=>> Building biology/salmon build started at Sun May 4 23:55:31 EDT 2025 port directory: /usr/ports/biology/salmon package name: salmon-1.10.2_7 building for: FreeBSD 13amd64-weekly-desktop-job-04 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1490 Mar 1 07:51 /usr/ports/biology/salmon/Makefile Ports top last git commit: 57a50b106b87 Ports top unclean checkout: yes Port dir last git commit: fa53920e7219 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1304000 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1304000 UNAME_v=FreeBSD 13.4-RELEASE-p4 UNAME_r=13.4-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/mnt/data/.m/13amd64-weekly-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/13amd64-weekly-desktop/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13amd64-weekly-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/13amd64-weekly-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/salmon/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/salmon/work/.cache HOME=/wrkdirs/usr/ports/biology/salmon/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/salmon/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/salmon/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=13.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/salmon" EXAMPLESDIR="share/examples/salmon" DATADIR="share/salmon" WWWDIR="www/salmon" ETCDIR="etc/salmon" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/salmon DOCSDIR=/usr/local/share/doc/salmon EXAMPLESDIR=/usr/local/share/examples/salmon WWWDIR=/usr/local/www/salmon ETCDIR=/usr/local/etc/salmon --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [13amd64-weekly-desktop-job-04] Installing pkg-2.0.6... [13amd64-weekly-desktop-job-04] Extracting pkg-2.0.6: .......... done ===> salmon-1.10.2_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_7 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by salmon-1.10.2_7 for building => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by salmon-1.10.2_7 for building ===> Extracting for salmon-1.10.2_7 => SHA256 Checksum OK for COMBINE-lab-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for COMBINE-lab-pufferfish-salmon-v1.10.2_GH0.tar.gz. => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-15_GH0.tar.gz. => SHA256 Checksum OK for samtools-htscodecs-5aecc6e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for salmon-1.10.2_7 ===> Applying FreeBSD patches for salmon-1.10.2_7 from /usr/ports/biology/salmon/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.37.pkg [13amd64-weekly-desktop-job-04] Installing bash-5.2.37... [13amd64-weekly-desktop-job-04] `-- Installing gettext-runtime-0.23.1... [13amd64-weekly-desktop-job-04] | `-- Installing indexinfo-0.3.1_1... [13amd64-weekly-desktop-job-04] | `-- Extracting indexinfo-0.3.1_1: . done [13amd64-weekly-desktop-job-04] `-- Extracting gettext-runtime-0.23.1: .......... done [13amd64-weekly-desktop-job-04] `-- Installing readline-8.2.13_2... [13amd64-weekly-desktop-job-04] `-- Extracting readline-8.2.13_2: .......... done [13amd64-weekly-desktop-job-04] Extracting bash-5.2.37: .......... done ===> salmon-1.10.2_7 depends on executable: bash - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: cereal>=1.3.0 - not found ===> Installing existing package /packages/All/cereal-1.3.2_1.pkg [13amd64-weekly-desktop-job-04] Installing cereal-1.3.2_1... [13amd64-weekly-desktop-job-04] `-- Installing boost-libs-1.87.0_1... [13amd64-weekly-desktop-job-04] | `-- Installing icu-76.1,1... [13amd64-weekly-desktop-job-04] | `-- Extracting icu-76.1,1: .......... done [13amd64-weekly-desktop-job-04] `-- Extracting boost-libs-1.87.0_1: .......... done [13amd64-weekly-desktop-job-04] Extracting cereal-1.3.2_1: .......... done ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> salmon-1.10.2_7 depends on package: cereal>=1.3.0 - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: libgff==2.0.0 - not found ===> Installing existing package /packages/All/libgff-2.0.0.pkg [13amd64-weekly-desktop-job-04] Installing libgff-2.0.0... [13amd64-weekly-desktop-job-04] Extracting libgff-2.0.0: .......... done ===> salmon-1.10.2_7 depends on package: libgff==2.0.0 - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: libtool - not found ===> Installing existing package /packages/All/libtool-2.5.4.pkg [13amd64-weekly-desktop-job-04] Installing libtool-2.5.4... [13amd64-weekly-desktop-job-04] `-- Installing m4-1.4.19_1,1... [13amd64-weekly-desktop-job-04] `-- Extracting m4-1.4.19_1,1: .......... done [13amd64-weekly-desktop-job-04] Extracting libtool-2.5.4: .......... done ===> salmon-1.10.2_7 depends on executable: libtool - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: autoreconf - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [13amd64-weekly-desktop-job-04] Installing autoconf-2.72... [13amd64-weekly-desktop-job-04] `-- Installing autoconf-switch-20220527... [13amd64-weekly-desktop-job-04] `-- Extracting autoconf-switch-20220527: ....... done [13amd64-weekly-desktop-job-04] `-- Installing perl5-5.36.3_2... [13amd64-weekly-desktop-job-04] `-- Extracting perl5-5.36.3_2: .......... done [13amd64-weekly-desktop-job-04] Extracting autoconf-2.72: .......... done ===> salmon-1.10.2_7 depends on executable: autoreconf - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on executable: aclocal - not found ===> Installing existing package /packages/All/automake-1.17.pkg [13amd64-weekly-desktop-job-04] Installing automake-1.17... [13amd64-weekly-desktop-job-04] Extracting automake-1.17: .......... done ===> salmon-1.10.2_7 depends on executable: aclocal - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [13amd64-weekly-desktop-job-04] Installing cmake-core-3.31.6... [13amd64-weekly-desktop-job-04] `-- Installing expat-2.6.4... [13amd64-weekly-desktop-job-04] `-- Extracting expat-2.6.4: .......... done [13amd64-weekly-desktop-job-04] `-- Installing jsoncpp-1.9.6_1... [13amd64-weekly-desktop-job-04] `-- Extracting jsoncpp-1.9.6_1: .......... done [13amd64-weekly-desktop-job-04] `-- Installing libidn2-2.3.8... [13amd64-weekly-desktop-job-04] | `-- Installing libunistring-1.3... [13amd64-weekly-desktop-job-04] | `-- Extracting libunistring-1.3: .......... done [13amd64-weekly-desktop-job-04] `-- Extracting libidn2-2.3.8: .......... done [13amd64-weekly-desktop-job-04] `-- Installing libuv-1.50.0... [13amd64-weekly-desktop-job-04] `-- Extracting libuv-1.50.0: .......... done [13amd64-weekly-desktop-job-04] `-- Installing rhash-1.4.4_1... [13amd64-weekly-desktop-job-04] `-- Extracting rhash-1.4.4_1: .......... done [13amd64-weekly-desktop-job-04] Extracting cmake-core-3.31.6: .......... done ===> salmon-1.10.2_7 depends on file: /usr/local/bin/cmake - found ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [13amd64-weekly-desktop-job-04] Installing gmake-4.4.1... [13amd64-weekly-desktop-job-04] Extracting gmake-4.4.1: .......... done ===> salmon-1.10.2_7 depends on package: gmake>=4.4.1 - found ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> salmon-1.10.2_7 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> salmon-1.10.2_7 depends on shared library: libtbb.so - not found ===> Installing existing package /packages/All/onetbb-2022.0.0.pkg [13amd64-weekly-desktop-job-04] Installing onetbb-2022.0.0... [13amd64-weekly-desktop-job-04] `-- Installing hwloc2-2.11.2... [13amd64-weekly-desktop-job-04] | `-- Installing level-zero-1.17.45... [13amd64-weekly-desktop-job-04] | | `-- Installing libfmt-10.2.1... [13amd64-weekly-desktop-job-04] | | `-- Extracting libfmt-10.2.1: .......... done [13amd64-weekly-desktop-job-04] | | `-- Installing spdlog-1.15.1... [13amd64-weekly-desktop-job-04] | | `-- Extracting spdlog-1.15.1: .......... done [13amd64-weekly-desktop-job-04] | `-- Extracting level-zero-1.17.45: .......... done [13amd64-weekly-desktop-job-04] | `-- Installing libpciaccess-0.18.1_1... [13amd64-weekly-desktop-job-04] | | `-- Installing hwdata-0.393,1... [13amd64-weekly-desktop-job-04] | | `-- Extracting hwdata-0.393,1: ...... done [13amd64-weekly-desktop-job-04] | `-- Extracting libpciaccess-0.18.1_1: ..... done [13amd64-weekly-desktop-job-04] | `-- Installing libxml2-2.11.9... [13amd64-weekly-desktop-job-04] | `-- Extracting libxml2-2.11.9: .......... done [13amd64-weekly-desktop-job-04] `-- Extracting hwloc2-2.11.2: .......... done [13amd64-weekly-desktop-job-04] Extracting onetbb-2022.0.0: .......... done ===> salmon-1.10.2_7 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Returning to build of salmon-1.10.2_7 ===> salmon-1.10.2_7 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-8.12.1.pkg [13amd64-weekly-desktop-job-04] Installing curl-8.12.1... [13amd64-weekly-desktop-job-04] `-- Installing brotli-1.1.0,1... [13amd64-weekly-desktop-job-04] `-- Extracting brotli-1.1.0,1: .......... done [13amd64-weekly-desktop-job-04] `-- Installing libnghttp2-1.65.0... [13amd64-weekly-desktop-job-04] `-- Extracting libnghttp2-1.65.0: ....... done [13amd64-weekly-desktop-job-04] `-- Installing libpsl-0.21.5_2... [13amd64-weekly-desktop-job-04] `-- Extracting libpsl-0.21.5_2: ........ done [13amd64-weekly-desktop-job-04] `-- Installing libssh2-1.11.1,3... [13amd64-weekly-desktop-job-04] `-- Extracting libssh2-1.11.1,3: .......... done [13amd64-weekly-desktop-job-04] `-- Installing zstd-1.5.7... [13amd64-weekly-desktop-job-04] | `-- Installing liblz4-1.10.0,1... [13amd64-weekly-desktop-job-04] | `-- Extracting liblz4-1.10.0,1: .......... done [13amd64-weekly-desktop-job-04] `-- Extracting zstd-1.5.7: .......... done [13amd64-weekly-desktop-job-04] Extracting curl-8.12.1: .......... done ===> salmon-1.10.2_7 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of salmon-1.10.2_7 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for salmon-1.10.2_7 (cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && ./bootstrap) + rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in io_lib-config + autoreconf -i libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' + cd htscodecs + autoreconf -i libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' parallel-tests: installing '../test-driver' ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/salmon/work/.build CC: gcc CC version: -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Detected non-ARM host. Setting USE_ARM to false. version: 1.10.2 -- CMAKE_BUILD_TYPE = Release -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test HAVE_LIBCPP -- Performing Test HAVE_LIBCPP - Success It appears that you're compiling with clang and that libc++ is available, so I'll use that Making Release build setting -DHAVE_NUMERIC_LIMITS128 CMake Warning (dev) at CMakeLists.txt:316 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. running /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/scripts/fetchPufferfish.sh 2>&1 -- fetch PUFFERFISH exit code 0 -- Found ZLIB: /usr/lib/libz.a (found version "1.3.1") -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library Found liblzma library: /usr/lib/liblzma.a;/usr/lib/libmd.a =========================================== -- Found BZip2: /usr/lib/libbz2.a (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: /usr/lib/libbz2.a =========================================== CMake Warning (dev) at CMakeLists.txt:438 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable BOOST_ROOT is set to: /usr/local For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:438 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/local/include (found suitable version "1.87.0", minimum required is "1.59.0") found components: iostreams system filesystem timer chrono program_options regex BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = /usr/local BOOST INCLUDE DIR = /usr/local/include BOOST INCLUDE DIRS = /usr/local/include BOOST LIB DIR = /usr/local/lib BOOST LIBRARIES = /usr/local/lib/libboost_iostreams.a;/usr/local/lib/libboost_system.a;/usr/local/lib/libboost_filesystem.a;/usr/local/lib/libboost_timer.a;/usr/local/lib/libboost_chrono.a;/usr/local/lib/libboost_program_options.a;/usr/local/lib/libboost_regex.a -- Found cereal: /usr/local/include (found suitable version "1.3.2", minimum required is "1.3.2") -- cereal found (include: /usr/local/include) -- Found TBB: /usr/local/lib/cmake/TBB/TBBConfig.cmake (found suitable version "2022.0.0", minimum required is "2021.4") FOUND SUITABLE TBB VERSION : 2022.0.0 -- libgff ver. 2.0.0 found. -- include: /usr/local/include/ -- lib : /usr/local/lib/ -- Found CURL: /usr/local/lib/libcurl.a (found version "8.12.1") Build system will compile Staden IOLib ================================================================== CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/bin/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 CMake Deprecation Warning at external/pufferfish/external/ntcard/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at external/pufferfish/external/twopaco/graphdump/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- setting COMPACT_VECTOR_DIR for graphdump to be /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump CMake Deprecation Warning at external/pufferfish/external/twopaco/graphconstructor/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp adding /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump to include path for libpuffer fetched path for compact_vector as [/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump] NO_IPO = FALSE TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = /usr/local/lib TBBGLOBS = /usr/local/lib/libtbb.so;/usr/local/lib/libtbb.so.12;/usr/local/lib/libtbb.so.12.14;/usr/local/lib/libtbbbind_2_0.so;/usr/local/lib/libtbbbind_2_0.so.3;/usr/local/lib/libtbbbind_2_0.so.3.14;/usr/local/lib/libtbbmalloc.so;/usr/local/lib/libtbbmalloc.so.2;/usr/local/lib/libtbbmalloc.so.2.14;/usr/local/lib/libtbbmalloc_proxy.so;/usr/local/lib/libtbbmalloc_proxy.so.2;/usr/local/lib/libtbbmalloc_proxy.so.2.14 -- Configuring done (2.8s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED FETCHED_LIBGFF -- Build files have been written to: /wrkdirs/usr/ports/biology/salmon/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for salmon-1.10.2_7 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 -B/wrkdirs/usr/ports/biology/salmon/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/salmon/work/.build//CMakeFiles/progress.marks /usr/local/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend /usr/local/bin/gmake -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend /usr/local/bin/gmake -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend /usr/local/bin/gmake -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles/libstadenio.dir/DependInfo.cmake /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make 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/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake /usr/local/bin/gmake -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f 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gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/tmp/libstadenio-mkdirs.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common/SignalHandler.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 4%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 4%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o [ 5%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/kalloc.c cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/dnachar.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/../common -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/graphdump.cpp [ 7%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o [ 6%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-mkdir cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 7%] No download step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-download [ 8%] No update step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-update [ 9%] No patch step for 'libstadenio' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-patch [ 10%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extd.c [ 11%] Performing configure step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && ./configure --enable-shared=no --without-libcurl --prefix=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install LDFLAGS= CFLAGS= CC=/usr/bin/cc CXX=/usr/bin/c++ checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem 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[ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz.c [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg.c [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o 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-fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF 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[ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c yes checking for C compiler default output file name... a.out checking for suffix of executables... [ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /usr/bin/cc accepts -g... yes checking for /usr/bin/cc option to enable C11 features... none needed checking whether /usr/bin/cc understands -c and -o together... [ 18%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 18%] Built target ksw2pp_sse4 /usr/local/bin/gmake -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/UnitTestsMain.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' yes /usr/local/bin/gmake -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/build checking whether make supports the include directive... gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' yes (GNU style) checking dependency style of /usr/bin/cc... [ 18%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/UnitTests.cpp gcc3 checking build system type... amd64-unknown-freebsd13.4 checking host system type... amd64-unknown-freebsd13.4 checking how to print strings... printf checking for a sed that does not truncate output... gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 18%] Built target ksw2pp_sse2 [ 19%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /usr/bin/cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... [ 20%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o BSD nm cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp checking whether ln -s works... yes checking the maximum length of command line arguments... 393216 checking how to convert amd64-unknown-freebsd13.4 file names to amd64-unknown-freebsd13.4 format... func_convert_file_noop checking how to convert amd64-unknown-freebsd13.4 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... [ 20%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o pass_all checking for dlltool... cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common/Fcontrol.cpp no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... [ 21%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o strip checking command to parse /usr/bin/nm output from /usr/bin/cc object... cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/Common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/ntcard/nthll.cpp ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/bin/cc supports -fno-rtti -fno-exceptions... yes checking for /usr/bin/cc option to produce PIC... -fPIC -DPIC checking if /usr/bin/cc PIC flag -fPIC -DPIC works... yes checking if /usr/bin/cc static flag -static works... yes checking if /usr/bin/cc supports -c -o file.o... yes checking if /usr/bin/cc supports -c -o file.o... (cached) yes checking whether the /usr/bin/cc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.4 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for inflateEnd in -lz... yes checking for zlib.h... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: no In file included from checking whether byte ordering is bigendian... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool openo rator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } //checking for egrep... NOO(cached) P/usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ yes checking for fcntl.h... yes checking for limits.h... [ 22%] Linking CXX static library libntcard.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/local/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake yes checking for unistd.h... (cached) yes checking for malloc.h... cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/ntcard && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/llvm-ranlib libntcard.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 22%] Built target ntcard [ 23%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp yes checking for zlib.h... (cached) yes checking for stdio_ext.h... no checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ 8 checking for inline... inline checking for mode_t... gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 23%] Built target ksw2pp_basic [ 24%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/../common -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/. -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/dnachar.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:27: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] yes checking for fileno... 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ yes /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cppchecking for fstat... :250:14: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 250 | auto c = seqVec[i]; | ^ yes checking for mallopt... no checking for /usr/bin/cc option to enable large file support... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:917:12: warning: variable 'totalKmersIshouldSee' set but not used [-Wunused-but-set-variable] 917 | size_t totalKmersIshouldSee{0} ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:1074:11: warning: variable 'loopCounter' set but not used [-Wunused-but-set-variable] 1074 | int loopCounter = 0; | ^ none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... [ 24%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp yes checking for working mmap... yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... [ 24%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp yes checking for fsync... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operyes ator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operatochecking that generated files are newer than configure... rdone ==(std=== configuring in htscodecs (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs) ::nullptr_tconfigure: running /bin/sh ./configure '--prefix=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install' --disable-option-checking '--enable-shared=no' '--without-libcurl' 'LDFLAGS=' 'CFLAGS=' 'CC=/usr/bin/cc' 'CXX=/usr/bin/c++' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' '--disable-shared' '--with-pic' '--srcdir=.' --cache-file= p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: yes unused parameter 'b' [-Wunused-parameter] checking filesystem timestamp resolution... 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:13: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ 2 checking whether build environment is sane... yes checking for a race-free mkdir -p... mkdir -p checking for gawk... no checking for mawk... no checking for nawk... nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... /usr/bin/cc In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructivechecking whether the C compiler works... _iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); yes | checking for C compiler default output file name... ^a.out /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.hchecking for suffix of executables... :2948:9: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to) ; | ^checking whether we are cross compiling... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::find_or_insert>>::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17no : checking for suffix of object files... note: in instantiation of function template specialization 'spp::sparse_hash_map>>::operator[]' requested here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ o checking whether the compiler supports GNU C... yes checking whether /usr/bin/cc accepts -g... yes checking for /usr/bin/cc option to enable C11 features... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: none needed /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: checking whether /usr/bin/cc understands -c and -o together... warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ yes In file included from checking whether make supports the include directive... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from yes (GNU style) /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:checking dependency style of /usr/bin/cc... 24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cppgcc3 26: :note: 1in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here: checking build system type... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp167: | 14 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp : 23 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h : 69 amd64-unknown-freebsd13.4 : checking host system type... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h amd64-unknown-freebsd13.4 : checking how to print strings... 241 :printf 36checking for a sed that does not truncate output... : warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]? t241y | p e n a m: std::inet eigtrearla_tcoorn:s:tant, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested herec yes o checking for BSD- or MS-compatible name lister (nm)... 195nstant' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]n ( t636y | lhsp_esneatmtee rs&td :o:preermaotvoer_=r(ecfoenrsetn clehs:e:tttyepre&) r&h&s ) | { ^ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(ok m_checking for sysroot... mno echecking for a working dd... m + (i * /bin/dd Bchecking how to truncate binary pipes... ITS) / U/bin/dd bs=4096 count=1 Bchecking for mt... ,mt checking if mt is a manifest tool... BITS, (i *no Bchecking for stdio.h... ITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 310 | (*cpos_offsets)[0] = 0; | ^ yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& yes ochecking for unistd.h... perator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destryes ucchecking for dlfcn.h... tive_begin(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cpp::29481:: 9In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp :note: 9in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp2948: | 10 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp : 636 : 15 : _warning: mdefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]o v e636_ | f r olmh(sm_osveetrt,e rh&t ,o pmeirna_tbourc=k(ecotnss_tw alnhtse_ds)e;t t e| r ^& /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.hr:h2745s:)26 :{ note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here| ^ 2745/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp | : 26 : 19 : note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here s p26a | r s e _ h a sahyes uchecking for objdir... ttoa bslpeo st[ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o m=.libs p (uMcd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/streamfastaparser.cpp oveDontCopy, *tnhdiesr,l yrieng().contigOffsets_[csonitigRank]; | ^ z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBaseIndex.cppe:_343t:o17):; note: in instantiation of member function 'PufferfishBaseIndex::contigRange' requested here| ^ 343/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h | :t3278e:m21p:l anote: tin instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested heree c3278l | a In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp s: 9 : PIn file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hppf:f12: eIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hppf i:checking if /usr/bin/cc supports -fno-rtti -fno-exceptions... 23: sIn file included from h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h B: a69 s: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h :I241 :n 36d: eiwarning: xfbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]< P( u241_f | rf ee sr if z:i sestyes _hdchecking for /usr/bin/cc option to produce PIC... dI:-fPIC -DPIC ned:checking if /usr/bin/cc PIC flag -fPIC -DPIC works... leitxnat(>e1;g) r) a | l ^_| c ^o n stant, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, VecHasher>::DefaultValue, std::vector &>' requested here __has_trivial_co nstructor(T) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 3813 252 | : std::in | t e gr a return rep.template find_or_liyes n_schecking if /usr/bin/cc supports -c -o file.o... ert(std::forward(key)).second; | ^ n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: sin instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, VecHasher>::operator[] &>' requested here t a414n | t yes ::type) && | ^ freebsd13.4 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for __builtin_prefetch... yes checking C compiler flags needed for ssse3... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typenameIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:i13t: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hppr:a647t:o32r:: :lhs_setter_type(m_mem + (i * BITS) / UB, BIwarning: Tunused parameter 'k' [-Wunused-parameter]S , (i * BITS) % UB) | ^ 647/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp | : 120 :m20e:r _note: bin instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested herea s e120_ | s t a triect(uurnns i(gned int k, c(o*nrsatn kchar* s) : super(k_) { | ^ _)[endPos] == 1); | ^ [ 27%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp -mssse3 checking C compiler flags needed for popcnt... [ 28%] Linking CXX static library libgraphdump.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphdump && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/llvm-ranlib libgraphdump.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 28%] Built target graphdump /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp[ 29%] Linking CXX static library libksw2pp.a :1cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& r"/usr/bin/llvm-ar" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/llvm-ranlib" libksw2pp.a hs) {gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | [ 29%] Built target ksw2pp [ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o ? typecd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/test.cpp name iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndexer.cpp:737:17: note: in instantiation of member function 'compact::vector_imp::vector, 64, true>, unsigned long, 0, unsigned long, std::allocator, 64, true>::operator[]' requested here 737 | posVec[idx] = kb1.pos(); | ^ [ 31%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp 13 warnings generated. [ 32%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp -mpopcnt checking C compiler flags needed for sse4.1... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: In file included from definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:12: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 636 4 | #p | ragma GCC diagnostic ignored "-Wmaybe -uninitialized" | ^ lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBaseIndex.hpp:26:19: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 26 | auto spos = underlying().contigOffsets_[contigRank]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishIndex.cpp:207:30: note: in instantiation of member function 'PufferfishBaseIndex::contigRange' requested here 207 | auto contigIterRange = contigRange(rank); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ -msse4.1 checking C compiler flags needed for avx2... /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:438:23: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 438 | auto sampledPos = sampledPos_[currRank]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:384:9: warning: variable 'inLoop' set but not used [-Wunused-but-set-variable] 384 | int inLoop = 0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:480:9: warning: variable 'inLoop' set but not used [-Wunused-but-set-variable] 480 | int inLoop = 0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:11: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ -mavx2 checking C compiler flags needed for avx512f... In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ 14 warnings generated. [ 33%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/edlib.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishSparseIndex.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishSparseIndex.cpp:379:19: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 379 | if (presenceVec_[idx] == 1) { | ^ -mavx512f checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... yes checking for function pthread_join... -lthr checking that generated files are newer than configure... done configure: creating ./config.status [ 34%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp config.status: creating Makefile config.status: creating htscodecs/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: no Libdeflate enabled: no have libbsc: no Have zstd: no CC: /usr/bin/cc CFLAGS: -Wall LDFLAGS: LIBS: -lm -llzma -lbz2 -L/usr/local/lib cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-configure [ 35%] Performing build step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake CC=/usr/bin/cc CXX=/usr/bin/c++ CFLAGS+= CFLAGS+= LDFLAGS+= CFLAGS+= CFLAGS+= CFLAGS+= gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake all-recursive gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making all in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake all-recursive gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making all in htscodecs gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Update version.h: #define HTSCODECS_VERSION_TEXT "1.5.0" gmake all-am gmake[8]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c -o pack.lo pack.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT pack.lo -MD -MP -MF .deps/pack.Tpo -c pack.c -fPIC -DPIC -o pack.o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITSmv -f .deps/pack.Tpo .deps/pack.Plo , /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c -o rle.lo rle.c (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:159:39: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 159 | if (res < numKmers_ and prlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rle.lo -MD -MP -MF .deps/rle.Tpo -c rle.c -fPIC -DPIC -o rle.o esenceVec_[res] == 1) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishLossyIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishLossyIndex.cpp:162:22: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here 162 | pmv -f .deps/rle.Tpo .deps/rle.Plo os /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c -o fqzcomp_qual.lo fqzcomp_qual.c = sampledPos_[currRank]; | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fqzcomp_qual.lo -MD -MP -MF .deps/fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o fqzcomp_qual.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ [ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:216:51: warning: 'const' qualifier on reference type 'decltype(* jointMemsList.begin())' (aka 'pufferfish::util::JointMems &') has no effect [-Wignored-reference-qualifiers] 216 | [best_pair_in_target, thresh](const decltype(*jointMemsList.begin())& jm) -> bool { | ^~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:61: warning: lambda capture 'coverageRatio' is not required to be captured for this use [-Wunused-lambda-capture] 239 | auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] | ~~~^~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:120: warning: lambda capture 'thresh' is not required to be captured for this use [-Wunused-lambda-capture] 239 | auto orphanFiller = [&jointMemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chain_sub_thresh] | ~~^~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/Util.cpp:239:128: warning: lambda capture 'ithresh' is not used [-Wunused-lambda-capture] 239 | auto orphanFiller = [&j16o warningisn generatedt. MemsList, &maxCoverage, &coverageRatio, &maxLeftOrRight, &leftOrphan, &rightOrphan, thresh, ithresh, orphan_chai[ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o n_sub_cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9b.cpp thresh] | ~~^~~~~~~ mv -f .deps/fqzcomp_qual.Tpo .deps/fqzcomp_qual.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c -o rANS_static.lo rANS_static.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static.lo -MD -MP -MF .deps/rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o rANS_static.o [ 37%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp mv -f .deps/rANS_static.Tpo .deps/rANS_static.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c -o rANS_static4x16pr.lo rANS_static4x16pr.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr.lo -MD -MP -MF .deps/rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o rANS_static4x16pr.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/rank9sel.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/rank9sel.hpp:27: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ 7 warnings generated. [ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp mv -f .deps/rANS_static4x16pr.Tpo .deps/rANS_static4x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c -o rANS_static32x16pr.lo rANS_static32x16pr.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static32x16pr.lo -MD -MP -MF .deps/rANS_static32x16pr.Tpo -c rANS_static32x16pr.c -fPIC -DPIC -o rANS_static32x16pr.o 14 warnings generated. [ 39%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp [ 40%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/../common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphconstructor/common.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT tokenise_name3.lo -MD -MP -MF .deps/tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o tokenise_name3.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:16: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ mv -f .deps/tokenise_name3.Tpo .deps/tokenise_name3.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c -o arith_dynamic.lo arith_dynamic.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT arith_dynamic.lo -MD -MP -MF .deps/arith_dynamic.Tpo -c arith_dynamic.c -fPIC -DPIC -o arith_dynamic.o [ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ 15 warnings generated. /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c -o htscodecs.lo htscodecs.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT htscodecs.lo -MD -MP -MF .deps/htscodecs.Tpo -c htscodecs.c -fPIC -DPIC -o htscodecs.o mv -f .deps/htscodecs.Tpo .deps/htscodecs.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c -o utils.lo utils.c In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.c -fPIC -DPIC -o utils.o 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(stdmv -f .deps/arith_dynamic.Tpo .deps/arith_dynamic.Plo ::n/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo `test -f 'rANS_static32x16pr_sse4.c' || echo './'`rANS_static32x16pr_sse4.c ullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const mv -f .deps/utils.Tpo .deps/utils.Plo com/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo `test -f 'rANS_static32x16pr_avx2.c' || echo './'`rANS_static32x16pr_avx2.c mlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -MD -MP -MF .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo -c rANS_static32x16pr_sse4.c -fPIC -DPIC -o librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o on& rhs) { | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -MD -MP -MF .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo -c rANS_static32x16pr_avx2.c -fPIC -DPIC -o librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:17: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter] 647 | mer_base_static(unsigned int k, const char* s) : super(k_) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp : 20l: hIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp_:s9: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hppt:t4e:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] r &4 | o#pragmap eGrCaC tdoiragnosti=c( cionst glnhosr_esd "e-tWtmaeyrb&e -ruhnsi)n i{t i a| l ^i z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: ein implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required hered" | ^ 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:154:35: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 2, unsigned long, std::allocator, 64, false>::operator[]' requested here 154 | kb.shiftFw(static_cast(refSeq[gpos])); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishValidate.cpp:479:14: note: in instantiation of function template specialization 'doPufferfishInternalValidate' requested here 479 | return doPufferfishInternalValidate(pi, validateOpts); | ^ 22 warnings generated. [ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp mv -f .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Tpo .deps/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo `test -f 'rANS_static32x16pr_avx512.c' || echo './'`rANS_static32x16pr_avx512.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -MD -MP -MF .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo -c rANS_static32x16pr_avx512.c -fPIC -DPIC -o librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o mv -f .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Tpo .deps/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.Plo /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -msse4.1 -mssse3 -mpopcnt -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_sse4.la librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.lo -lthr -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/librANS_static32x16pr_sse4.a librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o libtool: link: ranlib .libs/librANS_static32x16pr_sse4.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_sse4.la" && ln -s "../librANS_static32x16pr_sse4.la" "librANS_static32x16pr_sse4.la" ) [ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:53:24: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 53 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp : 15 : i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32f: warning: (unused parameter 'k' [-Wunused-parameter]n o 647 | mer_baset_ stativics(unsigned initted mv -f .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Tpo .deps/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.Plo [kv/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -mavx2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_avx2.la librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.lo -lthr -lbz2 -L/usr/local/lib ,] )cons t ch{a r* | s) ^ : super(k_) { | ^ libtool: link: ar cr .libs/librANS_static32x16pr_avx2.a librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o libtool: link: ranlib .libs/librANS_static32x16pr_avx2.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx2.la" && ln -s "../librANS_static32x16pr_avx2.la" "librANS_static32x16pr_avx2.la" ) /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -mavx512f -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o librANS_static32x16pr_avx512.la librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.lo -lthr -lbz2 -L/usr/local/lib libtool: link: ar cr .libs/librANS_static32x16pr_avx512.a librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/librANS_static32x16pr_avx512.a libtool: link: ( cd ".libs" && rm -f "librANS_static32x16pr_avx512.la" && ln -s "../librANS_static32x16pr_avx512.la" "librANS_static32x16pr_avx512.la" ) /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -version-info 3:2:1 -lpthread -fstack-protector-strong -o libhtscodecs.la -rpath /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib pack.lo rle.lo fqzcomp_qual.lo rANS_static.lo rANS_static4x16pr.lo rANS_static32x16pr.lo rANS_static32x16pr_neon.lo tokenise_name3.lo arith_dynamic.lo htscodecs.lo utils.lo librANS_static32x16pr_sse4.la librANS_static32x16pr_avx2.la librANS_static32x16pr_avx512.la -lm -lthr -lbz2 -L/usr/local/lib libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_sse4.a") In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:19: In file included from libtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx2.a") /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignolibtool: link: (cd .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a && ar x "/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/./.libs/librANS_static32x16pr_avx512.a") red "-Wmaybe-uninitialized" | ^ libtool: link: ar cr .libs/libhtscodecs.a pack.o rle.o fqzcomp_qual.o rANS_static.o rANS_static4x16pr.o rANS_static32x16pr.o rANS_static32x16pr_neon.o tokenise_name3.o arith_dynamic.o htscodecs.o utils.o .libs/libhtscodecs.lax/librANS_static32x16pr_sse4.a/librANS_static32x16pr_sse4_la-rANS_static32x16pr_sse4.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx2.a/librANS_static32x16pr_avx2_la-rANS_static32x16pr_avx2.o .libs/libhtscodecs.lax/librANS_static32x16pr_avx512.a/librANS_static32x16pr_avx512_la-rANS_static32x16pr_avx512.o libtool: link: ranlib .libs/libhtscodecs.a libtool: link: rm -fr .libs/libhtscodecs.lax libtool: link: ( cd ".libs" && rm -f "libhtscodecs.la" && ln -s "../libhtscodecs.la" "libhtscodecs.la" ) gmake[8]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making all in . gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making all in tests gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT rANS_static4x16pr_test.o -MD -MP -MF .deps/rANS_static4x16pr_test.Tpo -c -o rANS_static4x16pr_test.o rANS_static4x16pr_test.c In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cpp:16: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: 636unused parameter 'k' [-Wunused-parameter] | 25l | hstd::vecstor/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp : 167:: 26s:t dnote: :in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here: i n167t | e g ge rta l __ c o n s k t a n t < b o o l , m _ _?h atsy_pterniavmiea lie_[ 43%] Linking CXX static library libUnitTestsMain.a tdeerrsacd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake ttsorr(u:cc:olthnoscd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1 _rs(eTt)t e&r&_st ty p| se ^t( dm/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:_::m246e:m36 s:+ twarning: /usr/bin/llvm-ar qc libUnitTestsMain.a CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o /usr/bin/llvm-ranlib libUnitTestsMain.a builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins](r igmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' mv -f .deps/tokenise_name3_test.Tpo .deps/tokenise_name3_test.Po i246/usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT arith_dynamic_test.o -MD -MP -MF .deps/arith_dynamic_test.Tpo -c -o arith_dynamic_test.o arith_dynamic_test.c *n | g [ 43%] Built target UnitTestsMain B& I TfS a)s t/a U_B[ 44%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o f, i B:lI cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeeTsFiles/puffer.dir/FastxParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FastxParser.cpp ,St ,du i(n:it 3*2: _iBtnI TtSe)kg )r% a {Ul B_ )| c ^ o| n ^s t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishStats.cppa:n141t:<162b:o onote: lin instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here, _141_ | h a s _ t r i v i a l _ c o::type) && | ^ mv -f .deps/rANS_static_test.Tpo .deps/rANS_static_test.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fqzcomp_qual_test.o -MD -MP -MF .deps/fqzcomp_qual_test.Tpo -c -o fqzcomp_qual_test.o fqzcomp_qual_test.c mv -f .deps/fqzcomp_qual_test.Tpo .deps/fqzcomp_qual_test.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT varint_test.o -MD -MP -MF .deps/varint_test.Tpo -c -o varint_test.o varint_test.c mv -f .deps/varint_test.Tpo .deps/varint_test.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT entropy.o -MD -MP -MF .deps/entropy.Tpo -c -o entropy.o entropy.c mv -f .deps/entropy.Tpo .deps/entropy.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o rans4x16pr rANS_static4x16pr_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o rans4x16pr rANS_static4x16pr_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o tokenise_name3 tokenise_name3_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o tokenise_name3 tokenise_name3_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o arith_dynamic arith_dynamic_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o arith_dynamic arith_dynamic_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o rans4x8 rANS_static_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o rans4x8 rANS_static_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o fqzcomp_qual fqzcomp_qual_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o fqzcomp_qual fqzcomp_qual_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o varint varint_test.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o varint varint_test.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishExamine.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o entropy entropy.o ../htscodecs/libhtscodecs.la -lthr -lbz2 -L/usr/local/lib " | ^ libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o entropy entropy.o ../htscodecs/.libs/libhtscodecs.a -L/usr/local/lib -lpthread -lm -lthr -lbz2 In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -o libstaden_read_la-scf_extras.o mv -f .deps/libstaden_read_la-scf_extras.Tpo .deps/libstaden_read_la-scf_extras.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -o libstaden_read_la-translate.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iteratomv -f .deps/libstaden_read_la-translate.Tpo .deps/libstaden_read_la-translate.Plo r(W/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c * p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | vlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -o libstaden_read_la-compression.o oid bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWrlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -o libstaden_read_la-ztr.o iter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: 15 warnings generated. [ 45%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishKmerQuery.cpp:44:12: warning: variable 'rn' set but not used [-Wunused-but-set-variable] 44 | size_t rn{0}; | ^ mv -f .deps/libstaden_read_la-ztr.Tpo .deps/libstaden_read_la-ztr.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -o libstaden_read_la-ztr_translate.o 14 warnings generated. [ 46%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferFS.cpp /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o mv -f .deps/libstaden_read_la-ztr_translate.Tpo .deps/libstaden_read_la-ztr_translate.Plo [ 47%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/cc -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/xxhash.c [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp mv -f .deps/libstaden_read_la-deflate_interlaced.Tpo .deps/libstaden_read_la-deflate_interlaced.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -o libstaden_read_la-fpoint.o mv -f .deps/libstaden_read_la-fpoint.Tpo .deps/libstaden_read_la-fpoint.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -o libstaden_read_la-seqIOABI.o mv -f .deps/libstaden_read_la-seqIOABI.Tpo .deps/libstaden_read_la-seqIOABI.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c seqIOALF.c -o libstaden_read_la-seqIOALF.o 14 warnings generated. [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp mv -f .deps/libstaden_read_la-seqIOALF.Tpo .deps/libstaden_read_la-seqIOALF.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c expFileIO.c -o libstaden_read_la-expFileIO.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type)In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:2: &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/jellyfish/mer_dna.hpp&: 647:32: warning: | unused parameter 'k' [-Wunused-parameter] ^ 647 | mer_base_static (unsigned int k, const char* s) : super(k_) { | ^ mv -f .deps/libstaden_read_la-expFileIO.Tpo .deps/libstaden_read_la-expFileIO.Plo In file included from /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:3: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/clipp.h:1409:13: warning: variable 'i' set but not used [-Wunused-but-set-variable] 1409 | int i = 0; | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiunused parameter 'p' [-Wunused-parameter] les/puffer.dir/MemChainer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp 348 | Derived& operator=(stmv -f .deps/libstaden_read_la-seqIOPlain.Tpo .deps/libstaden_read_la-seqIOPlain.Plo d:/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c :nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c misc_scf.c -o libstaden_read_la-misc_scf.o unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ mv -f .deps/libstaden_read_la-misc_scf.Tpo .deps/libstaden_read_la-misc_scf.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsignlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c read_scf.c -o libstaden_read_la-read_scf.o ed b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ mv -f .deps/libstaden_read_la-read_scf.Tpo .deps/libstaden_read_la-read_scf.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-write_scf.lo -MD -MP -MF .deps/libstaden_read_la-write_scf.Tpo -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-write_scf.lo -MD -MP -MF .deps/libstaden_read_la-write_scf.Tpo -c write_scf.c -o libstaden_read_la-write_scf.o mv -f .deps/libstaden_read_la-write_scf.Tpo .deps/libstaden_read_la-write_scf.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c sff.c -o libstaden_read_la-sff.o mv -f .deps/libstaden_read_la-sff.Tpo .deps/libstaden_read_la-sff.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c srf.c -o libstaden_read_la-srf.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ mv -f .deps/libstaden_read_la-srf.Tpo .deps/libstaden_read_la-srf.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c array.c -o libstaden_read_la-array.o mv -f .deps/libstaden_read_la-array.Tpo .deps/libstaden_read_la-array.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-compress.lo -MD -MP -MF .deps/libstaden_read_la-compress.Tpo -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-compress.lo -MD -MP -MF .deps/libstaden_read_la-compress.Tpo -c compress.c -o libstaden_read_la-compress.o mv -f .deps/libstaden_read_la-compress.Tpo .deps/libstaden_read_la-compress.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-error.lo -MD -MP -MF .deps/libstaden_read_la-error.Tpo -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-error.lo -MD -MP -MF .deps/libstaden_read_la-error.Tpo -c error.c -o libstaden_read_la-error.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: mv -f .deps/libstaden_read_la-error.Tpo .deps/libstaden_read_la-error.Plo /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-files.lo -MD -MP -MF .deps/libstaden_read_la-files.Tpo -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-files.lo -MD -MP -MF .deps/libstaden_read_la-files.Tpo -c files.c -o libstaden_read_la-files.o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typenmv -f .deps/libstaden_read_la-files.Tpo .deps/libstaden_read_la-files.Plo am/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-find.lo -MD -MP -MF .deps/libstaden_read_la-find.Tpo -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c e iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-find.lo -MD -MP -MF .deps/libstaden_read_la-find.Tpo -c find.c -o libstaden_read_la-find.o S) % UB) | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:109:15: note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cppin instantiation of member function 'compact::vector_imp::vector, unsigned long, 2, unsigned long, std::allocator, 64, false>::operator[]' requested here : 109 | 1 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_cons mv -f .deps/libstaden_read_la-find.Tpo .deps/libstaden_read_la-find.Plo t /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-mach-io.lo -MD -MP -MF .deps/libstaden_read_la-mach-io.Tpo -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c ant>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-open_trace_file.lo -MD -MP -MF .deps/libstaden_read_la-open_trace_file.Tpo -c open_trace_file.c -o libstaden_read_la-open_trace_file.o 946 | Two_d_destructive_itera tor252 | & : std::integral_constant::type) && | ^ or=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>>, spp::sparsegroup>>, spp::libc_allocator>>>> *, std::pair>> *, std::input_iterator_tag, spp::libc_allocator>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp::327827: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/digestpp.hpp:5: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/hasher.hpp:136:10: warning: variable 'len' set but not used [-Wunused-but-set-variable] : 136 | size_t len = 0; | ^ 21: 12 warnings generated. note: in instantiation of member function 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemCollector.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemCollector.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp3813::mv -f .deps/libstaden_read_la-open_trace_file.Tpo .deps/libstaden_read_la-open_trace_file.Plo 348[ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o :37/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c : 29cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakewarning: Files/puffer.dir/PuffAligner.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp :unused parameter 'p' [-Wunused-parameter] note: 348 | in instantiation of function template specialization 'spp::sparse_hashtable>>, unsigned long, spp::spp_hash, spp::sparse_hash_map>>::SelectKey, spp::sparse_hash_map>>::SetKey, std::equal_to, spp::libc_allocator>>>>::find_or_insert>>::DefaultValue, unsigned long &>' requested here 3813 | Der iv ed& operator=(std : :libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-read_alloc.lo -MD -MP -MF .deps/libstaden_read_la-read_alloc.Tpo -c read_alloc.c -o libstaden_read_la-read_alloc.o nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] r 371 | bool operator!=(std::nullptr_t pe)turn rep.temIn file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:l27mv -f .deps/libstaden_read_la-read_alloc.Tpo .deps/libstaden_read_la-read_alloc.Plo a: tIn file included from /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-strings.lo -MD -MP -MF .deps/libstaden_read_la-strings.Tpo -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/digestpp.hpp :f19i: nIn file included from d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/algorithm/k12m14.hpp_:o9 r: {_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/digestpp/algorithm/detail/k12m14_provider.hpp i:n86s:e77r :t | e( svtodi:d: ftorrawnasrfodro(nksety )u)n.ssiegcnoendd ;c h a| r ^* /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cppda:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppt161:a:582,17: :u i32note: n:in instantiation of function template specialization 'spp::sparse_hash_map>>::operator[]' requested here t warning: 6 unused parameter 'lfs' [-Wunused-parameter]4161 _ | t n u m _ b l k s , spiazteh_[tr erfe_aclnlte]n.)r e s| i ^z e(contigCntP erPat582mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo h)/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c ; | ^ | bool operator==(stdlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o ::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { }In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: mv -f .deps/libstaden_read_la-traceType.Tpo .deps/libstaden_read_la-traceType.Plo definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c /657 | / lhsN_OOsPetter& oper ator=(const lhs_setter& r| hs) ^ { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp::libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-xalloc.lo -MD -MP -MF .deps/libstaden_read_la-xalloc.Tpo -c xalloc.c -o libstaden_read_la-xalloc.o 167:26: note: 845in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here : 167 | 22 : ? typeIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cppwarning: a:unused parameter 'b' [-Wunused-parameter]m e iterator::lhs 2_845: s | In file included from e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hppt :tv8mv -f .deps/libstaden_read_la-xalloc.Tpo .deps/libstaden_read_la-xalloc.Plo e: or/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c i_dIn file included from t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hppyb:p12: ieIn file included from t(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hppms:_(m23uen: msIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h+g (nei:d 69 *: b /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h):B 241I{T: S36}:) libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -o libstaden_read_la-vlen.o / /warning: / builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]N U O241BO | ,P B I| T ^:S ,std::integral _(constant, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested here : std::inte195g | r a l _ c o n s t a n t ' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 636 | lhs_setter& operator=(const blool, __has_trivial_assign(typename std::remove_reference::thys_setter& rhs) { | ^ p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here e 167 | ? typename i)terator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector, 64, false>, unsigned long, 0, unsigned long, std::allocator, 64, false>::operator[]' requested here & 310 | (*cpos_offsets)[0] = 0; | ^ | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21In file included from : note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/MemChainer.hpp 3278 | if :(8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] r 348 | Derived& operator=(sted::nullptr_t p) { | ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] i 367 | bool zoe_delta(1)) | ^ p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.he:3813:29r:a tnote: oin instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, VecHasher, spp::sparse_hash_map, unsigned int, VecHasher>::SelectKey, spp::sparse_hash_map, unsigned int, VecHasher>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, VecHasher>::DefaultValue, std::vector &>' requested herer = =3813( | s t d : : n u l lrpettru_rtn pr)e p.{t e m| p ^l a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppt:e371 :f34i:n dwarning: _unused parameter 'p' [-Wunused-parameter]o r _371 | i n sbeorotl< DeofpaeurlattVoarl!u=e(>s(tsdt:d:::nforwualrldpt( kpe)y ){) . s| e ^c ond; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp :note: 582in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, VecHasher>::operator[] &>' requested here : 414 | 32 : warning: unused parameter 'lfs' [-Wunused-parameter] 582 | b o o l o p e r a t o r = =e(qsItDd :=: neuqlMlappt[rt_litst] mv -f .deps/libstaden_read_la-hash_table.Tpo .deps/libstaden_read_la-hash_table.Plo ; l/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c | f ^s , const common& rhs) { | ^ libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } //mv -f .deps/libstaden_read_la-jenkins_lookup3.Tpo .deps/libstaden_read_la-jenkins_lookup3.Plo N/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c OOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o // NOOP | ^ mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/MemChainer.cpp:95:16: warning: variable 'mappings' set but not used [-Wunused-but-set-variable] 95 | uint32_t mappings{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:4: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:33946:33: : warning: In file included from definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: 69in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here : 2817 | for (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.hde:s241:t36ructive_iterator it = ht.destructive_begin(); | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278241: | 21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here : std::i nte g3278 | r al_ ciofnstan t(<_brool, e__has_trisviail_zdeestruct_or(T)d e&l& t a| ^ (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:1246):36: )warning: builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813 :29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned long, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned long &>' requested here 246 3813 | return | rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:264:33: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 264 | duplicateNames[dupInfo.txId].push_back(process edName); :| ^ std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PuffAligner.cpp:2: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:102:12: warning: private field 'k' is not used [-Wunused-private-field] 102 | uint32_t k; | ^ mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, std::string *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, std::string *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/FixFasta.cpp:490:20: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 490 | auto it = dset.insert(dname); | ^ 12 warnings generated. [ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:45: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SelectiveAlignmentUtils.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PuffAligner.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:48: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:56: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/SAMWriter.hpp:4: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BinWriter.hpp:31:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 31 | BinWriter(std::vector&& bin_data) :_bin_data(move(bin_data)) {}; | ^ | std:: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o : privacd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/metro/metrohash64.cpp te optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/PufferfishAligner.cpp:1022:31: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 1022 | gene_names.insert(processedName[ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o ); cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/src && /usr/bin/c++ -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/ LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp | ^ mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o 12 warnings generated. /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std:libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o :integral_constant::typelibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c string_alloc.c -o libstaden_read_la-string_alloc.o ) && | ^ mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | boolmv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo o/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c perator!=(std::nmv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo ul/bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c lptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operlibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o ator==(std::nulllibtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o ptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned omv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo ) /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo /bin/sh ../libtool --tag=CC --mode=compile /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo libtool: compile: /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -version-info 15:2:1 -lpthread -fstack-protector-strong -o libstaden-read.la -rpath /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz ../htscodecs/htscodecs/libhtscodecs.la -lm -llzma -lbz2 -L/usr/local/lib In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making all in progs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c mv -f .deps/extract_seq.Tpo .deps/extract_seq.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c mv -f .deps/extract_qual.Tpo .deps/extract_qual.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c mv -f .deps/makeSCF.Tpo .deps/makeSCF.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c mv -f .deps/index_tar.Tpo .deps/index_tar.Po mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scf_update.o -MD -MP -MF .deps/scf_update.Tpo -c -o scf_update.o scf_update.c mv -f .deps/scf_info.Tpo .deps/scf_info.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT get_comment.o -MD -MP -MF .deps/get_comment.Tpo -c -o get_comment.o get_comment.c mv -f .deps/extract_fastq.Tpo .deps/extract_fastq.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_tar.o -MD -MP -MF .deps/hash_tar.Tpo -c -o hash_tar.o hash_tar.c mv -f .deps/scf_update.Tpo .deps/scf_update.Po mv -f .deps/scf_dump.Tpo .deps/scf_dump.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_extract.o -MD -MP -MF .deps/hash_extract.Tpo -c -o hash_extract.o hash_extract.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_list.o -MD -MP -MF .deps/hash_list.Tpo -c -o hash_list.o hash_list.c mv -f .deps/hash_extract.Tpo .deps/hash_extract.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT trace_dump.o -MD -MP -MF .deps/trace_dump.Tpo -c -o trace_dump.o trace_dump.c mv -f .deps/hash_list.Tpo .deps/hash_list.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_sff.o -MD -MP -MF .deps/hash_sff.Tpo -c -o hash_sff.o hash_sff.c mv -f .deps/get_comment.Tpo .deps/get_comment.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT append_sff.o -MD -MP -MF .deps/append_sff.Tpo -c -o append_sff.o append_sff.c mv -f .deps/trace_dump.Tpo .deps/trace_dump.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ztr_dump.o -MD -MP -MF .deps/ztr_dump.Tpo -c -o ztr_dump.o ztr_dump.c mv -f .deps/hash_tar.Tpo .deps/hash_tar.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_dump_all.o -MD -MP -MF .deps/srf_dump_all.Tpo -c -o srf_dump_all.o srf_dump_all.c mv -f .deps/append_sff.Tpo .deps/append_sff.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_index_hash.o -MD -MP -MF .deps/srf_index_hash.Tpo -c -o srf_index_hash.o srf_index_hash.c mv -f .deps/hash_sff.Tpo .deps/hash_sff.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_extract_linear.o -MD -MP -MF .deps/srf_extract_linear.Tpo -c -o srf_extract_linear.o srf_extract_linear.c mv -f .deps/srf_extract_linear.Tpo .deps/srf_extract_linear.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_extract_hash.o -MD -MP -MF .deps/srf_extract_hash.Tpo -c -o srf_extract_hash.o srf_extract_hash.c mv -f .deps/srf_index_hash.Tpo .deps/srf_index_hash.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf2fastq.o -MD -MP -MF .deps/srf2fastq.Tpo -c -o srf2fastq.o srf2fastq.c mv -f .deps/ztr_dump.Tpo .deps/ztr_dump.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c mv -f .deps/srf_extract_hash.Tpo .deps/srf_extract_hash.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c mv -f .deps/srf_dump_all.Tpo .deps/srf_dump_all.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c mv -f .deps/srf_list.Tpo .deps/srf_list.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c mv -f .deps/srf_info.Tpo .deps/srf_info.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/cram_index.Tpo .deps/cram_index.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c mv -f .deps/scramble.Tpo .deps/scramble.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT scram_test.o -MD -MP -MF .deps/scram_test.Tpo -c -o scram_test.o scram_test.c mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_size.o -MD -MP -MF .deps/cram_size.Tpo -c -o cram_size.o cram_size.c /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_filter.o -MD -MP -MF .deps/cram_filter.Tpo -c -o cram_filter.o cram_filter.c mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib mv -f .deps/cram_size.Tpo .deps/cram_size.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:5: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iteratlibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 or& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 2817 | for (/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib destructive_iterlibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 amv -f .deps/cram_filter.Tpo .deps/cram_filter.Po tor /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2948:9: /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o index_tar index_tar.o -lm -llzma -lbz2 -L/usr/local/lib note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib _from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:2745:26libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 : note: libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o index_tar index_tar.o -lpthread -lm -llzma -lbz2 -L/usr/local/lib in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 hashtable tmp(MoveDontCopy, *this, resize_to); /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib | ^/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 if (_resize_del/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib ta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib ::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:143:47: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 143 | libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scf_info scf_info.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 plibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scf_update scf_update.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 ufferfish::util::ContigBllibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o get_comment get_comment.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 ock& cb = (*contigSeqCache_)[c.cid]; | ^ /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_tar hash_tar.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/RefSeqConstructor.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/include/Util.hpp:24: libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_extract hash_extract.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_list hash_list.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(colibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o trace_dump trace_dump.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 nst lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib 167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_sff hash_sff.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 ? typename iterator::lhs/bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib _setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/src/RefSeqConstructor.cpp:338:23: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 8, unsigned long, std::allocator, 64, false>::operator[]' requested here 338 | uint8_t edgeVec = edges[contig.contiglibtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o append_sff append_sff.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 Idx_] ; | ^ libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o ztr_dump ztr_dump.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_dump_all srf_dump_all.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_index_hash srf_index_hash.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_extract_linear srf_extract_linear.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_extract_hash srf_extract_hash.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_info srf_info.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o srf_list srf_list.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_index cram_index.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scramble scramble.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o scram_test scram_test.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_size cram_size.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making all in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -lpthread -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 -L/usr/local/lib libtool: link: /usr/bin/cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.a -L/usr/local/lib -lz /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs/.libs/libhtscodecs.a -lpthread -lthr -lm -llzma -lbz2 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-build [ 54%] Performing install step for 'libstadenio' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && gmake install gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' Making install in htscodecs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in htscodecs gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake install-am gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[7]: Nothing to be done for 'install-data-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libhtscodecs.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libhtscodecs.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.la libtool: install: /usr/bin/install -c .libs/libhtscodecs.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a gmake[7]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/htscodecs' Making install in . gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[6]: Nothing to be done for 'install-exec-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' /usr/bin/install -c -m 644 htscodecs/arith_dynamic.h htscodecs/fqzcomp_qual.h htscodecs/rANS_static.h htscodecs/rANS_static4x16.h htscodecs/tokenise_name3.h htscodecs/pack.h htscodecs/rle.h htscodecs/varint.h htscodecs/htscodecs.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/htscodecs' gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in tests gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[6]: Nothing to be done for 'install-exec-am'. gmake[6]: Nothing to be done for 'install-data-am'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/htscodecs' Making install in io_lib gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[5]: Nothing to be done for 'install-data-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a libtool: install: ranlib /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/io_lib' Making install in progs gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[5]: Nothing to be done for 'install-data-am'. mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' libtool: install: /usr/bin/install -c convert_trace /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/convert_trace libtool: install: /usr/bin/install -c makeSCF /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/makeSCF libtool: install: /usr/bin/install -c extract_seq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_seq libtool: install: /usr/bin/install -c extract_qual /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_qual libtool: install: /usr/bin/install -c extract_fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/index_tar libtool: install: /usr/bin/install -c scf_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_dump libtool: install: /usr/bin/install -c scf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_info libtool: install: /usr/bin/install -c scf_update /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scf_update libtool: install: /usr/bin/install -c get_comment /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/get_comment libtool: install: /usr/bin/install -c hash_tar /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_tar libtool: install: /usr/bin/install -c hash_extract /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_extract libtool: install: /usr/bin/install -c hash_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_list libtool: install: /usr/bin/install -c trace_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/trace_dump libtool: install: /usr/bin/install -c hash_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_sff libtool: install: /usr/bin/install -c append_sff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/append_sff libtool: install: /usr/bin/install -c ztr_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/ztr_dump libtool: install: /usr/bin/install -c srf_dump_all /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_dump_all libtool: install: /usr/bin/install -c srf_index_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_index_hash libtool: install: /usr/bin/install -c srf_extract_linear /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_linear libtool: install: /usr/bin/install -c srf_extract_hash /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_extract_hash libtool: install: /usr/bin/install -c srf2fastq /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fastq libtool: install: /usr/bin/install -c srf2fasta /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf2fasta libtool: install: /usr/bin/install -c srf_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_filter libtool: install: /usr/bin/install -c srf_info /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_info libtool: install: /usr/bin/install -c srf_list /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/srf_list libtool: install: /usr/bin/install -c hash_exp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/hash_exp libtool: install: /usr/bin/install -c cram_dump /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_dump libtool: install: /usr/bin/install -c cram_index /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_index libtool: install: /usr/bin/install -c scramble /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scramble libtool: install: /usr/bin/install -c scram_merge /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_merge libtool: install: /usr/bin/install -c scram_pileup /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_pileup libtool: install: /usr/bin/install -c scram_flagstat /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_flagstat libtool: install: /usr/bin/install -c scram_test /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/scram_test libtool: install: /usr/bin/install -c cram_size /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_size libtool: install: /usr/bin/install -c cram_filter /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin/cram_filter gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/progs' Making install in tests gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib/tests' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4' /usr/bin/install -c io_lib-config '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/bin' mkdir -p '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man1' /usr/bin/install -c -m 644 man/man4/Read.4 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man4' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/share/man/man3' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/io_lib' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib' cd /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/staden-io_lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-install [ 55%] Completed 'libstadenio' /usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles/libstadenio-complete /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/salmon/work/.build/libstadenio-prefix/src/libstadenio-stamp/libstadenio-done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 55%] Built target libstadenio /usr/local/bin/gmake -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend /usr/local/bin/gmake -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/salmon_core.dir/DependInfo.cmake gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/alevin_core.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o [ 56%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o [ 57%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/jellyfish/mer_dna.cc [ 58%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DNDEBUG -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/xxhash.c cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/backtrace.cc cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/edlib.cpp cc: warning: argument unused during compilation: '-stdlib=libc++' [-Wunused-command-line-argument] [ 59%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/TranscriptGroup.cpp 14 warnings generated. [ 60%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SingleCellProtocols.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/jellyfish/mer_dna.cc:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:117:16: note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here 117 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:123:16: note: in instantiation of function template specialization '__int128_ns::__print' requested here 123 | __int128_ns::__print(os, x); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | char padding[nb_padding]; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ 3 warnings generated. [ 61%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp [ 62%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/LibraryFormat.cpp [ 62%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GenomicFeature.cpp [ 63%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinUtils.cpp [ 64%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/VersionChecker.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EffectiveLengthStats.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal:6: warningass generateds. ign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived())[ 65%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o ; | ^cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:501:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 501 | return setConstant(Scalar(0)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:38:7: note: in instantiation of member function 'Eigen::DenseBase>::setZero' requested here 38 | eel.setZero(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EffectiveLengthStats.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EffectiveLengthStats.cpp:42:10: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 42 | return eel; | ^ 2 warnings generated. [ 66%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FastxParser.cpp [ 67%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/StadenUtils.cpp [ 67%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp [ 68%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ [ 68%] Linking CXX static library libtwopaco.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/external/pufferfish/external/twopaco/graphconstructor && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/llvm-ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/llvm-ranlib libtwopaco.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 68%] Built target twopaco [ 69%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonExceptions.cpp [ 70%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonStringUtils.cpp [ 71%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SimplePosBias.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant_:c:otnysptea) && | ^ nt::type) && | ^ [ 72%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SGSmooth.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:2: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: note: read of non-const variable 'nb_padding' is not allowed in a constant expression /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:95:11: note: declared here 95 | ssize_t nb_padding = os.width() - (prefix.str().size() + buf.str().size()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ [ 72%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/src/pufferfish/metro/metrohash64.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cppc:t18: oIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppi:z12e: In file included from =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp :15: bIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppol(MightVec:t6o: rIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppz:e23): In file included from &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h&: M69a: yLinearize /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h&:252:36:& warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]DstHa s 252 | D i r: escttdA:c:cienstse g r| a ^l _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hc:o607:n20stant: >, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested herel , 607_ | _ h atsy_pterdievfi atly_pceonpaym(e TA)ssignment Trai&t&s : :| P ^a c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hk:e1818t:T32y: pnote: ein instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here P 1818a | c k e t T y p e ; b o| o ^ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :u739n:u10s:e dnote: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here = 739 | Kern eplh mkaepr:n:eils(_dtsrtiEvviaallulayt_ocrop,y _sconrscEvaluator,t ructible::vafluunec&,& d| ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ht.const_cast_derived()); | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5:2053 :note: 45in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here: note: 879 | in instantiation of default argument for 'optional_data>' required here c2053all_dens | ec_aslsiagss nompetnito_nlaoolp (:d stp,r isrc, fuvnc); | ^ a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ht:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here e 836 | A ssoipgtnimoennatl<_AicnttuearlnDaslt:TypeC:loeaned,Src,Func>::run(acptualDst, src, func); t| ^ i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.honal_dat:a804:<3: note: Tin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here > 804 | , | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here c 2820 | a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp l:p_102ha:msa16s:p i:warning: g:variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]n m oe102pn | t t_ incooh_naaarl lip;; | a| ^~~~~~~~~~l ^ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h::11721:13:o: 16note: :in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herec note: in instantiation of function template specialization '__int128_ns::__print<__int128>' requested here21_ | ; 117i n | t e| ^_r _n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hi:n2832t:a28:1l 2:note: 8in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here_: c na2832sl | :l:__a_csplrsaiisngstn (mnoeosnd,te (xt_hh)ia;sn-d>lde e r:| i ^vp eu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppdb:lic102 no:d16e:_ hnote: a(read of non-const variable 'nb_padding' is not allowed in a constant expressionn) d, l 102P | l a icnhOabrj epcatd:d:iCnogn[sntba_npta(drdoiwnsg(]);, c o| l ^s (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp):,e95_:ob11a:s enote: t_d ad si sn| ig ^g n=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp_ :oo125ps:<.41Sw:ci adnote: ltin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested hereah r( ,)125S | c- a l( ap rr >e (f )i )x . s tdre(c)o.yssi.zien(s)e r+t (bhuefa.dset;r - >| r ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppf:[57i:]15.:n anote: min instantiation of member function 'Eigen::DenseBase>::operator*=' requested heree ) ;57 | | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp :c18o: uIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppt:s12_: In file included from */wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp=: 15sr: aIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppm:o6n: :(In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp):m.23s: iIn file included from za/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.he:(69): )t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h;h::LOG_0:; | ^ 241 : 36| : ^warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppt:d102::16: warning: :variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]i n t102e | g r aclh_acr paddoinnsgIn file included from t[/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DistributionUtils.cpp:3: aIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppb:_5p: aIn file included from d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppd:i5n: gIn file included from ]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense;: 1 : | In file included from ^~~~~~~~~~n t' requested here:V enote: cin instantiation of template class 'phmap::is_trivially_destructible>' requested heret o r254i | z e = b oiosl_ (tMriigvhitaVlelcyt_odreiszter)u c&t&i bl eML:i:nveaalruiez>e {&}&; D s| t ^H a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hs:D1818i:12332r:e | cnote: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested heret A c1818c | e s s | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :b607o:o20l: unote: nin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereu s e607d | = _ t_pyhpmeadipen:f: itsy_pternitav1mie2 a8A_snssi:g:n_m_epnrtiTnltl(ryo_sc,o pxy)_;c o n| s ^t rauicttsi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:b:lPeae:t:Tvyapleu eP&a&c k e| t ^T y:p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.he:;2053 : 45| : ^ note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hin instantiation of default argument for 'optional_data>' required here102 : 739::205310 | 16c:l anote: sread of non-const variable 'nb_padding' is not allowed in a constant expressions o102p | t i ocnhaal r:: ppnote: arin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested heredidviantge[ nob p_ t739iona | l_ipn at deKdreinranlg:n]:;o pe t| i ^ol n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppa: l95k_:de11a:rt anote: n,95 | | ^~~~~~~~~~~~~~~~s es/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hli:z2820(e:_37t: nnote: bin instantiation of template class 'phmap::optional>' requested here_ p da2820sd | d i n g p=h moasp.:t:woipdttiho(n)a l-< a(lpElroevfcaialxtuo.rs_ttry(p)e.>si zael(l)o c+_ ;b u f| . ^ as/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.htt:or2832r:,(28 :s rnote: cin instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested hereE v a2832l | u)ca.ltasosris,z enf(oud)nec_,h adn)sdtl.ec o:;n p u| b ^sl t_icca snto_dedrei_vheda(n)d)l;e _ b| a ^s e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h<:879P:o5: note: lin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here i 879 | c call_ydTernasiIn file included from et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp_s:a,1s : AsIn file included from li/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hppl:o6c: >In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp : 4| g: ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppn:m:22125: :In file included from 41e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:n: 1tnote: : _in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested hereIn file included from l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreo :o125p420 | (: d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h s: t86 :, 63 :s r warning: c converting the enum constant to a boolean [-Wint-in-bool-context], d86fe | uc no cy )s ;.M ia n| ys ^Le ir/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hnt:e16(a836 warningrhsV:ee46a generatedc:dt. eonote: rrin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here-i z> er836 e | =f [ biAo]so.slni(agMmniemg)eh;nt tV r:ecIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp::15A: rIn file included from cu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppc:n6e: (sIn file included from as/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppc: t23u : aIn file included from l/usr/bin/llvm-ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/llvm-ranlib libpuffer.a | D ^s t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h,:: 69s: gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' 607r:c20,: fnote: u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested heren c )607;:[ 73%] Built target puffer | | 259 ^t: y17/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:: 728warning: :builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 17 259 | : p e note: d in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested heree fb o o728l, | t y_ p_ha s_et rn ia vmiiaeln_ tAesrsniagln:m:ecnatlTlr_aaistssi:g:nPmaecnkates_tnTsoyip_ea lPiaagcsk(etthTiysp-e>n;d e r| i ^v e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hd:(739):,10 :o tnote: hin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested heree r .739d | e r iKveerdn(e)l, kienrtneerln((daslt:E:vaaslsuiagtno_ro,p e(_)r)e;f esrte_ndceere:d:(t)y)p;e ) | & ^& /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :| 879 ^:5: note: | in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h879 | : 278 : 15/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h ::c1819a: l22l:_ note: dnote: ein instantiation of template class 'phmap::is_trivially_copy_assignable>' requested heren sin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here e1819 _ | a s s i g278 n | m e n Base::_tset_no alias_(o tlh eo ro); pp| (h ^d st/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp,: 84s:r3c:, note: mfin instantiation of member function 'Eigen::Matrix::Matrix' requested hereu n c84 | ) ; G Ca| F ^r a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hg:M836o:d46e:l (note: Gin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested hereCp F r836a | g MAosdseilg&n&me)n t=< AdcetfuaaullDts;t T y| p ^e C:leaned,Src,Func>::run(:aictualDst, src, sfunc); | ^ _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here t 804 | r icvially_copy_assignaballle_>' required here, func); | ^ 2053/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: | note: c(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)l a s782s | o pctailoln_aals s:i gpnrmievnatt(ed soptt,io nsarlc,_ iintnetrenranla:l::assig:n_oopptiS,rc::Scalar>()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here | 710 | internal::call_assignmen ^~~~~~~~~~~~~~~~t(this-> derived(), other.derived()); /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 2820 225 | : ret37u:rn Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here in instantiation of template class 'phmap::optional>' requested here 327 | retu 2820r | n d e rpihvmeadp(:) :=o pCtoinsotnaanlt<(arlolwosc(a)t,o rc_otlysp(e)>, avlallo)c;_ ; | ^| ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h501::283210::28 :note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested herenote: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 501 | 2832 | crleatss node_handle : pubulrn setConstant(Scalar(0)); i | ^ c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:47:14 :n onote: din instantiation of member function 'Eigen::DenseBase>::setZero' requested heree _ h47a | n d l_em_abragsien | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:In file included from 20/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9:: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32note: : warning: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>>, Eigen::internal::evaluator, Eigen::Array>>, Eigen::internal::add_assign_op>' requested hereunknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 607 | 4 | typedef typename AssignmentTrai#tpragma GCC dsia:gnosti:c ignPoared "-Wmaybe-unciniktializede"tT y | ^ pe PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>>, Eigen::internal::evaluator, Eigen::Array>>, Eigen::internal::add_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:29:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment>, Eigen::CwiseNullaryOp, Eigen::Array>, Eigen::internal::add_assign_op>' requested here 29 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::add_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:48:22: note: in instantiation of member function 'Eigen::ArrayBase>>::operator+=' requested here 48 | _marginals.array() += _prior_prob; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp63: warning: :converting the enum constant to a boolean [-Wint-in-bool-context] 375 86 | MayLinearVe:ct10: owarning: rvariable 'clusterID' set but not used [-Wunused-but-set-variable] i 375 | sizzee = bool(MightVectorize) && MayLinearize_ t && DstHasDirectAccess | ^ c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: lin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested hereu s 607 | typedef typename AssignmentTraits::PacketTtyepe PacketType; | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: Iin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here D 739= 0; | ^ | Ker/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:472:10: warning: nvariable 'clusterID' set but not used [-Wunused-but-set-variable] e 472 | size_t clusterIlD = k0; e | ^ rnel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, -1, 1>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 45 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::div_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:237:55: note: in instantiation of member function 'Eigen::DenseBase, -1, 1, true>, -1, 1>>::operator/=' requested here 237 | _probs.col(pos).segment(nodeStart, rowsPerNode) /= tot; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::div_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::div_assign_op>' requested here 45 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::div_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:245:25: note: in instantiation of member function 'Eigen::DenseBase, -1, 1, true>>::operator/=' requested here 245 | _marginals.col(pos) /= numStates; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp86:3210::3463:: warning: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]converting the enum constant to a boolean [-Wint-in-bool-context] 321086 | | M a y L i ngeeanreVEexcptso[rgn].push_back(move(eri)z)e; | ^ = | std:: bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>, Eigen::internal::assign_op>' requested here 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseUnaryOp<(lambda at /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:251:18), const Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:254:10: note: in instantiation of function template specialization 'Eigen::Matrix::operator=>>' requested here 254 | _probs = _probs.unaryExpr(takeLog); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SBModel.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/UtilityFunctions.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::add_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::add_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::add_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:177:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::Matrix, Eigen::internal::add_assign_op>' requested here 177 | call_assignment(derived(), other.derived(), internal::add_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SBModel.cpp:288:60: note: in instantiation of function template specialization 'Eigen::MatrixBase>::operator+=>' requested here 288 | void SBModel::combineCounts(const SBModel& other) { _probs += other._probs; } | ^ 7 warnings generated. 13 warnings generated. In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:501:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 501 | return setConstant(Scalar(0)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:2717:27: note: in instantiation of member function 'Eigen::DenseBase>::setZero' requested here 2717 | contextCountsFP.setZero(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, -1, true>>, Eigen::internal::evaluator, -1, -1, true>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, -1, true>, Eigen::Reverse, -1, -1, true>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:144:20: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, -1, true>>::swap, -1, -1, true>>>' requested here 144 | leftCols(half).swap(rightCols(half).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1, true>, -1, 1>>, Eigen::internal::evaluator, -1, 1, true>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1, true>, -1, 1>, Eigen::Reverse, -1, 1, true>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:148:29: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, 1, true>, -1, 1>>::swap, -1, 1, true>, -1, 1>>>' requested here 148 | col(half).head(half2).swap(col(half).tail(half2).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, -1, 1>>, Eigen::internal::evaluator, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, -1, 1>, Eigen::Reverse, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:154:19: note: in instantiation of function template specialization 'Eigen::DenseBase, -1, 1>>::swap, -1, 1>>>' requested here 154 | topRows(half).swap(bottomRows(half).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Swap.h:20:11: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op, 1>' requested here 20 | : public generic_dense_assignment_kernel, BuiltIn> | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel, 1, 1>, -1, 1>>, Eigen::internal::evaluator, 1, 1>, -1, 1>>>, Eigen::internal::swap_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:418:7: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, 1, 1>, -1, 1>, Eigen::Reverse, 1, 1>, -1, 1>>, Eigen::internal::swap_assign_op>' requested here 418 | call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Reverse.h:158:29: note: in instantiation of function template specialization 'Eigen::DenseBase, 1, 1>, -1, 1>>::swap, 1, 1>, -1, 1>>>' requested here 158 | row(half).head(half2).swap(row(half).tail(half2).reverse()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3048:28: note: in instantiation of member function 'Eigen::DenseBase>::reverseInPlace' requested here 3048 | seqFactorsRC.reverseInPlace(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonUtils.cpp:3158:10: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 3158 | return effLensOut; | ^ 21 warnings generated. [ 74%] Linking CXX static library libsalmon_core.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o "/usr/bin/llvm-ranlib" libsalmon_core.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 74%] Built target salmon_core 4 warnings generated. [ 74%] Linking CXX static library libalevin_core.a cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/llvm-ar" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o "/usr/bin/llvm-ranlib" libalevin_core.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 74%] Built target alevin_core /usr/local/bin/gmake -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/unitTests.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o [ 78%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o [ 78%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable 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-I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -stdlib=libc++ -DBOOST_HAS_INT128 -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -pthread -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/src/pufferfish/rank9b.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), coIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpps:(6): ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppv:a22l: )In file included from ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense : 1| : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h::420627: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h10::86 :note: 63in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here: warning: 627converting the enum constant to a boolean [-Wint-in-bool-context] | 86r | e t u r nM asyeLtiCnoenasrtVaenctt(oSrciazlea r=( 1b)o)o;l ( M| i ^g h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppt:V56e:c15t:o rnote: iin instantiation of member function 'Eigen::DenseBase>::setOnes' requested herez e )56 | & & M a ycLoiunnetasr_i.zsee t&O&n eDss(t)H;a s D| ^i rectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp :t6: yIn file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppe:d22e: fIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denset:y1p: eIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corea:m420e: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hA:s86s:i63g:n mwarning: econverting the enum constant to a boolean [-Wint-in-bool-context]n t T86r | a i t s :M:aPyaLcikneetaTryVpeec tPoarcikzeet T=y pbeo;o l (| M ^i g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hh:t739V:e10c:t onote: rin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herei z e739) | & &K eMranyeLli nkeearrniezle( d&s&t EDvsatlHuaastDoirr,e cstrAccEcveaslsu a t| o ^r ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :f607u:n20c:, note: din instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested heres t .607c | o n stty_pceadsetf_ dteyrpievedn(a)m)e; A s| s ^i g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hn:m879e:n5t:T rnote: ain instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested herei t s879: | : P a c kceatlTly_pdee nPsaec_kaestsTiygpnem;e n t| _ ^l o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ho:p739(:d10s:t note: ,in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here s r739c | , fKuenrcn)e;l k| e ^r n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: ein instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here l (836 | d s tAssEivgnmentn:s:tr_ucna(satc_tduearlivDesdt(,) )s;r c ,| ^ f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu:n879c:)5;: note: | in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h879: | 804 : 3 : cnote: ain instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested herel l _804d | e n scea_lals_saisgsnimgennmte_nlto_onpo(_daslti,a ss(rdcs,t ,f usnrcc),; f | ^u n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hc:)836;: 46 :| ^note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 782836: | 3 : Anote: s(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)s i g782 | n m ecnatl::run(actrunaallDst,: sr:c,a sfsuingcn); _ | o ^p , Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heree D804s | t:: S ccaallal_ra,stsyipgennmaemnet _Snroc_:a:lSicaasl(adrs>t(,) )s;r c | ^ ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h: 710f:u17n:c )note: ;in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here | 710 ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h : 21 : 13 :i nnote: tin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heree rn a21l | : : cianltle_ranssaignment(this->delr:i:vceadl(l)_,a sostihgenmre.ndte(rtihviesd-(>)d)e; | r ^i v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.he:d225(:)20,: Pnote: lin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested herea inObje c225t | : : C o n s traenttu(rrno wBsa(),csols(),othee:r:)_s,e t(ionttheerrn)a;l : :| m ^u l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h_:as327s:i20g:n _note: oin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested herep < S327c | a l arre,tSucranla rd>er(i)v)e;d ( )| ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp=: 57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here C o57n | s t a n t ( rcoowusn(t)s,_ c*o=l ssa(lmon)::math::,L OvGa_l0);; | ^ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/LibraryTypeTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp : 6 : MIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppy:L22i: nIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densea:r1V: eIn file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coret:o420r: i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hz:e86 :=63: warning: bconverting the enum constant to a boolean [-Wint-in-bool-context]o o l86( | M i g h MtayLinearVectorize =V ebcotoolr(iMzightVee)c t&o&r iMzaey)L i&n&e aMraizyeL i&n&e aDrsitzHea s&D&i rDescttHAacscDeisrectAccess | ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 607| : ^20 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :note: 607in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here: 20 :607 | note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here t y607p | e d etfy pteydpeefn atmypeename Assi gAnsmseingtnTmreanits::PatcketType PackTetType; | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:a739:10: note: iin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested heret s 739 | : Kern:el kernel(dstEvaluator, srcEvPaluator, afunc, dst.const_ccast_dekreitvTeyd()p)e; P a| ^ c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hk:e879t:T5y:p enote: ;in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here | 879 ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 739 :c10a:l lnote: _in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested hered e n739s | e _ aKsesringenlm eknetr_nleolo(pd(sdtsEtv,a lsuract,o rf,u nscr)c;E v a| l ^u a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ht:o836r:, func, dst.const_cast_derived()); | ^ 46/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5:: note: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herein instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | 879 | A s s icganlmle_ndte :s:rrcun(,a cftuunacl)D;s t ,| ^s r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hc,: 836f:u46n:c )note: ;in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here | 836 ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h :A728s:s17i:g nnote: min instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested heree n t728< | A c t u a l DisnttTeyrpneaCl::lceaalln_eads,sSirgcn,mFeunntc_>n:o:_raulni(aasc(ttuhailsD-s>td,e rsirvce,d (f)u,n co)t;h e r| ^ ./wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hd:e804r:i3v:e dnote: (in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here ) 804 | , icnatlelr_naasls:i:gansmseingtn__noop_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h(:))21;: | ^13 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h :note: 278in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here: 15 :21 | note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here i n278t | e r n a l : : cBalals_ea:s:s_isgentm_ennoatlia(st(hoitsh-e>rd)e;r i v| e ^d (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp):,84 :P3l:a inote: nin instantiation of member function 'Eigen::Matrix::Matrix' requested hereO b j84e | c t :G:CCFornasgtaMnotd(erlo(wGsC(F)r,acgoMlosd()e,lo&th&e)r )=, dienftaeulrt; | ^ nal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/GCSampleTests.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ 7 warnings generated. 7 warnings generated. 4 warnings generated. [ 79%] Linking CXX executable unitTests cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -lpthread -fstack-protector-strong -Xlinker --dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/lib -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib -L/usr/local/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib:/usr/local/lib" /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a /usr/local/lib/libtbb.so.12.14 /usr/local/lib/libtbbmalloc.so.2.14 -lgomp -lrt -lgff /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a -lgomp -lrt Copying unitTests cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E copy /wrkdirs/usr/ports/biology/salmon/work/.build/src/unitTests /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/tests/unitTests gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 79%] Built target unitTests /usr/local/bin/gmake -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' cd /wrkdirs/usr/ports/biology/salmon/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src /wrkdirs/usr/ports/biology/salmon/work/.build /wrkdirs/usr/ports/biology/salmon/work/.build/src /wrkdirs/usr/ports/biology/salmon/work/.build/src/CMakeFiles/salmon.dir/DependInfo.cmake gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/gmake -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [ 80%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o [ 82%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o [ 83%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o [ 84%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 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-fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/Graph.cpp.o -MF CMakeFiles/salmon.dir/Graph.cpp.o.d -o CMakeFiles/salmon.dir/Graph.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 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-DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -MF CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/EMUtils.cpp.o -MF CMakeFiles/salmon.dir/EMUtils.cpp.o.d -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:20: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:28: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:40: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant:r:typeu) &}c&t or(T) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: | builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] ^ 252| | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258: 40 : warning: :unused parameter 'src' [-Wunused-parameter] s t258d | : : ivnotiedg rcaolp_yc_oanlsltoacnatto:r :(warning: tTbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]y) p e&In file included from 241)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp | & : 22 &: | &In file included from ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp :: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h 12| :s: ^246tIn file included from d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp::::15i36: nIn file included from t:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppe:g6r: aIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp_:c24o nwarning: sbuiltin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]t a n: t246In file included from a(:s ^&l( ft syr,ph escn)oa nm{se t s| ct ^o mdm:o:nf:&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp e: warning: r1h: rsIn file included from unused parameter 'b' [-Wunused-parameter])/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp e: 6{785: | In file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp| : c ^8 : eiIn file included from t30a:: t:In file included from ot/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppr:y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp(13p:W: e785*)In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp&p27&:,: 23 u : warning: nIn file included from unused parameter 'b' [-Wunused-parameter]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.hs : i69785| g | ^ n: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.he :di241 t:be36,r: a utwarning: nobuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]sr i( gW241n* | e dp , o )u: n s| s ^i tg/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppdn::e806:d:i 22nb:t, e gwarning: urunused parameter 'b' [-Wunused-parameter]na sl i_806gc | no en ds tova)n ot <| ib ^do o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppbl:i,806t :s_22(_:uh nawarning: ssunused parameter 'b' [-Wunused-parameter]i_ gt nr806ei | dv i bav)lo _i{dd e }sb ti/rt/us c(NtuOonOrsP(i Tg )n| e ^&d & b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp| : ^845 :)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h22 ::{246 :warning: }36unused parameter 'b' [-Wunused-parameter] : / /warning: 845 builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] | N O Ov246P | o iIn file included from d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp| b ^i :t :49s: (In file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppns:t:ds15i: g845nIn file included from ::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hppe:22di :n: tb12): In file included from {/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp :}24 : /In file included from //wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp :N10eOgO: r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppa:l348_:c37warning: o:n swarning: tPunused parameter 'p' [-Wunused-parameter] | 348 ^ | unused parameter 'b' [-Wunused-parameter]a nIn file included from D/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cppt:e <34r845b: i | oIn file included from v o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hppe l:dv,15&o : i_In file included from od_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hppp h:eba12ri: saIn file included from t_t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpps:to(24ruri: nv=In file included from sii(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppags:lnt10_ed: d:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppc::348o nn:bs37):t ur lu{warning: cunused parameter 'p' [-Wunused-parameter]t lo p }348r | ( /T/ )D te Nrr&Oi&Ov_e Pd t| & ^| p o ^)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :p 252e{:r ator =36| ( ^ :s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppt: 367warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]d :: 34252 | : s::t ndwarning: :uunused parameter 'p' [-Wunused-parameter]:lint egrall_const pa367ntt | ^:r :taype/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp)t: o371&r& : | ^ =34=:( swarning: tunused parameter 'p' [-Wunused-parameter]d : :371n | u l blool operator!=(psttd::nullptr_t p) { | ^r _t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp34:582::32: warning: warning: unused parameter 'p' [-Wunused-parameter]unused parameter 'lfs' [-Wunused-parameter] 371582 | | bool o pbeoroalt oorp=e=r(asttodr:!:=n(usltldp:t:rn_utl llpftsr,_ tc opn)s t{ c o| m ^m on&582 :r32h:s )warning: unused parameter 'lfs' [-Wunused-parameter]{ 582| ^ | bool opeIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppa:t5o: rIn file included from =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp=::785(11:s: 27tIn file included from :d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp ::warning: 5:: unused parameter 'b' [-Wunused-parameter]nIn file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp l:785l | 7p : t ri_tIn file included from te /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppl:f8rs: ,In file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppc:o30nt: soIn file included from tr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp (:cW13o*: mIn file included from m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp :po23n: :&69 : r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.huh:snIn file included from 241)s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp: i36{g:: n1 ewarning: : | builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]In file included from ^d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp :2416o: | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8 : )In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp: 30:| : ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppIn file included from s :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppt785/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:d::13:80627: :::i 22nwarning: In file included from :unused parameter 'b' [-Wunused-parameter]t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp e:warning: g24785unused parameter 'b' [-Wunused-parameter]r: | aIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppl 806:_i | 10t e: cr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp a:otv348onor:s(i37tdW:a* n bwarning: tpiunused parameter 'p' [-Wunused-parameter],lg| &_r ^ara hls/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hs_s:)ic246 og:{nn36s( t:t a y| nwarning: p ^tbuiltin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]e < nb ao246mo | el , s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp t_:d _785::h:: a27rss:_ettm drwarning: oi:unused parameter 'b' [-Wunused-parameter]vv: iei _an785lrt | e_e fcg eoriprayeltn(_eTccre)oa tr: a( :nWt| t* ^y< pb/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hpo:e,o259 )l:u ,n& 17&s_: _ ih| gwarning: anbuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] ^s e_ dt259 r | bi ,v i ua nl s_ ic go nn es dtb roouo)cl t, o | r_ ^(_ Th/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp)a: s806&_:&t22 r: i | vwarning: ^iunused parameter 'b' [-Wunused-parameter] a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h _:806a252 | s: s36i :g nv(warning: tobuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]y ip de252 n | b ai mt es (:unsigned b) { } // NOOP | ^ ss/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppt:t845dd:::22:::r iewarning: nmunused parameter 'b' [-Wunused-parameter]to evger _a845rl | e_ fc eovrnoesintdca enbbs:o(:outlny,sp ie_g)_ h&a&s _ t| r ^i vianle_dc obp)y ({T )} &/&/ | N ^O O/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hP:259 : 17| : ^ warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | boolIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppo:p1e: rIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppt:o4r: =In file included from =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp(:s8t: dIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp::n44u: lIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppp:tr30_: tIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppl:f13s: ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppc:o24n: sIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp :c10: o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:m348m:37o:n i&v erdh&s )o p{e r a| t ^o r=(std::nullptrIn file included from _t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp :p1/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp): 785: {:In file included from 27 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:| : ^warning: 8 unused parameter 'b' [-Wunused-parameter]: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp367785:: | 4434 : : In file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppwarning: t:unused parameter 'p' [-Wunused-parameter]e30 r: aIn file included from 367t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp | o: r13 (: bWIn file included from o*/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppo :lp24 ,: o In file included from pu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppen:rs10ai: tg/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppon:re348=d:= 37(b:s, t warning: duunused parameter 'p' [-Wunused-parameter]:n :s ni348ug | ln le pdDt eror_)it v pe| )d ^ & { /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppo :p| 806e ^:r 22a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:t: o371warning: r:unused parameter 'b' [-Wunused-parameter]=34 (: s 806twarning: | dunused parameter 'p' [-Wunused-parameter] : : vn371ou | il dl pbbtoirot_lst ( ouppn)es ria{gt no er| d ^! =b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp():s 367t{:d 34:}:: n /uwarning: /lunused parameter 'p' [-Wunused-parameter] l Np Ot367r | _O t Pb o po )l| ^{o p e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp| :r845 ^:22: warning: a unused parameter 'b' [-Wunused-parameter] t 845 | void obirts(unsigned b) { } // NOOP | ^ =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp=:(582s:t32d:: :warning: nunused parameter 'lfs' [-Wunused-parameter]u l l582p | tbro_otl po)p e{r a t| o ^r =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp=:(371s:t34d:: :warning: nunused parameter 'p' [-Wunused-parameter]u l l371p | t r _bto ollf In file included from so/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp,p: e30cr: oaIn file included from nt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppso:tr12 !: c=In file included from o(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hppms:mt15od: n:In file included from :&p )warning: r unused parameter 'version' [-Wunused-parameter]h{ s ) | 73 ^ | { | v ^o id /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpps:e582r:i32a:l iwarning: z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppunused parameter 'lfs' [-Wunused-parameter]e: ( 785A582:r | 27cb:ho iowarning: vlunused parameter 'b' [-Wunused-parameter]e &o p785ae | rr ,a ticotoren=rs=ta( tsutnodsr:i(:gWnn*ue ldpl ,pi tnurtn_ stvi eglrfnssie,od nc) o bn{,s t u | nc ^so imgmnoend< Do,) I ,| ^B ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp :W806,: 22U:> &warning: unused parameter 'b' [-Wunused-parameter]r h s806) | { v o| i ^d bits(unsigned b) { } // /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppN:O785O:P 27 :| ^warning: unused parameter 'b' [-Wunused-parameter] 785/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: | warning: unused parameter 'b' [-Wunused-parameter] i t845e | r a tvoori(dW *b ipt,s (uunnssiiggnneedd bb,) u{n s}i // gNned o) | ^ O/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] O P806 | | voi ^d bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, coIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Salmon.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: sIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] u 73 | void serialize(Archive& ar, const unsigned int version) { | ^ nsigned int version) { | In file included from In file included from ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp: :134: : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:6: :In file included from 18/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp: :In file included from 5/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp: :In file included from 37/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:573: :In file included from 50/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:: 1warning: : unused parameter 'version' [-Wunused-parameter]In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core :73415: | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h: 139 :v14o: iwarning: ddefinition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] sIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp139r: | i 1a : l In file included from i /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppzD:ee(4rA: irIn file included from vc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppeh:di8&v: eIn file included from o&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppp:44e: rIn file included from aa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppt:ro37r,: = /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp(c:co73on:ns50st:t uwarning: Munused parameter 'version' [-Wunused-parameter]a n t73s | ri i gvnxoeBidad s iesn&et roIn file included from vit/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cppeah:rle1is: zrieIn file included from )(;A /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppr:o8 : c| h ^i v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.he:&90 :a65r:, note: cIn file included from onin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppn) s t90 : | 44ut{: en mIn file included from s p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp| l:a37t: ei/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hppiv ec&l aasrs, CcwoinssetN uulnlsairgynOepd; i n| t ^ v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he:r176sion) :{ | ^ 10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: lIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp,: 11i: nIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppr:n17a: lIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh::29s: c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:a258l:ar_constant_op(value));26 : | ^ warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hunused parameter 'dst' [-Wunused-parameter]: 327 :25822 | : note: vin instantiation of member function 'Eigen::DenseBase>::Constant' requested hereo i d327 | c o prye_turan dlelroicvaetdo(r)( A= &Consdtsatn,t (croownss(t A) ,& scrocl,s (s)t,d :v:afla)l;s e _| t ^y p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:e627): 10{:} note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here| ^ 627/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh | : 258 :r40e:tu rnwarning: sunused parameter 'src' [-Wunused-parameter]e tC o258n | s t avnoti(dS ccaolpayr_(a1l)l)o;c a t| o ^r (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppA: 56&:d15s:t ,note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested herec o n56 | s cto uAn t&s_.ssertcOn,e ss(t)d;: : f| a ^ lIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cppe:_1t: yIn file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hppe:)6 : {In file included from }/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp : 5| : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template clasIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp :22C: wIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpps:e12N: uIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hppl:a15r: yIn file included from O/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppp:;6 | ^ : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176In file included from :10: note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here: 23 : 176In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h : 69r: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ht:u252r:n36 :D ewarning: nbuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]s e B252a | s e < D e:r isvtedd:>::i:nNutlelgaryExpr(rows, rcaoll_sc,o nisnttaenrtn: (In file included from &v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppa:l&23u: eIn file included from )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h| :) ^69; : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :| 252 ^: 36/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:: 327warning: :builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]22 : 252note: | in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327: | 1818: : 32sr:te dtnote: :uin instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here:r in n t1818de | eg rr ia vl e_ dc (o )n s t =ba onCotl>::setConstant' requested here r note: u in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested herec627 t | i1818 b | l re e< t u r Tbnoo>l : s:uenvtuConsatasnletud( S=c aphmalp::iesa_trivially_copy_constrr&u(&c1t)i)b;l e <| T ^> ::va/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpplue&& | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:562053:45 :: note: | 15in instantiation of default argument for 'optional_data>' required here: ^ note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here:2053:45: 2053 | note: 56c | l a s s o pctoiuonntasl_ .:s eptrOinveasin instantiation of default argument for 'optional_data>' required heret( e) 2053;o | pc tl| ia ^os nsIn file included from a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpplo:_p1it: niIn file included from to/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hppen:ra6nl: a:In file included from l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:p::r5oi: pvIn file included from ta/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppi:t5o: nIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseel: _1od: paIn file included from tt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreia:o<348nT: a>/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.hl,:_ 92i :n| 29t ^~~~~~~~~~~~~~~~:e r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hwarning: n:definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]2820 a:l 37:92:: | onote: pin instantiation of template class 'phmap::optional>' requested here t i o2820nn | oa _l a_ sd sapithgamn:n,:t o_ po| tp ^~~~~~~~~~~~~~~~ie or/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hna:at2820lo:>' requested herece ar ta2820ot | ro _r t= y( pcpeoh>nm saatpl :ln:oooc_p_at;si so in| ga ^nl m>, std::allocator>' requested herear t_ ot2832ry | &pc)el;>a s as| l ^ln oo/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hcd:_e90;_: h65 a:| n ^dnote: lin implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.he : 2832:90: | 28pt:ue bmnote: lpin instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested hereil ca t2832ne | onx dT ly ep| _e ^b> a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpps :e 125< : P 41 o: clanote: ss Cin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested herewl ii s125e | Nc uy l l Ta rr ay iO tp s; , d| Ae ^lc lo/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hoy:c176>:s 10 :. | note: i ^in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required heren s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp e:176r125 | t: (41 h:re eanote: tdin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested hereue rr n-125 > | Dr ee nf s[ ei B] a. sn ea :In file included from d:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cppeN:cu30ol: ylIn file included from sa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp.r:iynEsxerptr((hreo12aw: dse,In file included from r /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp-c:>o15rl: esIn file included from f,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp[ :ii6]n: .tIn file included from ne/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppar:mn23ea: )lIn file included from ;: : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.hs| :c ^69a : lIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ha/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppr::_22241c: :oIn file included from 36n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpps::t12a : nwarning: tbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]_ oIn file included from p241< | S c a l a:r >/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp(s:v15ta: dlIn file included from :u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp::ei6)n: )tIn file included from ;e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp g: r23| a: ^lIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hc::o69327n: :s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h22t::a241 n:note: t36in instantiation of member function 'Eigen::DenseBase>::Constant' requested here<: b owarning: 327obuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] | l , 241r_ | e_ th ua rs n_: t drseitrvdii:va:elid_(nd)e st=te rgCurocantlso_trca(onTnt)s( traon&wts&<( b)o,o lc, o| _l ^_ sh/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ha(:s254)_:,t7 r:vi avnote: liin instantiation of template class 'phmap::is_trivially_destructible>' requested here)a ;l _254 d | | e ^s t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hr :u 627c :ti10os:r_ (tnote: Trin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here)i v i&627a& | l l y| r_ ^ed te/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hus:rt254nr: u7sc:et tinote: Cbin instantiation of template class 'phmap::is_trivially_destructible>' requested hereol en <254T | >s : t: av an lt ui(esS>_c t{ra}il;va ir a(| l1 ^l) In file included from y)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp_;:d: 1818e5 s: :| tIn file included from 32 ^r:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp u:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppnote: c11in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here:t : 56 i1818In file included from :b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp | 15l ::e14 < : note: TIn file included from in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp > : 15:56 : : | In file included from v a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp lb: uo9 e: o >l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp :c{4uo}n:uu32;ns: te sd| warning: _ unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]= ^ p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h4h: | 1818m:a32p::# .:pnote: srin instantiation of template class 'phmap::is_trivially_copy_constructible>' requested hereieas tg _Omt1818nr | aie v si G( aC )C ;l ld iy | ab_ ^gco onopolys _tucinocun ssietdgrIn file included from In file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppu=oc tp:i1hbrmlaee:d: pIn file included from : :In file included from atIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppy:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:b5r: :ieIn file included from v-/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp::vu55a: iIn file included from n: a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/DenseliIn file included from :ln/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp1:l: iuy13In file included from t: _i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoreaIn file included from lcie:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppo420z&: e:&p yd _| 14c": oIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp ^n::15s: In file included from t86/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h| ::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hppr632053: ^:u45 :c:9t i: warning: bnote: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hppconverting the enum constant to a boolean [-Wint-in-bool-context]in instantiation of default argument for 'optional_data>' required herel : e 4< 86:2053T | 32 | >:c : l :warning: av unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]sMa sla yu4oeL | &pi#tnp&ei ra oa| rng ^aVm elac /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h t::G2053o C:rpC45ir :zid veinote: aain instantiation of default argument for 'optional_data>' required heretg=e n obo2053so | ptotcililc(ao Mnsiisaggl nh_ootiprVtneetidcoe trn"oan-ralWi lm::za e:yp)obr pei&t-v&iu aoMtnneiaa nloyi_pLtdtiiainatolaenii_d,zi"en t& | e| ^~~~~~~~~~~~~~~~&r ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hnD:as2820lt::H37:a:os pDnote: tiin instantiation of template class 'phmap::optional>' requested hereir oe cn2820taA | lc _c de ast as< T >| , ^p h /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h| m: ^~~~~~~~~~~~~~~~a607 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hp20:::2820: :onote: 37pin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here:t i note: o607in instantiation of template class 'phmap::optional>' requested heren | a l 2820mo ena alAlls n note: tain instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested hereT l 2832 | crllaoacs_is;t sn :o| :d ^Pe a_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hhc:ak2832ne:dt28lTey: p :enote: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested herePp au cb2832kl | eictclT aynspseo ;dn oe d_e| h_ ^ahn ad/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hln:e739_:db10la:es e:note: < in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herePpo ulb il739ci | y T rKaceir ntneosld, e k_Aehlralnnoedcll>(e d_ sb ta| Es ^ve a, phmap::priv::hash_policy_traits>, std::allocator>' requested herer c E125av | ia tl su ,a t Ao lr l, o cf >u nd ce ,c| o ^dy ss/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp.t:i.125nc:so41en:r snote: ttin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here(_ hc e125aa | sd te _r d- e> rri ev fe[ di (] ). )nd;ae mc eo| )y ^;s ./wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :| i879 ^n: s5In file included from e:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cppr :tnote: 30(in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here: h In file included from e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppa879:d | 12e : r In file included from - /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp> :rc15ea: lfIn file included from l[/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp_i:d6]e: .nIn file included from ns/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppae:m_23ea: )sIn file included from ;s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h i: g| 69n: m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h ^e: n259tIn file included from :_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp17l::o22 o: warning: pIn file included from builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins](/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp d: s12259t: | ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp s: r15 c: ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp f: u6 n: c In file included from )b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp;o: 23o : l| In file included from , ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h :_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h69_:: h836/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ha::s46259_::t rnote: 17iin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here:v i warning: a836builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]l | _ a 259sA | ss is gi ng (n tm ye pn et n< aAbmcoeto ulsa,tl dD_:s_:thrTaeysmp_oetvCreli_evraienafeled_r,aeSsnrsccie,gnt:cy:>pt:ey:npraeum)ne ( &as&ct td u:| a: ^lr De/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hsm:to1819,v: e22s_:rr cenote: ,fin instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here e fr ue1819nn | cc )e ;< T > | : ^: t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hy :p 804e :) 3 :& &pnote: hin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here m | a ^p804 : | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h: :i 1819sc:_a22tl:rl i_note: vain instantiation of template class 'phmap::is_trivially_copy_assignable>' requested hereis as li1819lg | yn _m ce on pt y_ _n ao s_ sa il gi na as b(pldhesm>' required here_a am se2053s | iscgtlndam:se:snr teo(mpdotsviteo,_n casvlr< c :, | pi ^rn it/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hve:ar2053tn:ea45 l:o: pnote: :tin instantiation of default argument for 'optional_data>' required hereai so sn2053ia | glcn__lionptay,lp e :n| a ^~~~~~~~~~~~~~~~pm re/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hi: v2820Sa:rt37ce:: :onote: Spin instantiation of template class 'phmap::optional>' requested herect ai lo2820an | ra >l (_ )i )np;th em ra| np ^a: l:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:o::p710ot:p17ti:io onnote: nain instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herea ll <_710ad | la lto ac o, r i_ nt| ty ^~~~~~~~~~~~~~~~ep re/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hn>:a 2820la::37l:: cnote: lain instantiation of template class 'phmap::optional>' requested herel lo _2820a | s s i g npmche_m;na tp (:| :top ^htio i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hns:a-2832l:_d28typee> alloc:r_;i v e| d ^() , ot h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hernote: .:in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested hered2832e: r28 i:v enote: din instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here( ) )2832; | c l| a ^s In file included from 2832/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hs:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp225 : | :n20c:1 olnote: d: ein instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here_a hIn file included from s a225/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppsn: | d8n : l In file included from o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppd :e _rheatnudr47e: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h::n946: l:394 33:p:eu18 bwarning: B:definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]a: swarning: e :variable 'readspmol' set but not used [-Wunused-but-set-variable]946:p | _u bs ll iiecct n394(o od e | tT_hnwhooe dr_aed n)_d_h ldae n; e_ sdtb r aul c| suete_i< ^iPb oa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hvslneei<_ctPyiTt:1re327a:o6ir20t_:sa,tt o rA¬e: lr lleoin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested hereaopdicse>r p ca tyo| r327m | =To( ^l c r {oa0n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpps}:i125r:t41;te:st ,u r| T ^nAnote: wlin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here od el125_r | doi c_v> de e ds ( t )| r ^ = u /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppcC: o125t ni: vs41 etd_:eac inonote: ttin instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested herey(es r.r oia125nwt | sos er( r) t, &( oh c)e o;a d l e| sr ^ (- )d>/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h,er c:eo2817yf:v[40ali:)s] ..inote: n;in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here n | s ^a m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he2817er | t:(627):h10e;a:d note: ein instantiation of member function 'Eigen::DenseBase>::setConstant' requested here r | - ^ 627 | > r rfeotru r(nd essettrCuocnetsfit[vaien]t(S.cnaalma_er)(;1 ) )| ; ^ i| ^ t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppe:rator 56i:t15 := note: hin instantiation of member function 'Eigen::DenseBase>::setOnes' requested heret . d56e | s t r counts_.setOuncetsi(v)e;_begin() ; | ^ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | In file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp:1: mIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: vconverting the enum constant to a boolean [-Wint-in-bool-context] e _86f | r o m ( mMoavyeLr,i nearhVte,c tmoirni_zbuckets_wanted); | ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here = 2745 | b o o l ( M i gshptaVrse_hashtable tmpe(cMtoovreiDzoen)t C&o&p yM,a y*thiLsi,n eraersiizzee _&t&o )D;s t H| a ^s D/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hi:r3278e:c21t:A cnote: cin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested heree s 3278 | s | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 607 : 20 : note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here i607 | f (t_yresizep_eddeelft atyp(e1n)a) m e| ^A s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hs:i3813g:n29me:n tnote: Tin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested herer aits::PacketType Packe t3813 | T y p e ; | ^r e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ht:u739r:n10 :r enote: pin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here . t739 | e m pKleartnee lf ikernel(dstEnvdaluator_,o rs_rcEvaluaitnosre,r tfc(assttd_der:i:vfeodr(w)a)r; d| < ^ K/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hT:>879(:k5:e ynote: )).second; | ^in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28 :87914 | : note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | c a eldlg_eds[sourecne].insert(ssei_naks)s;i g n| m ^e nt_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(thIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:s47: -/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h>:d946e:r33i:v ewarning: ddefinition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]( ) ,946 | P l Tawion_Odb_jdeecstt:r:uCcotnisvtea_nitt(erroawtsor& operator=((c)o,colsn(s)t, oTtwhoe_rd)_,d eisnttreurcntailv:e:_miutle_raastsoirg n&_oo)p;< S c| a ^ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here a 2817 | for (destrructive_iterator it = ht.destructive_begin,(Scalar>()); | ^ )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57;:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9In file included from In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/EMUtils.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp :note: :1In file included from in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here34: : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EMUtils.hpp2948/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp: | :6 14: : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp: :5 15: : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:m:5o9: v: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hppe/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:_:4f1:: rIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corem32:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp(420:m: : warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hunknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]: 86 :463 | :# powarning: rconverting the enum constant to a boolean [-Wint-in-bool-context]a g m8624a | G C C Mdaiya: gLnosIn file included from iti/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedEMOptimizer.hppcn e:vai8grnVoercetdo r"i-e: WrIn file included from mza,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppyeb e=- ubno oiln(iMtii:hg14ta: ,lhIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpptmz:iVe15endc: "t_In file included from ob /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hppur| :ci ^9kz : ee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hppt):s 4_&:w&32a :nM tawarning: eyunknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]dL )i ;n4 e | a#| rp ^ir zae/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hg :m&2745a&: 26GD:s tCnote: HCin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested herea sd Di2745ia | rg en co ts At ci cc e sissg p na| o ^rr se/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hed:_ 607h":a-20sW:hm tanote: ayin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested herebb le e-607 u | tn mi pnt(iyMtpoievadeleDifo zntetydCp"oe pn ya| ,m ^e *Atshsiisg,n mreentsTirzaeits:_:tPoa)c;k e t| T ^yp e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h Pa:c3234k:e9t: Tnote: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here y pe; 3234| ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | K e r n_erle skerinzeel_(ddeslttEava(l1u)a;tor , s r c Ev a lua t o r, f u n c , d s t. co nst _/cas/t_ daedrdiivnedg() )a; n | ^ o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hb:j879e:c5t: ,note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested hereg r 879 | o w i fca lnl_densee_easdsig nmebnet _lo op| ( ^d st,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :s4225r:c67, : fnote: uin instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested heren c )4225; | | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here s 836 | t d A:ssignmentt::run(earatorc,t bool> uinsert(P&& obj) { return rep.insert(stadl::forward

(obj))D; } | ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here t 28 | edges[source],.insert(sink); | ^ src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:368:16: warning: variable 'muSum' set but not used [-Wunused-but-set-variable] 368 | double muSum{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:247:12: warning: variable 'totalNumFrags' set but not used [-Wunused-but-set-variable] 247 | uint32_t totalNumFrags = 0; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:217:22: warning: variable 'muSum' set but not used [-Wunused-but-set-variable] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp 217 | : 450 : 12: warning: variable 'totalLen' set but not used [-Wunused-but-set-variable] 450 | d o u b ldeo umble utSotaulmL e=n {00..00}In file included from ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp : 1| : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp;: 8 | : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cppv:e502_:i14ter:a twarning: ovariable 'asum' set but not used [-Wunused-but-set-variable]r & 502o | p e r a t o rd=o(ucbolnes ta sTuwmo _=d _{d0e.s0t}r;u c t| i ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppv:603:10: warning: evariable 'totalLen' set but not used [-Wunused-but-set-variable] _ 603 | i t edroautbolre &too)t; a l| L ^e n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h{:02817:40.:0 }note: ;in implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here 2817 | | ^ for (destructi ve_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp2948:776:10: :warning: 9:variable 'totalLen' set but not used [-Wunused-but-set-variable] note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here 776 2948 | _ | m o vdouble totalLen{0e._0f}r; o m| ( ^m over, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, boost::hash>>::DefaultValue, std::pair &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Graph.cpp:10:24: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cppnote: :in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, boost::hash>>::operator[] &>' requested here 34 10: | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp : 18 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp : 22: iIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: dIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corex:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h=: 139v:e14r:t Mwarning: adefinition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]p[node]; | ^ 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:34: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:18: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppa:l1:: :In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppc:a4l: aIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp_:8: cIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppnIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp47:: 5/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h: :In file included from 946/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp::3311:: In file included from warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]: 5 : 946 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp : 7 : TIn file included from w/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppo:_5d: _In file included from d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppe:s5t: rIn file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densec:t1i: vIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core_:i415t: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hr:a139t:o14r:& warning: odefinition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]p e r139a | t o r = (Dceornisvte dT&w oo_pde_rdaetsotrr=u(cctoinvset_ iMtaetrraitxoBra s&eo&); | o ^t h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.he:r2817):;40 : | note: ^in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h :281790 | : 65 : note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required heres 90f | otre m(pdleasttern ( ) ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hc:l2948a:s9s: Cnote: win instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested herei s e2948N | u l l a r y O p ;_ m o| v ^e _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hf:r176o:m10(:m onote: vin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required heree r ,176 | h t ,r emtiunr_nb uDceknestesB_awsaen ^: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hN:u2745l:l26a:r ynote: Ein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested herex p r2745( | r o w s , c o lssp,a trasnet__hoapst(mvpa(lMuoev)e)D;o n t| C ^o ipnyt,e r*ntahli:s:,s craelsairz_ec_otnos)t;a n t| _ ^o p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h<:S3278c:a21l:a rnote: >in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here( v a3278l | u e ) ) ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h : 327 : 22 : inote: fin instantiation of member function 'Eigen::DenseBase>::Constant' requested here ( _327r | e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hs :r327e:t22u:r nnote: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here i dz327ee | r i vr_edteuedlrt(a)n =d Co(ne1sr)iv)ed () t| =a ^n t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h(:r3813o :wCso(n29s):, note: tcaonlin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested heret ( s3813r | (o w s () ) ,, vc aorlle)st;(u)r,n vraelp).;t e m| p ^l a| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ht ^:e 627 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:f:10i627:n: 10note: :in instantiation of member function 'Eigen::DenseBase>::setConstant' requested hered _note: oin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here r _627 | i 627n s | ree rt turt( generated(. sSntcdsa:tl:aafnrot(r(1wS)ac)ra;dl < aK| T ^> (r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppk(:e156y:))15)):.; s note: e in instantiation of member function 'Eigen::DenseBase>::setOnes' requested herec| o ^ n 56d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp | ;: 56 : | 15 ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppnote: c:in instantiation of member function 'Eigen::DenseBase>::setOnes' requested hereo 28u:n14t: s 56_note: . | in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested heres e t 28O | n e s[ 87%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o ( c) ;o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy u | n ^e dtstem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp gIn file included from se/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp_s:.[5ss: eoIn file included from tu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hppOr:nc11ee: s]In file included from (./wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppi):n;5s : e In file included from r| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hppt ^:( 7s: iIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppk:)5;: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp| : ^5 : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281::14: 34warning: : definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp :28118 | : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp : 22D: eIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densei:v1e: dIn file included from &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core :o420p: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:a86t:o63r:= (warning: cconverting the enum constant to a boolean [-Wint-in-bool-context]o n 86 | s t D eMnasyeLBianseea&r Voetchteorr)i;z e | = ^ b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.ho:o48l(Mi:g34: note: hin implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required heret V e48c | ttoermipzlea)t e&<& tMyapyeLnianmeea rizDee r&ived> class MatrixBase | ^ &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here D 90 | template> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp cr:i xt946T8A | y: c pIn file included from c e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppe :s>30 : TIn file included from ws /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp o:_ d _13d| : e ^In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h ::607t24:: r20In file included from cu:lc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppa: 10ts: is/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppvnote: :ein instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested hereC_657 wi:i 15st:e 607warning: eNdefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] | ru al657tt | yol pa reldhes&f_ steyropytpeOetprne;aa rmt e&o| r ^oA= pse/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hsr(:aitcg176ononmre:=n10(t:T rnote: asin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herei tct o176 s | n:s:tT wPla hcrokeste__tduTs_reyndp teDe tPeseantrcr&skeueB tacTrtsyhep t :e| :r ^a| t o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppN ^r:u l&167lo:)26;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :a | note: ^in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here:r 739y :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h167: | 2817 :E40 10x :: p note: r in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required herenote: ( in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here r o w2817739s | , | cK oe lr s n, e li n f to kerer rn a(l nde:e?l:s(tdss ctrtaEuylcatpvrieavln_auceo_nisatmttearneat ot_rio,otpe rt:ho(tlr.h,d sefsutn_vrscuac,t eidlstvuttee.e_crb)oe_)ngtsi;nt( y_ p)c| ;ae ^s( t m| _ ^m e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hm: 2948+: 9(:_i note: *in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here B I2948T | d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he S ) r : /i327 v: Ue_22dB:(m onote: ,v)in instantiation of member function 'Eigen::DenseBase>::Constant' requested heree) _ ;f B327rI | ToSm| ( m ^o, vre/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr(e:,t879iu *h:t ,B r5mIiTnS_)b u%nc : kUe dtnote: Bsein instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here_rw i) va 879e n | dt| (e ^ ) d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp= :)645 c:;22Ca ol nl:s t| note: _ ^d ein instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h a: 2745645: | 26 : note: nin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested heres e _n a2745 | t gs(c sBiigtrAnrmreanyt__[ lio ]ow os p=( ()s1d,p; c o| l ^s (as)r,s tev,_ahl a)ss;rh c In file included from ,t| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp ^a:f b27u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hl: n:eIn file included from c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense627t)::m;110p: : ( In file included from Mnote: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreoin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here| :v 415 ^e : D627/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h | o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:n 13917 :t:rC warninge836o14tsp:u generated r:. warning: n46ydefinition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] :, s enote: *139tin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested heret | C h oi 836ns | s , t aDrAneestrs(i[ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o Ssicd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp 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/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp eiea_dglt&nao mr)o(e;pn1 et) r)<| aA; ^t c o t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h| u: ^ar 3234l=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:D:(956s:c: o15note: ntin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here:s T t note: 3234 | yin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here Mp ae tC56 r | li ex a B_n rae esd se, i&Scz rootceu,h_nFdeterslu)_tn.;ac s(>e 1:| t):O ^;r n ue/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h n:s ((90 a) :;c 65t : u | ^a note: In file included from lin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp :D 5 s: 90 In file included from t | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp,t: e11 sm: rIn file included from p cl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp ,:a t5 ef: , Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heret348 m,: e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h804 M: | ga92 rt:r oi29cxw:T iawarning: yfldefinition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] p lne_ e>a92e s | ds i bg en nm oe | _n ^a t sc_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hsln:iao4225sg_:sna67 ml:Cei wannote: istin instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here(sd_se to,N spu4225relc | r,l fa at uorn rcsyt)&d;:O : ppa| i ; ^ro< ip/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h et| :e782 ^r:r aa3t:o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hrt,note: : (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)o 176b o782:o | r10 l=: >( ccnote: oinnin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required heress aet r 176lnl | t_oa _s (sarPse&i&st giunomgrbnnje)m n t ( e dD snte t ,{n _ssore cpr,e tBeuirrananst etos s:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h(::isNg90unt:l65l:a r_ynote: Eodxppin implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required herer<:(t: rfyo op90w | srt,wea remcnodpmt(leeso <,Dt byijpnetnesartmn:)ea):;S l N}cu:a ll:a r| , ^ts lyc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpppaa:r28l:yaeOrnp_23a,:mc eo tS nynote: srtpin instantiation of function template specialization 'spp::sparse_hash_set::insert' requested hereacen: nt a28_ | omp e < MS: acS cta lar a liearxrdTgy>e>sp(ev(>[)a )ls o;u ur e c )| )e ^] .;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hi n s | :c ^e710 r:l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ht17a(:ss327s:i:n 22note: Cin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herek w:) i ;snote: 710ein instantiation of member function 'Eigen::DenseBase>::Constant' requested here | N | u ^ l l327 a | ir yn Ortpee;t ru nr| an ^l d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he:r176i:v10e:d (note: )in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here =: :176Cc | oa nl slrt_eaatnsutsr(inrg onDwmesen(ns)te,(B tachsoeilr,di evvreaidlv>)e:d:(N);u,l loatrhyeErx.p dr e(| rr ^io vw/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hesd:,(627 ):c)10o;:l s note: ,| in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here ^In file included from i n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppt627:e:225r | 19:n 20: a:In file included from rl /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:note: ::in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested herees1 tc: au225lIn file included from | arr _nc o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core n s: ts a415rneet: tt_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hCuo:ropn139n< :SBcsaa14slt:aear: >:n(warning: vt_definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy](as Slec uta139e(l | )ao )tr; (h 1e ) | )r ^D;)e ;r i| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hv: ^e| d ^& 327 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:o:22::p327 56:enote: :r20in instantiation of member function 'Eigen::DenseBase>::Constant' requested here15:a : t o327note: note: | rin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested herein instantiation of member function 'Eigen::DenseBase>::setOnes' requested here= ( cr32756oe | | nt s urt e r Mnt au rtdn ercriioxv uBedndae(ts)rse i&_=v .eoCstdoeh(nt)eOsrnt )ae=;sn ( t )C(| ;o n ^rs | ot ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.haw :nsIn file included from 90t(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:():65r,19o warning27 w: :sc (note: o)lin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required hereIn file included from ,s generated90/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denses:. ( 1 | ): ct,oIn file included from e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corelmvs:pa414(ll): a)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h,t; :e 281v< a| :tl14 ^y) :p; /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he :warning: n definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]627a| : m ^ e281 In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp 10/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:N : u:l 627D1l:e10 arnote: i: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested herevrIn file included from :ye/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp d: &O4 p ,: In file included from o627t | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppy:p8pee n[ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o a: mrenote: cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp 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CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp In file included from aort re627/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppt | :ri u44 =rre: t(In file included from nu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppcr:o22 : snesttC oxDnIn file included from en n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densess:Tesye1ttBa: anCsptIn file included from o(een>& S /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core :c415o: ta/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hsl:h139a:t14 a: rn te( S c(arlwarning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] )1;c) a)l;r (| a ^1 139)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpps: | 56) s;: | C 15w ^ D e:irsi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h enote: v:in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here| N ^ u l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppl:a56r48y56e:d34 | &::15 : onote: p in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required heree r note: a48t | oin instantiation of member function 'Eigen::DenseBase>::setOnes' requested heretreO= m(p pcl oant;s e < 56| tt ^y | p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :cMeanota rmuinx176e :Bt as _D es.e &r i10covteos:udn enote: h>in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required heretteO n sec_l.sa rs())s176; | s ; M | ^ar e tte/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hr:i90tx:B| 65 ^Ou:a rsnnnote: ee in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here sD ( )| ;In file included from ^ e90 n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h | | : ^90 ts:e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppe65m::Bp 5lanote: : asin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required hereIn file included from te t: eIn file included from :Ni i x1 Tny: p et> In file included from e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoreM r a ny:ca420cllla:as:: ss/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hcLsa:ls86a r:Ci 63_Cwcwnoiensas:tae nwarning: iconverting the enum constant to a boolean [-Wint-in-bool-context]tN_ uo slper86r(MyvoaOlrpallya;iu L zr| iey ^ne )e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hO :)176apr;V: 10;=:e note: | | in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here ^ c t o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h176:r | 327i : ^zr eeb t22/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h=o:: 176bnote: o:in instantiation of member function 'Eigen::DenseBase>::Constant' requested hereoluo10(r: M lni(note: MgDi hgin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here327htet | VV e176ecn | tsr eceo ttrrBoiaersuierztnzi : nM:saNveyeuLdli(MnBleaaaya)rLs yie=r ECnx, :c& t:oHNlasc(&us)olD,i rvellc saat,DArsy lti)HcEan;csxe Dp it| s ^rs e ec/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hrrt(:nAa627rcloc:e:sssc: w a 10l| :| as r ^ ^note: ,_ c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hin instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereo :n607s :tc20a :o627 n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hlt:note: | sin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607_ ,o: 20ir ne607ptt>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested herea rl aantr ylp>607s: | e ( :evtdaeCtlfos utycypaeln)aspret)da_;ecfe onnt nta| s(m ^eyt p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hS:ace327aA:nn22as:lst im_note: aoin instantiation of member function 'Eigen::DenseBase>::Constant' requested hererpg (ts1T()tvri)gu;na mlra n| ie tuds ^n:e et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp)::r)Pi56T;vraaecd k: ei15(tt:T| )sy : ^pnote: =:in instantiation of member function 'Eigen::DenseBase>::setOnes' requested heree/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h P: C56P327 | a ac:c ko kn22eesttt a: n T Tnote: tyycpin instantiation of member function 'Eigen::DenseBase>::Constant' requested hereoe pu( rePnoat;327sc | w_ k. esst(e| ) ^T,r e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hctotOlunsreyns(p )(d,)e:e ;vr;a li )739| ;: ^ 10 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h| | :v ^note: e ^in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here739/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hd : 627 In file included from ::739(10 | 10:) : note: =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppKin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested herenote: ein instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereCr: n19 e 739ol | 627: k nK | se treanrnIn file included from etr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denselen(:er1lt: ( In file included from oukwd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coresr:(se414)tnr,E: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.hcsn:v281oe:lats14lC(u:e)ol ,awarning: ndefinition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]tsv (tod as281ar | n,t t( lES)vs;ca l rauc l| aEaD ^tr ov(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hea1l:urr627),:ai10)vt: eo;s d r& r| ,c ^note: oE fin instantiation of member function 'Eigen::DenseBase>::setConstant' requested herepuv/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppn :ecar ,la627u | ad t56s otrre:=.15(tc:tocu onnote: orin instantiation of member function 'Eigen::DenseBase>::setOnes' requested herenrnss tt, s 56f_D | ce unanescte ,CB s ato snd_se ds&t ea tcnr.ootitc(uhvSneocdtn(sa)sle_ta)rr;)( .1;_) c | | s ^ ^ ) a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h;es:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h 879tt: :O| 548 ^_n:d: eer note: 34i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppsv::(e)in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here56;d: ( )879note: 15) | in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here; | : ^ 48 note: In file included from | | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cppc ^in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here: at 27l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h: l:e In file included from m879_:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densepd5:e:l56 na1stnote: | e: e In file included from in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core <: 348879 ta : | y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h p c: eo 92 nuc:an29am:ste ls l_warning: D.definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]es sr_iegid vnt92mee | enOd s>nn eets c_(ll _a)nsaoo;so_ ps asM (a| isd ^tgsrts, ni In file included from ims/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppgr:ecnx,nm1te: _BnIn file included from a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppfo:us4no: cIn file included from et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp )p ;:_ 8o: (| In file included from pd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp ^e: sr| 44/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hat ^: tIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp90,o:: r:s83665&:r22 46: o::pIn file included from enote: note: rcin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required herein instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested herea ,t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseo 836r : | 90f=u1 ( | : ctIn file included from noecAn)ss;s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coretim :gpnln 414oa: _m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h| ta ^e:s esn281/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hi:, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]_note: au in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested herema oel 281p | 836D | s eNtr auT tl olDrA&ya)seprr;esyi OCiplv eg,e| an ^d n me&ed/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.htn: y90,to:Sp65 | :=:sr(tMutTne(caaocttnyrupismaxlteDTsCt ,ly eppalDaeet>ne snuahsren:r :y)crC)uOw;n p;i,s ( | t e ^| ya Nc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hp ^:uteln804la uama:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.her:3yl48OD: p:Ms atnote: 34;in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heret , r s:| r i804 ^cx | T note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h y:in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here,176cp:e 10 :>f48 u nac note: | )in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herel lt;_ a 176 | e s s| r eictgmunpl ^ramn ls/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hse: anD etCn804_s:nw3teo:_ Banote: eiain instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereviseO:grd:c>N,p u;cn fl male| ulsn ^acsr) n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hyMt:;E_ x176 pa| : ^rn10(t: orr_i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hao:lx iwBs782a,note: s ea:csin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required hereo(l s3 :, | 176 dnote: ^is n(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h t t:782, e | rs90n r:rc65a, e:ct ulfrnote: :nuin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required herena:c l) l 90;Ds | ec _t aenlmsaper| a_ls ^aBct oesn, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereavyr Ocrp >,e21, d(i>vn | t: ae lritu:ney)npate)ln;ea :N r:mnaea | ls ^:M us:al/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hci:tlgraanl327ri:lxy_22TE_yax:opsppser< >inote: (in instantiation of member function 'Eigen::DenseBase>::Constant' requested heretr y op327 wegn | sa mn e, m r e c cnDotelst(tsl:t,a:hSsu sicr asli-na>Crnd,w titydeseerprneirneivaaNmevldeeu (d:)(:Sls,r) c Pc=a: llCla:oaranyrSOsic_ptn;caO lba jo| ea ^nc ntr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hst(:tr>176:o(:w):asC10(n)to_)o;pn<, S :c so| ctlnote: a ^ansin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herel( atr )>176,( ( | vr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hvo:a a710lw l)r:su17(;e):et , )c unote: )rin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here| n;o ^l Ds /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h| ( ^e710 ):/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h, | :n o627327t::s22he10eB:ra )note: :,in instantiation of member function 'Eigen::DenseBase>::Constant' requested heres note: e iin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here n< D 327 t | e e rr in rienv627aet | dl> t:e:rm:nu:alul_:a:scsNa rlirlgu_lnane_sospliaxdprre ( rro>wiss(,ve=e cdotlCso)C()o)n,,s nt ;oati nhntsetrt e(.ranr| daonlw: ^est :((/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp)rSi,scc avcl:o57elda(:s15):(r) ),;( 1v| ) ^note: a a)ll;) ; in instantiation of member function 'Eigen::DenseBase>::operator*=' requested herea /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hr| : ^225| : ^20 57_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h: | :56c627: :15 10 :: note: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here :in instantiation of member function 'Eigen::DenseBase>::setConstant' requested herec o note: 56no | in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here627 | sr e ttcuu o225aur | nnnt nss_ et._t soCetotnO sntpe)In file included from (;v=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense :t s1u| : ^aIn file included from r l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreuae/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:ln:34856: :m)15/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:: 92 note: )o:in instantiation of member function 'Eigen::DenseBase>::setOnes' requested heren29: :B;: a 56warning: | m| definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] as ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ht: 327h92: :: | _:s e22t:: L ( octnote: h eornin instantiation of member function 'Eigen::DenseBase>::Constant' requested here)uo O;_ Gans327t_ | ssi_g .nsmeetn| Ot0n_e so;( ^)p e;r r ae tt| | uo ^ ^r &r n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ho :pd327ee:rr20ai:tv oenote: In file included from dr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp(=:)(in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 27c : =o nIn file included from sIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/DenseC/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cppt327: 1o:nn | : o In file included from _ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core34sr: eaIn file included from ts/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:tsau420ni: t:g(r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hnrn18mo: : In file included from 86we:dn63/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpps:e:tr(22 i_warning: : o)In file included from vp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense,e:converting the enum constant to a boolean [-Wint-in-bool-context]re ad c1to : l86In file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core | s(r:( 420) : & ) )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hM;,:a =y | 86vC:Loa ^n sli)63/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h;tn::e 90aa : | rn ^65V warning: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.heIn file included from :t627(:crt oconverting the enum constant to a boolean [-Wint-in-bool-context]o note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here10w86s | ( r ) , : :M58acy Lii znote: 90: nin instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereeIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppo: l as (627) | | , rr evtau=r10l: nVIn file included from )t s;eecbt otoCl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppo(rM :i| g40 ^: iIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hmzo:n627:hept lsVtaa4et: =n: In file included from 10t:e bnote: oin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here< (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh t627ycSo | tple( n:ao29r: mc eaMli/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hhr:i258a:rg( 1h)z26e:t eVNwarning: u))l leat;unused parameter 'dst' [-Wunused-parameter]&urcr ty& O258M | a| ny ^ op ,s rt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppLi:ey56i:n15v:ztp Ceo)ieonenote: dan in instantiation of member function 'Eigen::DenseBase>::setOnes' requested herea smter 56i | z &e&c o MpM ya _ acao&ut&yr innaxlTlLyitDopse_n>csta(etaot .rH (r A s&idaeS s s tcOz t ec a,ln Dleas&(&s )acr;s i| ( ^1o) )n;rsCD wset iH| cttaA cAcs ^s In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppD/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp::56ie:srs1 e: ec&N tIn file included from 15A| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp ^u ::4 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hnote: :l: lsIn file included from cr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp607acin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here,c e:: rs56y8O20: s | : p s ;note: tIn file included from in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp | | ^: 44d ^ 607: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:In file included from | :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp :cf 607a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:o:u176l:2022ns: :: In file included from note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseein instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested heret:_y t10tyspp:_e e1. d607): snote: | {eeIn file included from f }/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core t: t 348y| : in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required hereO/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.htn:p ^e92 es: (29/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hhn:)176; | :y a warning: 258pdefinition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] : rme| eedt4092 ^: | e Ausrsfi warning: n unused parameter 'src' [-Wunused-parameter] gt ny mp258nee | nn Doae_ mtnvesToraia dIn file included from eiA tBsscss:oi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppaspigyn:s_gmnamlePnltoea:_coepkneec5epde: sr:P:att/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppoN5u:a:l:c10l: ,In file included from kaerr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp: yt=ET:yxP40pae: cIn file included from ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp (In file included from pk/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp ce:r7 t:T4y(: rpo| c ^w ooIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:ns: n:e739 In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp29P: ta,s t:c:n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hhok10e:t c_oa :Anote: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herelsT5s: &yIn file included from ss258p,r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:cieg , : is;t 26 739| : | 5n ^dm: : : warning: In file included from unused parameter 'dst' [-Wunused-parameter]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densen::ft739e:ran101ael nK:e rnote: tn s_e: oIn file included from in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereel :lp : s ce/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core258_:k | 420trearlaa739: yntr p | e oe)v oKi_l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :e(rcr86&d) ;n de:l{so cton}Esktv63 e:a a plwarning: | u nrt| ^y nconverting the enum constant to a boolean [-Wint-in-bool-context]_ ^ea a_lot/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.ho(lr:,90 : 65dsplt(cElvvuin implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required hereaalt oyu aLalrt90o | ur,i ,aen )fttusno)c;e rr,ea (c rdEm| pV ^Asv etl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h.accl&a:u327dats:ot22,t:t oe nc>::Constant' requested herenyts ip ertz327_ nAcea | &as m r,sc =ft, eu_n sNrut ecltduebrol,oradi:l:vfne ( rddsdt(y)aeOlp)Mr.,cii;gvo eh s de| (n_ ^)t tVt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hye: c=pt879e sC:otynopr_ic5azsne:a esnote: t)m) _e{in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hered }& M& a e t879a| tMnrtr ^ai(i y | r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hhxoLTviy pwen:see258(:) , da40>r (:) )cio zcwarning: ea lunused parameter 'src' [-Wunused-parameter]sl ; l ( _ )| ^, 258d &e | v avl &n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h)c;: osl879e:_5a i: dsa sDnote: | sstin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested hereH assCDwiiisg ^en mNeunltl_ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h879roaec:o627pcyo_:rpyt10(:d | Asc t ,cO seps;s note: | ain instantiation of member function 'Eigen::DenseBase>::setConstant' requested here r ^l c ,l627 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :| o ^c acft | 176/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hoa: : lr10l:_u(rneA607 cnote: :d20in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required heree) :t ;& nuds r| ^note: nin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested heree/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h_ a176sst: 836s :si | ,607g46n:m een note: tin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested heret _clroeC | o nos t puo(tntd sr836A | yns&ttsapn e DA,edstr ncsse(BsSirgc,na,e c fmseef stunnyaty :::p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppe:eANs46uCsl:e al56l:anote: r15nin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested heree )d :836 | , inote: yASsEs{grin instantiation of member function 'Eigen::DenseBase>::setOnes' requested herex}pcr ( ,56i | r o| gnnw ^mFmue sne ntn,< tA cTc crotauli>at lsD:s: t PcTo:yap:cekCsleu,r tiueTnatynnp(eeed n,tPsSra_r.csceak,enFtcuttTnauyaclp>O:n::secl:D;er ua n| ( ^sa tsc(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ht:u739a):;l 10 ,D:s| tl ^a r , _note: scin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested heresro rnIn file included from cc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpps,t: 19, f739au: | n cnIn file included from )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense :;1 Kf uen| : tIn file included from r ^n_c oe)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h;l: 728/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corep:k17:e< 420Src:: n ae l| l ^a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h( rd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hnote: :>in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested heres(: 804t86 :E:v728v | 3aa:63l ule ):)u ; a note: warning: converting the enum constant to a boolean [-Wint-in-bool-context]t o ri, in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heren tser| rc ^n Ea/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hv:a327l: l:u86:a | cta ol 22r:l 804, | _ a sfnote: usn iin instantiation of member function 'Eigen::DenseBase>::Constant' requested hereM gcnc amy,ae327Llinn | lt __edna os_ssaairlginarVmste(enetth_icnso-t_u.ta>olrdriicezornae s n(=iddvseest d,b(oro t)lsi_vr,cc ae,o (tsfduhMnec(i)t)gr;_ dh= t V.eeCcrd ioe| nrvtisvet ^o ed/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(:d782r()))a;, n : 3| i ^t :i(n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hz r:tnote: eo(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)) e879w r782 ns:a& | (l ) :5&:c :,aM alylLainote: nse sacriin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heregi_zansosel_sio gpn m(e<)Sn,c 879 t | (vd as t&,la l )s;r ca, r| c, &atlyl ^ _Dps dieen/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hnntat:seH627rm:ee10 n_a:aa ssDnote: iOsin instantiation of member function 'Eigen::DenseBase>::setConstant' requested herei gt n627mh | e rrle:Dc :tarseseieAngrti_vntlcueodr:_:oocpStssatn(:t20():)rS:;c cS c aa| lnote: a,rin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herel, t ^a r yf p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h(eun1an607:m)278c: | e)15 );S: r;c :note: :t| S c ^ayin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here pl a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h| re ^>:( 836)278d:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppe46 | f: t note: : y)56pin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here e:; n 15a: m836 note: e| | ^in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here A s s iA/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h s:sg710inBgmane:m56sn17ete | n:: T :tnote: r, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here a i t 710s _: | c:AoPcastc eu ka elttDTu_y nsp tnets oT_Piyanaptl.eesCreilcteaOanknsan(eleodset:(t:)h,;ec raS Tlr)| ylc ^;_p,e aF ;s u sn| i ^c| g> ^n:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:e84:In file included from n739:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppr:3:u:101tn:((t : hnote: aiin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here sc- In file included from t >note: u739din instantiation of member function 'Eigen::Matrix::Matrix' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppae : | l4rD : sIn file included from ti,Kv 84/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppes | r: 8r: cIn file included from ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppn :e44 G: CdFf(rIn file included from )e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp,: 22o: lau In file included from tk/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseh:necgr1M)noe: edlre;l(In file included from d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core(.sd e:rti420vG: CEeF/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hrd| v:(a)a86lg:M ^)oud e63a:;t olwarning: r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hconverting the enum constant to a boolean [-Wint-in-bool-context], : & s&86r | c| )804 ^ E :v3 a lMu:=aa ynote: tLo irin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heren, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.he afdrueVnf ce,ca :u804d225t | s: tl20 to.;c:ca onote: lr nl si_| ta_ ^zscsais in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested heregten _m de e=nr225ti | _vbn eood _(o a)l l)(iM;ia gs h In file included from t| r( ^eV td/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BuildSalmonIndex.cpp:s879etu:,:c 5tr:34n snote: oin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hereBrr: aciIn file included from ,z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp 879es | :ef) u15 n :c &: )&In file included from c;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hppa::l12_l _ : d| In file included from e ^Mnsa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppeystL e(:_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h24ia: n:seo21aIn file included from s:ti13hgreni/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppz:me re :note: n)in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heret _; l21 10o | o &: &| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp ^:p iD657n:s(15dttseH:tr a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h,n a:ssrwarning: Dldefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]i: r:327cc:e20,ca:t lfAl657u_ | ca csnote: ns cin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested herel) h;es i_s gs sn| e t ^ mt| ee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h327r ^ | &n : o836 t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(r::e60746tt:h:pu20e i:note: s r-note: a>in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested heret din instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here ro607n | er rd836=ie | r( vi cveotAnessydsp(tei) g,ndd (lm)hP elnateisnf=<_ sACetoOyntsctbpejtetureaca&ntn l:rD:tasC(homrnstosTewt)s (Aysap{ne) s,Ci lg tne(ca| onmerel ^osdwn s,t(S(r)In file included from ,Tc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppr,aFi uvn:ct>)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpps:::a:r58,: luP:In file included from acc167nko(:e26/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppt:a)l;cTs ytp10e: ( :In file included from u) | Pa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppa: ^clknote: 44D: sin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required heree ,tt ,167T | yspro ce/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hIn file included from :,627; f:u10t hn c :)| ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h note: e30| : :In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp ^in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here739 :r )13: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h 10::804 ,:627 : note: | 3in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here :In file included from inote: rin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heree739n t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp :e | tr804u n r K | 23 : aeclIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h r:ln?e:n t:69l: smyuell_p eta_C/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hao:s241nskinssgensrtnmeiegln(tdna:__sntoE_vaal36oi:pas( )tnd| ::):;c ,note: ::(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)i ^ dn ls tte.h 782/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp| | s :_ gc ^r aolcs/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppanl56:l:s57__e15ats::c_ tcostnote: 15inegrs:tan_astin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here tmynet_>::operator*=' requested hered vp eeod57s | (t(),) ;s l r,| 56 ^ | _c_ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 879mh,_a:s 5 i:n mte_note: tin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested herer cme +i vr 879(o | uin a *i la BnI t:TlsSc_)d:_oc.esa aeulsts/Otnlt rsUnie_Bgssd(,euncnt_os_eo _*rpa, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here> ( )836246M):a ; | y LA | s ^si | note: n e in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested herei/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp: g n:71084r: mVe17n:t , Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herec t : euIn file included from 645: | c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh ta l os t710 : | r29Di: s tz d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh T ey p:e C l 258= ieg:acn:b26B:ieoIn file included from no:ld t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppwarning: :unused parameter 'dst' [-Wunused-parameter]t,5A e(rSr rirnaaM: ncl258: | :,iIn file included from yFc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp _vtaeg:oghrl[11li_: utaina]ls c_dV sce>cctiIn file included from o:go/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppn:rnso:rp5u: mi=In file included from zenne/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hppt()t a:y7 ac: (1n&t&t ;u_Ma lthaIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp5 : oIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppl| ol ^c:d Day5eLsro: ttliIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densev:,, esor rcd(_(,A_1) ,f: &hIn file included from danu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coress:n420c: ) _;o tte t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h,r:aih| e ^r .v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr: di86caei804lozrn:i:63v:_ swarning: etdceconverting the enum constant to a boolean [-Wint-in-bool-context]o n3s :( ) )t86; note: | & rin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here| &uA c ^ t Dos& rs(rTc )804, | M&t&a H y Lc| ian ^s ta/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:e252a:rl36l::d :warning: s:225_faVDaibuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]rlesc :s es20_t252iA | t:y e g cp note: ecc)in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here {n:te so225m | se r}i n | stz e_ ^ =t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h| :n ^bd oo 607_::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh a lo::r20liea258s:i40((:Mditsut:,r n n s rBctnote: geagwarning: shin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here,unused parameter 'src' [-Wunused-parameter] t V ercft258a lou_ | 607 ren cc:v:o_i | d) sceotp;o( oiy t h| z_n ^ese ta)ltay rln)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h t;: p::operator=, Eigen::Matrix>>' requested here a cLsoA_ctnrsi siat327lsvl iiA | _ a &nglan mss_resreacroenpiiztteygc nT,m( e&nu&sr Tttn()dD dss: t&,dre &s r:taf ariH| c ^al,i vs/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :D259seidnei(r)e _t:etr17nt:c= twarning: ayA plsceCc):o builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]: :: Pe{naacss259sk | tea t sT y n }| pte ^ Ps /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(:r607oai : c g20kn:_w o | se (note: p ^t T) in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here<,y pt ey b607;poe | o c onl a| m,et ^yl D pss_te_(d:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hh)a:,:sS739_cetaf: 10lv:ra irv,itnote: tain instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested hereayllp)_ aysep;ne s739ai | mn eg a | mKSeen ^( rrIn file included from tAy/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpppsnsce::i:lg nSmce e90n: tanlaa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hkT/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/radicl/BasicBinWriter.hppe:r:rmr22627a:>n10:e(i etls60s):)(::td ds:;warning: Punqualified call to 'std::move' [-Wunqualified-std-cast-call]:: at cnote: kin instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereE | v rael e62722mu | a ^t | t T/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hy:p710oB: 17 v:eroe ra,P ssirnote: ain instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herec tkueectBc T_710r | eEr nyfipv anl W e re uer;a ts ei| o ^rntc etirCn t,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(:ee s739otnd::10sftu(c:tco:anote: S,in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested herec:atlrl ayr< (clh1d_s)t apa)739;se.s)i | r > &cKg&e& n r| m ^on &e e n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :t56n(s| b ^t:li t n_k15ce_:rhanIn file included from edsla(tdas)i st-:> note: _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppEt:vbail1d_unaetrin instantiation of member function 'Eigen::DenseBase>::setOnes' requested herei: v_ ddoaerIn file included from e,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppd:t10 (sar56c: | rEi)vIn file included from a, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp( v ol tuheeda( r .)c)mt;od:eo44 u: nIn file included from trsi_v.esd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp(e or| t)O:)30; ^, nv/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hee ( f: suIn file included from b: n| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp ^c:i13,(879n) _;d: sdIn file included from att.a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp)::225)c {23::| o5 ^} n;:20 s:note: t : in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here_note: cIn file included from in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested herea| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h ^ s t :In file included from 879225 | 69_ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp : | std:: | : 19 d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h: In file included from ec:In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppa:r l:l _ d1ie58n241 s:r36e:ve: _: tIn file included from In file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppau/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Cores: rwarning: d420ns:i g: nbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]m10 e(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hBna:s86et _: :In file included from 241/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp | l :o: o63p:()d s: )_;t ,warning: converting the enum constant to a boolean [-Wint-in-bool-context]s s44 r86c | : ,eIn file included from ftu(n o c t:| ) ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpph ;: 30 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.heM: rIn file included from a)y;L :i n879/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppe a| | ^r:s:5 ^ tV/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he:d13327: c:t o20r:i :: z:In file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppinote: nnote: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested herein instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here t :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h24 =: 327:In file included from e | 836 g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp :r46a l879r:ebt_ unote: r | in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested heren :c 10od oeo: rn l836s(tc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppaM:i | 348i:l37 g vhaeAtsndt:V< (lbswarning: )_unused parameter 'p' [-Wunused-parameter]eicdgennm etn=to l: ^e:: l r ucp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hn:(246at | note: A ^in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here: tc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h36:cc:836t e s swarning: 627ur | builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]_:ta46 : lnote: pin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested hereD | )836s | {t ^, | 246sArs ^rcs, | f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppu :e gtn:m367607u:n34::r20e:c n nt)<; s eAnote: warning: t in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here:| unused parameter 'p' [-Wunused-parameter] C cst 367t | ^ u d607: | : oa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hn:ls t804a:Dn3bs:i ttnote: o(o in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herenSTty pye C804pceldaelfa | ttryelpege( aonnpreael _ c1rd)c,a)Sar;otacn,mFouls enrlct >| _ =A ^s =:(ssi:ag/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppratsnnsmieudnn:(:at:tngcnTmrtau56u:l<15i:baelnpltDts_sn:o:tP aonote: ocl_,kt e,r_in instantiation of member function 'Eigen::DenseBase>::setOnes' requested heret _ h sT56_ayarps | t_e l ptir c a)i,cso(P uan cdfv{kteusnics) at_ t.;T,syeplet_| c ^ o; nsOrnce s ,( )| ; ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp ^ :| fs371 t ^ru/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hun::c 34 739:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h c:t:728o):r17;:( warning: 10unused parameter 'p' [-Wunused-parameter]T| note: ^:in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here) note: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp: :& 728&37121 | in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here1 : : b | 13In file included from o o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp::739l onote: p | ein instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here| 4 ^ r: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :iIn file included from n /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppt 252:aet21: | 8o: rKn In file included from rear nli!n:t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp=eer(l: :scn4436ka: laIn file included from lt:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppdle:::22 :c_warning: ra: n:aeIn file included from nl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseul:ll(s_1builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]a: sd ss lsIn file included from itg/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coren:p252mtE420ri_vega: nl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hnuta :p86m: | t o63 rt,:e () t{warning: :nconverting the enum constant to a boolean [-Wint-in-bool-context] s tr| c_ nsh ^o t ids:-86>_E | a: dienvtla/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppri l:iuvae ds582a(et(: )oMta32yrgL:ri,n e aPrwarning: Vunused parameter 'lfs' [-Wunused-parameter]elca,la_iht co ins582r i | zfbooO-ones>ld tue=ro binpbeoajcov,rlne aetc, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herezoen < ^&Dn&a,lc: : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.haDs :o879lssi | tsH( Ia s D ,c)a259,gon i_l:Brt,oh 17elpW<_c:e,rSdce) tUAa, nlwarning: >s ac&iec _rbuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]a rhe,stsyssp neti259nes | armgn) a n| l ^ : e { : m uOl _ t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h| h ^me: r607 eD: 20 aens t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:s:r785_:lioi g 27o:nv_po(pdesnote: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here< bwarning: Sdcta,ol oalr, ,s607r | cSunused parameter 'b' [-Wunused-parameter]:, c_:_a lSacrhafl>a(a us)n)c_);; r t| r ^ >785i | | ( ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 836v :)46i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp a)i:t57;: :t15 :| y ^ le_r pae/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hd:note: a278tin instantiation of member function 'Eigen::DenseBase>::operator*=' requested hereoenote: :sin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here15 : r sf inote: g(57Wn836( | * | in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here A s ps i g n ,c ott ymyup278ne | u psni tes e_nnnaa mme* A=eg n est ssst oc:yt:>h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:etp:rer)yu;pn (P aae| In file included from ): c&c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp ^k:t 27&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppeu:ta: 84 lIn file included from :806 3:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense| D22 ^Ts yt::,:p1 : e sIn file included from ;note: warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corerunused parameter 'b' [-Wunused-parameter] in instantiation of member function 'Eigen::Matrix::Matrix' requested here: c ,| 806 ^420 | f: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h 84:n | :cv86 o)739;i: 63:Gd:C | b10 ^:i warning: note: F tconverting the enum constant to a boolean [-Wint-in-bool-context]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here :s 804( :u863n | 739s | :ir g an g note: eKM in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereo edd e rb n)804e | Ml l a (y{cG LCk ailFelrn}ea _aa/gs/rMrs oVnNeeiOdcOtgPn moeelln(&td_s&rn)ot_ E=av la| id ^ielzae sf (udaas/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp=tt uobl:to845,o rs;,l:r(cM,i 22f :u n| ^cwarning: sgunused parameter 'b' [-Wunused-parameter]r) hc ;Et845 vV | a e | c l ^tv oo/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.huir:ai21dtz :eo13)br: i,& &tnote: Msin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereaf y(u Lun21ncis | ,in egIn file included from nd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppe: sdt 1ib: anIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpper.ir):c nz10{: oe n}&s& ta/_/Dcls a:NsOIn file included from t:Oc_a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppdPe tlr Hl:ia44| _va ^e: sIn file included from D/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppdsi :rs(ei30)gc: n)tIn file included from m;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppe:A 13cn : tc| In file included from e( ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppts sh /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hi :s:| 24-879: > ^:d In file included from e5/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:i:v10e: :d 607(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppnote: ::)in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here34820,: 37: : P879note: lwarning: | aunused parameter 'p' [-Wunused-parameter]in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here i n 348O | 607 b j | e Dc t :ec:rtCiayovnplsetedl&adnetf( _r todoywesp(pn)ese,In file included from ner/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppc_aotlaoa:smse95s(: rIn file included from A)=i,g(so/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppsnisg:tmt44deh: n:mn:In file included from ten_eul/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppnr:ol30tlToprp)(adt,s: r ti,_t tiIn file included from sn: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppsp:tr13P)acc: , In file included from ekf{/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppr :e u23tn| : T ^In file included from yn/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppca:p:le:69):367: ;m:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hu 34: lP241_a ac| sk: ^e36 st:T:y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hp :iwarning: 836warning: g:unused parameter 'p' [-Wunused-parameter]builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]46 : e n367note: | ;241_ in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here | o b o 836p < | | o l ^: S Asc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hts doap:se:r:aiigl739natr:nemgt,eS10rnoar:=c= (tnote: sin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here< all A739_ca | rtt uca>o (KdlnDss:e:t)t)rnT;a uynpltnlee15Ei:av:a:lrl _uudane(satt)conote: t rin instantiation of member function 'Eigen::DenseBase>::operator*=' requested herer u,{ cs tu oarrcl( DTEs)| t ^ ,v&57a l | u&ast or /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp| c ^, :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h371fr : u 246n:c36:)34:;, c warning: o| ubuiltin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]f ^nu : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h246:t | s804_n c ,warning: unused parameter 'p' [-Wunused-parameter] : 3d s:t *371= | .:cs o anl smto_ncsanote: :sin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heretb_to:d om l804a t:od:hpeerriiva:e | dt(:)oL)Or;! = G| ( ^sn _ 0ttdc;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ha: : l:l879| _:ena ^gs5u:sri gl anlnote: lpm_terin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested herec_ tno tpn879)_s | n t {oa _ n a t | l, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 86 s | d t21d | :& s: &t n, su Mra ylilcL| ,i npn ^ttfre _et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.haru:nnc )l;252 f ar:Vls:36:e,cc:ta lclo no_srti zwarning: a| ceo builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]=s ^m smb/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ho oo:iln(<252gM836D:,46 :I , | nBim ,gnote: het in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested hereWV,e nct Ut836( | >to:rhii s&A-ss tsz>dird:gh:snie)e ){m re&i&v eMn naty| L ^ ^h:taas rn_(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:tt:rruWin(v607(rio:w20a*a:ls note: c_tpu(in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here,a cu) n607osli | ,gpD cy snt(etTdyo),lp es b&,(ds&rec ,)f f| uut ^ynncp,se )io;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h gn :n| eatdm ^259 eh eor)) , | i ^n t:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp728A17e:::17s:s r806i:nwarning: a22note: :lbuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]:g in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here:nm warning: munused parameter 'b' [-Wunused-parameter] e 259 n728t | T r | a 806u | i t lis_n:t a: evro iPs sadnca l ibgint :s_k: oecpae t({t sTr}()yi pt)v;he/ ii/s a| ^N O-/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp>:dOle;rP57 i _ :| v| ^a 15 ^es: ds (i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp)g:note: ,nin instantiation of member function 'Eigen::DenseBase>::operator*=' requested here :o (57t | 845th :y22e p:r e 739 .:dne10r: iawarning: c vmoenote: edin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereunused parameter 'b' [-Wunused-parameter]u n (s) t ,dt845 | 739:si : | _ v rKnoeer*indtme =o lsev abkilemreto_ns:nrra:(elmfna:te:uelnar(shis:gedsn:ncLeedOsi}tp o:a(s)t)_;d e r| i ^v e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hd:(278):)15;: note: | in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h278: | 879 : 5In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp : note: 1 in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppB879:a | 4s : e In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp: :_c8sa: elIn file included from tl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp__:nd44oe: anlIn file included from sie/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppa_:sa22(s: osIn file included from ti/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densehg:en1rm: )eIn file included from ;n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core t: _420| l: ^o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h o:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppp86:(:84d63:s:3t: , warning: note: converting the enum constant to a boolean [-Wint-in-bool-context]sin instantiation of member function 'Eigen::Matrix::Matrix' requested here r c 86,84 | | f u n GcMC)aF;yr La ign| Me ^ao rd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hVe:el836c(:tG46oC:rFi rznote: aein instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested hereg M= o 836db | eo lo &lA&(s)Ms ii=gg hndtmeVefenactutc:t:Access | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:un(ac607t:u20a:l Dnote: sIn file included from in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested heret /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp, 607s | r c: ,30t : yfIn file included from pu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppen:d12ce: )fIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp;t: y15 p: | eIn file included from ^n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp a:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hm6:e: 728 In file included from A/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpps:s24i: :gIn file included from n17/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppm::e10 n: note: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested hereT: r657 a:728i15t:s | :warning: :definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] P a c657k | e t T lyihpnset_ esPreantcatklee:rt:&Tc yaoplpele;_r In file included from aa s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpps:it58g: | on ^mIn file included from er n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppt=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:_10(: :nIn file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppIn file included from oo:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp44:n95739: : sIn file included from In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp10:ta:l :i37 : note: lin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereh s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp _44739s: | e t tKeerIn file included from r&n /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpper:a:lh73 :3050s:k)se r{n e( lt| h ^( i: d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpps:t167E:v26a:l sunote: -In file included from ain implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required heret> warning: do r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp,167e | s r :c E v 13a l ur ia t unused parameter 'version' [-Wunused-parameter]: oIn file included from r 73 | , v e f u n cdv ( ),o d s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp?,i:t24 d. ctso: oeyIn file included from nt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppshpretie:n_10aacrlm.ae: s id/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppzi:et(etA348e_:rrdireacrv37itve:doehr d:(i:warning: )(lunused parameter 'p' [-Wunused-parameter]) )vh;e s&348 _ | as, e | tr i ^Dt ee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:_,879t rc:on5iy:ptn enote: ve(rein instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested heremsd tn_ a&ml 879e | um + o:( icnp :e*aa rlsliaBgstInsT_Sei)og rd=de/ (ninsns t_e tUo_dBap,:v , unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here:e ^ r warning: i /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hunused parameter 'p' [-Wunused-parameter]v645: e | 836 d :367: 46 | : : S cnote: b aoin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested hereo ll aor >p e( 836r)a)t;o r =| = ^( s | t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hd::278::n15u:l lnote: pgtin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested herer _ t278 c | B Aip st sA) ir gr{na my e _| n[ ^Bti a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp(::s84:t:rd3u::n: (nnote: auin instantiation of member function 'Eigen::Matrix::Matrix' requested hereclt lu pa84t | lr D_ stGt C,pF )rs ar{gc M, o | df ^eu ln(cGC)FragMo;d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp e: l582| &: ^&32 ):/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h :=warning: 728 unused parameter 'lfs' [-Wunused-parameter]:d e17 f:582a | unote: blin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested hereot o; l 728 | o| p ^ e r a t oirn==t(estrd:n:anlu:l:lcptarl_lt_ alsfssi,g ncmoennstt_ ncoo_mamloinaW/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppd,:e 12rU: i>In file included from v&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hppe :dr15(h: )sIn file included from ,)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp :o{6t : h In file included from e| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppr ^:. 24: dIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp657::515: :iIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hppwarning: :definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]11 : In file included from 657/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp | : 5 : lIn file included from h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpps:_7s: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppe:t785t:e27r:& warning: ounused parameter 'b' [-Wunused-parameter]p e rIn file included from 785/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp | : 8 : iIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppe:r30a: tIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppart(oWv:*re13=: (In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp opn,s tud nls:h(is24_: sIn file included from eg/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpptn:t10e: re/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppd: 657b:)&, 15 :u nwarning: sdefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]i g nr657hes | d ol)h s _| s ^e t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp)t: e806r:&22 :o pwarning: eunused parameter 'b' [-Wunused-parameter]r a t806o | r = {( vcooinds tb ilthss(_us n| s ^i g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppn:e167d: 26b:) note: e{t t}e r/&/ ,rNhOsOin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here)P 167| | ^ { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp : 167 :i26 : note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here: 845 :16722 | : warning: unused parameter 'b' [-Wunused-parameter] 845 ? t y | p e nvaomied biittesr(a u n?s itgynpeedn abm)et oirt:e:rnalth{to s}_ s/e/tet rN:O:OrelPnrha_ lt: y:spa_eIn file included from s| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpps ^(i:gs30n: mIn file included from e__/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpptomt:pee19m<: r SIn file included from _+ct/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp y:(ap18ile: a(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hr*m:, _946tBm:Ie33yTm:pS e)+warning: n definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/a( mi Ue 946B* , | O tB BhI IeT TSrTS)Dw, e o/r(_ idiUv_ Bed*,de :s B:tBISITcTSraSul),ca tr%(i> iv(U e)B*_)) i;B t I e T| r| S ^a ^)t o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h%r:: &278645U ::Bo1522)p::e r note: note: ain instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here| tin instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here ^o r 278=/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp645 | : | (645 c: o 22 : n s note: t in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here T B w645 ao | gs c_ eBd i: _:t d_A esr ser ttar _yun co_gta[ciliBvi]ei a_t=siA (r1or;tta eh rey| a_rt ^[o)ir; &] | o= ^) ;1/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :; 84 | : ^3| : ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :note: 2817in instantiation of member function 'Eigen::Matrix::Matrix' requested here : 4084 | : note: Gin implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required hereC F r2817a | g M o d eflor( G(CdFestructive_iteratroagMro dietl &&) == ht.destructive_begin( )d; | e ^ f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here a 2948 | _move_from(moveru, ht, min_buckets_wanted); | ^ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: tin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here ; 2745 | sparse_hashtab l| e ^ tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp: 30 : ifIn file included from (_resiz/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppe:_de13l: taIn file included from (1/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp):)24 | : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h10:3813: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: 29definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] : 657 | lhs_setter& operator=(const lhs_se tnote: ter& rhs) { | ^ in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | 3813 ? typename iterator::lhs_setter_type(m_mem + (i * BITS | ) / UB, BIT S, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | r ^In file included from e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppt:u95r: nIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppr:e44p: .In file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppe:m37p: l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hppa:t73e: 50f:i nwarning: dunused parameter 'version' [-Wunused-parameter]_ o r73_ | i n voisde rsteIn file included from : v(In file included from es/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp&t: d44a:: r:In file included from ,f /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppoc:ro37wn: as/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpprt:d 73uIn file included from <:nK/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppsT50i>::(5g kn: warning: eeIn file included from unused parameter 'version' [-Wunused-parameter]d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hppy ) :In file included from )i11.ns: te In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppv73o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:n | :de722;r: : In file included from sIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppo :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppn:18 v): 19o| : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hIn file included from ^ i:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp{ :d94618 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp : :s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h33:e:946:: 3351:: 17warning: warning: | rdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]: ^ i note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here946 | 51 | T w ob a_rdc_o946ddeeGsrtoruupc | t[ibv ea_rictoe rdaet]o r[&ua molTpiwie]ozr _e=ad t(_1oAd;rr =ec (sh| ci ^vt oern&u caIn file included from srtt,i /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cppvTIn file included from w:e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp30 : c_oIn file included from n:istte/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp ou:_1r: andt19o_rd&seIn file included from i : osIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hppp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppe:r18ag: tn/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht:e9464:rd33o:: u In file included from warning: idefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]rcn= (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpptt: i c8vo946: vnIn file included from esetr s | iT/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppw _oo_ :d 47i t: enT/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hw_odr)_aedts :o_rt946 {&r: u oc)tdi33e| : ^; vs ewarning: t| _rdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]i ^ tu ce/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht946r:ia | 2817tvo :r e40 _ :i& oTt)note: we;in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required herero a _ | dt2817 ^o_ | dr e&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :s ot2817 p:r 40ue :rc at note: itfin implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required herevoo err_= (2817i( | tcd oee rn ss at tt ro urT cwf&to ioorv_ pede(__drieatdtseeotrsrrtaur=tc(uotccirtvo ineiv_steti _t =iTe trwhaeott_ro.ardd _teiodsre s&ttro u)=c; t hitt vr| .eud ^_c iet/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hsti:etvrr2817eua:_c40tb:ote irgnote: viin implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required heree&n _o( b))2817e;; | g i n| | ( ^ ^) ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :: 28172948 | :: ^940f ::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ho : r2948note: note: :in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here20in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here9( warning : d 28172948 | snote: generated | ein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here s t r2948 | . u fc o t _ri mv o(e dv_ eei_s_tmfteorrrvuoaemct_t(ofmirrvo oveim_et(ri mt,=e o rhvhaettt,r. ,odmr eih snitt_,trb uum=ci ctnkhi_tevbt.esdu__cebwkseategntritsune_c(wtd)i)a;;vn e [ 89%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o t _e| cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isybd ^e)stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/WhiteList.cpp g| i; ^n ( /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h)| :; ^2745 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h| 26::: ^29482745 ::note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h926:in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here:: 2948 : 2745note: 9 | note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here: note: 29482745in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here | | 2948 | s p a r s_se mp _o hva_aersm_sohfetvr_eaoh_bmalf(sremh oottmva(mebpmrl(,oMe v ohevttrem,,pD ( mohMinotntv,_C ebomDupoicynnk,t_e bCt*oustcp_hykwie,as tn,s*t t_erwhdeia)sns;,it ez red| e)_;st io z)| ^e; ^ _ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h2745o| ::) ^262745; :: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h 26 :note: :3278| in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here ^: note: 21 in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745: | 3278 note: :in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here2745 21 : | 3278 note: | in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | s sp p a ar r s s e e_ _ h haia sf sh ht(t a_iabrfble les(e i _tztrmemep_ps(di(MeMzoleovt_veadD(oen1tlC)otp)ya, *(teh 1iD| )so ^)n, t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h rC:| eos ^3813p i:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hzy29e:,:_3813t o )note: :;* in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here29 | t ^ h: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hi 3813:s3278:note: 21:, | in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested herenote: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested herer e 32783813 | s | i z e _ t r o e) t ; u rri efn| t( _ ^urr ree/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hnsp: i.z3278rte:e_ed21eplmt.a:(p1t l)enote: a)min instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here tp l| e ^a3278 t | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hfe :i3813 : 29:nf dinote: _nin instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here o d r _3813 | _o ir n _ s i e n r sr ete t_Vo(reas__tlidnduse:eelr:tfefaa(u(los1trtV)awdl)u:ae :>r (fd| sotaa:rrd(3813dT) (>)knote: (.ein instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested herekys)e) .eys c)e3813o)c | n.o dsn ;ed ; c o | | n ^ ^d ; /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp :51r ::26e| :51t ^:note: u in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here17 r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp: n:51 51 | note: r: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 17e : p 51note: .b | tin instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested herea er m c 51po | l d bae taG re c bofadirencGrdroo_dououeprGp[_[rbiobanaursprce[corobdtade | (1| ^s ^; t d :| : ^f orward(key)).secoIn file included from In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp::n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp22d: 5:In file included from : ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp58 In file included from :: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp19In file included from | : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp ^In file included from ::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp11 12:: : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppIn file included from In file included from 18/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:: ::75113/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h: :: :In file included from 17In file included from 946/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:: 3318:note: :14: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hwarning: In file included from :definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp 946:51 :15 | 94633: | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp: : warning: 9bTdefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]: aw /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hppro :c_9464od: | _32 d d e :sTetwrouG c_rtdiwarning: v_unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]eo _duie ps4t[ | tebrr#aauprcrtcaotgormidav&ee ]_Go[ipCutCeme rriaadtt]ooir a&r=g = n(o1cop;soe trn asit| toc ^ r T=iw(gocn_oodnr_edsde st"t -rWumTcawtyoib_vede-__udinetisentriratuticoatrli iv&zeoe_)di;"t e In file included from r | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppa| : ^t1 ^o: rIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:8:&: 2817In file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47:: )40/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h;:946:33: :warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] note: | in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here946 | ^ Two_d_d e st r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hucti2817v:e | _2817ite r:a t40or& op: e ra tnote: o in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required herer = ( cfo2817nos | tr T w o(_ dd_des tructieves_tirtuecrtaitvoer_ i & o ) ;f o r| ^( d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.he:s2817t:r40u:c tnote: iin implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required herev e _2817t | e r a t o r i tf o=r h(td.edsetsrturcutcitviev_ei_tbeergaitno(r) ;i t | = ^ h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht:.2948d:e9s:t rnote: uin instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested herec t iitveer_abteogri ni(t2948) | ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2948_:m9 o=:v enote: _in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested heref r o2948m | ( m o v e r , h_ th,t .mdiemsotvreu_cftriovme(_mboevgeirn,(n)_;b u c| k ^e t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hs:_2948w:a9n:t enote: din instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here) ; 2948 | | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2745 : 26 :_ mnote: oin instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested herev e _2745f | r o m ( m o v e rs,p ahrts, eh_th,a smhitna_bbluec ktemtps(_M wmainnt_ebdu)c;k e t| s ^_ w/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ha:n2745t:e26d:)o ;vnote: ein instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here | ^2745 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2745 : 26 : note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested heres p a2745r | Dsoen_thC o p y , * t hsiapss,h traebsliez et_mtpo()M;o v e| D ^o n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht:C3278o:p21y:, note: *atrhsies_,h arsehstiabzin instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested hereIn file included from le /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppe_ :t3278 o1 | t)m: pIn file included from ;( /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp M: 12o : | v ^ In file included from e D /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ho/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp :n:t327813 C:: o In file included from p 21y : , i fnote: * in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested heret( _hr ie3278s | s i, z e r_ de s iez l te a_ ( 1 ) )t o | i ^f ) /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h(;:_3813r: e29 s:| i ^z note: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hin instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here_: d3278 :e213813l | :t anote: ( in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp 1 )3278 ) | : In file included from 14 r | e ^t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppu r:: n97 In file included from r e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hppIn file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp381315: : : p 11.29: t:In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppe/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp::149m: p l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp: : note: aIn file included from 4in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp::32t 15:: eIn file included from warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp i:ff3813unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] | i( n4 | 9 # : p /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpprda :g_4 om: 32ar: eGtwarning: Cuunknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]_ Crrr _ei nnssed4i | a#r tigprznereo<_psdDa.eettgfeammlaiup ltltcaaG V(aClituC1eg )d>n)ei ( sotafd| g:ni:n ^fr deood/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h rs:_wo3813ra_"r:tid29i<:nK-s WTmecnote: rain instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested hereyt <>Dbe (f3813akiu | eg lnt- Ve ay )oul r)u. sen>eei (d csrto"en-ntWdiumdrtaiy:n;:b afero- eur npl| .witza ^reeiddm<"np l K| i ^a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppTt>:e51 (t :kif26eaiyl:n) id)znote: _.ein instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested hereos dre" _c51 io | nn | sd ^ e; r t in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here[( bs at51rd | c: o: df eo ]rb[wauarmrcido]r1o;u( p [k| b ^a eryc)ode][umi] = 1; | ^ ).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:129:13: warning: lambda capture 'beta' is not used [-Wunused-lambda-capture] 129 | [&, beta](const BlockedIndexRange& range) -> void { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:124:22: note: while substituting into a lambda expression here 124 | arena.execute([&]{ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedGibbsSampler.cpp:476:7: note: in instantiation of function template specialization 'sampleRoundNonCollapsedMultithreaded_>>' requested here 476 | sampleRoundNonCollapsedMultithreaded_( | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/WhiteList.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/WhiteList.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp:4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp:60: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' (aka 'const basic_string') [-Wrange-loop-construct] 168 | for(const std::string trueBarcode: trueBarcodes){ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeModel.hpp:168:13: note: use reference type 'const std::string &' (aka 'const basic_string &') to prevent copying 168 | for(const std::string trueBarcode: trueBarcodes){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | & /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:281:17: warning: lambda capture 'alphaIn' is not used [-Wunused-lambda-capture] 281 | [&eqVec, &alphaIn, &alphaOut, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:278:20: note: while substituting into a lambda expression here 278 | arena.execute([&]{ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:939:7: note: in instantiation of function template specialization 'VBEMUpdate_>>' requested here 939 | VBEMUpdate_(arena, eqVec, priorAlphas, alphas, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp:189:17: warning: lambda capture 'priorAlphas' is not used [-Wunused-lambda-capture] 189 | [&eqVec, &In file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppr::i4885o: r:A19lIn file included from :p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp h:warning: a11loop variable 'trueBarcode' creates a copy from type 'const value_type' (aka 'const std::string') [-Wrange-loop-construct]s : , In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp488&: | a7 l: p In file included from In file included from fh/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppo:a:r1I18 : n: (In file included from ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp ::o4946&:n: 33aIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpps:lt8 : pwarning: In file included from hdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppaa:u47 Ot: u ot946 | ] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h t( :r946 cuT:wo33o:e_ nBda_rwarning: dcsodefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]etds t er946B:u | lt orc cu etBk airvceoedT_dietIsew)nor{a d_t ed| x ^R_oa rdn/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp&:e 488gs:o8pete:&rr unote: ruse reference type 'const value_type &' (aka 'const std::string &') to prevent copyingc aa nt488g | t io evfro)er= ((cc_-oion>sntt evsTtr oaawitudtoo_o r {td&r_ ud oee| pBsea ^rrctordue :a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cppctt:o186rtr:u=i20(ve:cB aorenote: c_nwhile substituting into a lambda expression hereosdit tee sT186r)w | a{t oor _a d& or| )_;e ^~~~~~~~~~~~~~~~~~~~~~~ dn ea| s ^ t r| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h.u:e2817 &:cx te40ic:vu etnote: _ein implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required herei( t[ e&2817r] | a{ t o r| ^ & o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedEMOptimizer.cpp ): ;950f :o 7r| : ^ ( note: d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hin instantiation of function template specialization 'EMUpdate_>>' requested heree: s2817 t:950r40 | :u c note: t in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required herei v e2817E_ | Mi Ut pe dr aa tt eo _r ( faiortre n=(a d,h etes.qtdVreeusctc,rt upicrtiiovreA_lbpehgaisn,( )a;l p h| a ^s ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :a2948l:p9h:a vsnote: ein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested hereP _r i2948iIn file included from t | m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp ee :r)117 a;: t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppo :r | 16 ^:i 3t_: m =owarning: vexplicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted]he t_ .f16dr | eo s tFrmourcgt(iemvteot_vibneegrgM,ia nsh(st)C,;a lm c| iu ^nl _a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hbt:uo2948cr:(kF9eo:tr sgnote: _ein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested herewt at ni2948tn | eg dM )a ;s s C a| l ^ c _u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hmloav:te2745o_:rf26&r:&o )mnote: (in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here=m o d2745ve | ef ra ,u l ht t; , m| si ^pn a_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpprb:su141ec:_k14he:at ssnote: h_move constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructortw aa bn141lt | ee d t)sm;tp d( :M| :o ^mv ue/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.htD:eo2745xn: t26fC:fo Mpnote: uyin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested heret, e x*2745_t | ;h i s | , ^ r /usr/include/c++/v1/__mutex/mutex.he :s 30is:zp3ea:_r tsnote: oe'mutex' has been explicitly marked deleted here)_ ;h a30 s | | h ^t am/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hbu:l3278te:e 21tx:m( pcnote: o(in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested herenM so v3278te | D m uo tn et xC &o )p y , * t h i s , i fr e (s=_i rzdeees_litezote)e_;;d e l| | t ^ ^a (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp1::)327816):: 2158 ::| ^note: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested herereplace 'default' with 'delete'/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 3813327816: | | 29 : Fnote: oin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here r g e3813 t | t i n g M a s s iCrfae lt(cu_urrlnea strioezrpe(._Ftdoeermlgptealt(at1ti)en) g fM ia| nsd ^s_ Coa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hrl:_c3813iu:nl29sa:et ronote: trin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here<& D& e)3813f | a= u ld te Vf aa lu ul etr>;e( ts ut| rd ^~~~~~~n: : rf| eo deletepr .w/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppta:er17md:pewarning: ( explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted]kf ei yn17)d | )_ .o srFe_ocirongnsedet;rt ti >::operator[]' requested hereea >t (o28sr | t& d :o :p fe or ra wt aoerrdd=g<(eKFsTo[>rs(gokeuetrytc)ie)n].g.sMieancssosenCrdat;l( cs ui| ln ^ak t)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppo;:r 32& :&| 13) ^: =note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested hered e f32a | u l t ; | t ^i d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppM:a141p:[14t:x pnote: ]move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator. e m141p | l a cset_db:a:cmku(teeqxI df)f;M u t| e ^x _; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp : 1 T: wIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp_:d4_: dIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpps:t8r: uIn file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppt:i47v: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h_:i946t:e33r:a twarning: odefinition of implicit copy constructor for 'Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]r & 946o | p e r a tTowro=_d(_cdeosntsrtu cTtwivoe__di_tdeersattrourc&t iovpee_riatteorra=t(ocro n&sot) ;T w o| _ ^d _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hd:e2817s:t40r:u cnote: tin implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required herei v e_i2817t | e r a t o r & o )f;o r | ( ^d e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hs:t2817r:u40c:t inote: vin implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required heree _ i2817t | e r a t o r i tf o=r h(td.edsetsrturcutcitviev_ei_tbeergaitno(r) ;i t | ^= /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hh:t2948.:d9e:s tnote: rin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested hereu c t2948i | v e _ b e g i n (_)m;o v e| _ ^f r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ho:m2948(:m9o:v enote: rin instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested here, h2948In file included from t | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp, : 120m : i In file included from n /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp_: b55 u: cIn file included from _k/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/SAMWriter.hppme:to4sv: _e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BinWriter.hppw_:af31nr:ot60me:(d m)warning: o;unqualified call to 'std::move' [-Wunqualified-std-cast-call]v e r| 31, ^ | h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h t: ,2745 : m26 i: n _note: Bbin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested hereiu nc Wk2745re | it ts e_ rw (a sn tt de :ds:p)va;er cst eo| _r ^hb30&l:&e note: btin instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested hereim np _(2680dM | ao tv ae )D o :n _t bC io np _y d, a st*pata(hrmisose,v_ hera(esbshiitnza_ebd_laet at)tm)op )({;M} o; v | e ^D| o ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hn :t 3234C| : std::o9 :p ynote: ,in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here * t3234h | i s , s z ) ; _ r| e ^s i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hz:e2846_:d13e:l tnote: ain instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_maybe_shrink' requested here( 1 )2846; | _ m a y b e _ s h r/i/n ka(d)d;i n g| ^a n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :o3799b:j45e:c tnote: ,in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::pair, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::resize' requested here g r3799o | w i f vnoeiedd rbees i z| e ^( s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hi:z4225e:_67t:y pnote: ein instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here c n4225t | ) s t d : :{p arierp<.rietseirzaet(ocrn,t )b;o o}l > | i ^n s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.he:r3801t:(41P:& ¬e: in instantiation of member function 'spp::sparse_hash_map, unsigned int, boost::hash>>::resize' requested hereo b j3801) | v o i d{ rreesteurrvne (rseipz.ei_ntsyepret (cnt)s t d : : f{o rrweasridzc(notb)j;) )}; /}/ c| + ^+ 1/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp1: 28 :| 23 ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppnote: :in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here39 : 1828: | note: in instantiation of member function 'spp::sparse_hash_map, unsigned int, boost::hash>>::reserve' requested here 39 | evdegretse[xsIonudrecxeM]a.pi.nrseesretr(vsei(nnku)m;C l a| s ^s es); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:120: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:298:62: warning: lambda capture 'invalidScore' is not used [-Wunused-lambda-capture] 298 | [&scores, hardFilter, &msi, decoyThreshold, invalidScore]( | ~~^~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:429:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 429 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:768:10: :warning: 4variable 'locRead' set but not used [-Wunused-but-set-variable]: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp768: | 8 : In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppi:z47e: _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht: 946l:o33c:R ewarning: adefinition of implicit copy constructor for 'Two_d_destructive_iterator, std::pair>>, spp::sparsegroup, std::pair>>, spp::libc_allocator, std::pair>>>> *, std::pair, std::pair>> *, std::input_iterator_tag, spp::libc_allocator, std::pair>>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]d { 0946} | ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp : 826T:w10o:_ dwarning: _variable 'numMappingsDropped' set but not used [-Wunused-but-set-variable]d e s826t | r u cstiizvee_t n_uimtMearpapintgosrD&r oopppeerda{tor=(co0n}s;t T| w ^o _d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, std::pair>>, spp::sparsegroup, std::pair>>, spp::libc_allocator, std::pair>>>> *, std::pair, std::pair>> *, std::input_iterator_tag, spp::libc_allocator, std::pair>>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp3278::123721:10:: note: warning: in instantiation of member function 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::_resize_delta' requested herevariable 'locRead' set but not used [-Wunused-but-set-variable] 32781237 | | s i z e _ t l o c R e a di{f0 }(;_ r e| s ^i ze/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp_delta(1)): 1240 :| 12 ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hwarning: :variable 'localNumAssignedFragments' set but not used [-Wunused-but-set-variable]3813 : 291240: note: | in instantiation of function template specialization 'spp::sparse_hashtable, std::pair>>, std::vector, boost::hash>, spp::sparse_hash_map, std::pair>, boost::hash>>::SelectKey, spp::sparse_hash_map, std::pair>, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, std::pair>>>>::find_or_insert, std::pair>, boost::hash>>::DefaultValue, std::vector &>' requested here u3813i | nIn file included from t 6 4 _ t l o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpprceatlu:rN1n: In file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppe:p10.: utIn file included from me/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppAm:sp44s: liIn file included from ag/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpptn:e22e: dIn file included from fF/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denseir:nadg_moern_tisn{s0e}r;t 1< DefaultValue>| (s ^t: d :In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:f:1307o415:: r10/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hw::a139 r:warning: d14variable 'numMappingsDropped' set but not used [-Wunused-but-set-variable]<: K Twarning: 1307>definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] | ( k 139es | yi )z )e ._ stDe cnounmdM;a p p| i ^n g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpps:eD285rr:o20p:p enote: idin instantiation of function template specialization 'spp::sparse_hash_map, std::pair>, boost::hash>>::operator[] &>' requested herev{ 0 e}285d; | & | ^ o p e reator=(cqocnlasssHash[tg enMeastVrixBase& otehcer]).; f i| ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:s65t: note: +in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here= 90 | 1t;e m p| l ^a te class CwiseN/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppu:l5l: aIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp:y11: OIn file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp; : | ^ 7/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:: In file included from 176/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:10:18: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 946 | 176 | Two_d_destrreutcutrinv DenseBase:e:_NiutlelraartyoErxpr(rows, cols&, oipnetreartnoarl=:(:csocnaslta rT_wcoo_ndstant_op_: (In file included from v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppa:l8u: eIn file included from )c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp):t;47 : i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h| v: ^e946 _:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hi33:t:327e :rwarning: 22adefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]:t o note: r946in instantiation of member function 'Eigen::DenseBase>::Constant' requested here | & 327 o | ) T w;roe_ td u| _r ^dn e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hsdt:er2817ru:ic40vt:ei dv(note: e)in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here_ i t2817e | r = a t o r & oIn file included from fp oerr a(tdoers=t(rc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppuo:n58s: tCIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppT:w10o: _cdot_idvees_tirtuecrIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppai:t44n: vIn file included from os/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppre: _22i: itIn file included from tta/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense en:r=t1a (: thrIn file included from to/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreo.:rwd 415s&: oe()/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h;s) t :,r139| u ^:c 14c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ho::tl2817i sv:(ewarning: 40)definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]_:, b note: ev139gin implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required herea | i l n)2817( ;) | ;D e| r ^| i ^ v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h e:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hd 627& :: f2948oor: 10p9:(:e drnote: note: ein instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested hereain instantiation of member function 'Eigen::DenseBase>::setConstant' requested heres t to 2948rr627 | =u | ( cc otr nie vste tu_ iMta et rr_rnimxaotvoer_ firto =ms (BehmatotsCve.od&ee nort,h eshttrr)u;s, ct t| am ^in iv/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.ht:en90_(:b_65b:uS ceckgnote: iaenin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required herel( ) ;ta 90sr _ | | t ^e m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hwpalnatteed<)t(;y :p2948e:n9a:m enote: 1in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested hereN )| u)2948 ^; | l l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h a: r2745 y: O26 p: ,| note: in instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here ^_t m oy2745/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppv | p: ee 56n _:af 15mr:e onote: mMin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here a( tmsr oip56vxae | Trr sy, ep e_ h> h a ts ,hc ot mua nib tns l__ e.b uscetlctmkaOpsen(stMe ssoC_(vw)wie;as ne DNt| ueo ^ld nlIn file included from )at/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppr;:Cy1 O: opIn file included from | p;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp ^ y: 10, | : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h* /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:2745h:44:i176: 26s:In file included from :,10/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp ::r 22enote: : snote: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required hereIn file included from i /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densein instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested herez : e1761 | : _2745 In file included from t | o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core r): 414e: ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.ht: 281u: 14 r: nwarning: | definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]D ^ e ns/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h281sp | :ea 3278Br: as21 es: _eD , unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested heresr vhi tev3278dae | &bd >lo e:p :e Nr uta ml l pta o(r Mry =oE( xc pvor en( Ds ornttioCf owD sp(,y_e,r e*s inzcestoh_iesl,Bsda ,sr eei&en ltstoeiatz(r1e)hn_e)at r l| ) ^: ;: os )c;| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h a ^| l ^ a:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hr3813:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:_29:c327848o::n2134s::: t note: anote: note: nin instantiation of member function 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested herein instantiation of function template specialization 'spp::sparse_hashtable, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, const unsigned short &>' requested herein implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required heret _ 3813 | o 48p | 3278 | e t( ui327 d:ecln22ldt:a_ asnote: o(sin instantiation of member function 'Eigen::DenseBase>::Constant' requested herer 1M _)a327it) | n rs ei| xrr ^Bt ea, unsigned short, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned short &>' requested herea90 vl: ue3813e65d | :> (( )snote: t in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here = d : :C f90 oo | rrtewnteasmuptrrladnanypop(w.ektsne(eya)m)m,p)e l. caNstoeelc uosfnl(idln);ad,r _ ovy| raO ^_lp i),/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppn; :s 747te y:r| 36pt:e< n ^Danote: ein instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested heremf/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h e:a 627 uM:747a10l | t:tr Vi note: x ain instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereT l y up e627e | >> ( s r t e d t: :u r f n o r s cwealatrraCbdsosn sCtwain /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppk:e56y:r15::) a176note: )g:in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here.C 10s o56: | eu c nnote: o in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here nt d s ; c[ 176g o | i| u ^ d n ]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpprt[e:sit286t_:.u37.f:sri nrnote: ein instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested heresDtteO ]nn se+286es | =B( a) is t; e. l58 :a: | :sIn file included from ^Ns u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppHl:al10sa: hrIn file included from [y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppgE:ex44np: erIn file included from s(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppVr:eo22cw: ]In file included from s./wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense,s: e1cc: ooIn file included from ln/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coresd:,[414 r: ie/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.hna:td281es:rp14nm:oa llwarning: ]:definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] : +s =c281 a | 1l ;a r _ | cD ^oe nrsitvaendt&_ oopp((cvoanlsute )D)e; n s| e ^B a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hs:e327&: 22o:t In file included from note: h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppin instantiation of member function 'Eigen::DenseBase>::Constant' requested heree: r5 ): 327In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hpp : 11r: ;eIn file included from t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppu:r7n: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppd| :e ^18r : i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hv::e48946d::(3433):: =note: warning: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required heredefinition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned long *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]C o n48946s | | tt ae nm tp (lTrawotowe_sr; a ct lo| ar ^s& s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h o:Mp627ae:tr10ra:it xonote: Bin instantiation of member function 'Eigen::DenseBase>::setConstant' requested herera =s e(627 | c o| n ^rs et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.ht :uT90rw:no65 _:sd e_note: tdin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required hereCe osIn file included from nts/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp rt:90ua1cn | t: ttIn file included from ie/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp(vm:Spe4lc: _aaIn file included from lt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppiaetr:, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] ^:y 15O /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:p:946 ,2817 | note: : in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here40t :y p 56note: e | in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned long *, std::input_iterator_tag, spp::libc_allocator>' first required here n T aw 2817m o | e _ dM c_ ao dtu ern sit tsx rT_fu.yocsprteei t>(vO de ne_e si stt( re)u ;cr t ai| vt ^ eo _cIn file included from ir/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpptl&:ea1r : saoIn file included from stp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppoeC:rrw10a it: isIn file included from to/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppe :r=N44= u: h(In file included from ltcl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp.oa:dn22es: srIn file included from tt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densery:u O1Tcpw: ;to In file included from i_ vd| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coree_: ^348d_ : be/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hes::gt92ir:n176u29(:c:)10 ;twarning: : i definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] v | note: ein implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here ^92_ i | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht176 e | :r 2948a t:ro 9enr:t o u_&rnote: aoin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested heres) sn i; 2948g | Dn me| en ^ns t e _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h B:oap s2817e e:r<_40aD:mte oorvnote: irein implicit copy constructor for 'spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int>>> *, std::pair, unsigned int> *, std::input_iterator_tag, spp::libc_allocator, unsigned int>>>' first required here&_ vf ore2817pd | oe> mr:( a: mtNoo uvr le= rl (,a crf oyohEnrtx s,p(tr d (emnrsiootn_wr_aubsscu,sct ikigcevontem_sel_niwtsa_tno,tpee erdiarn)tta;ote ro rr| n& ^)a i;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hl t:: :2745| =s: ^ 26c ha:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.htl :.anote: d90rein instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here_ :sc 65to2745:rn | uscnote: tt in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required hereai nv te __90 o | bp te e< gmSipcsnlpa(aal)tar;ers <>e t(_| yv ^hpa aels/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hnhu:at2948maeeb: l)N9e)u:; l tlnote: min instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_move_from' requested herep| a( ^rM yo2948/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hOv | :pe327 ,D: 22 ot:n t ynote: C pin instantiation of member function 'Eigen::DenseBase>::Constant' requested here eo n_p amm327yoe | v , eM _a*frttrerhtoiuimsxr(,nTm yodrpveeeer>rs i,iv ez hde t( _,) t o m= )i ;nC c_ol bn| auss ^tcsa k /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.heCn:wtti3226s(:s_re9wo:Naw nusnote: tl(in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested hereel) da ,)r3226 ; | yc Oo p| l; ^s ( /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h) :, | 2745 :_v ^26r a:el/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h s):note: i176;in instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::sparse_hashtable' requested herez : e10 _| :2745 ^d | note: e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hlin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here : t 627a :176( 101 | : ) ; rnote: se in instantiation of member function 'Eigen::DenseBase>::setConstant' requested herept au rr627 sn | e _ Dh e anr sse het tBu aa rb slne e < sD te em rtp Ci( ovM/eno/sdv t>ea:aDdn:odNtni(utSnClgcola playana,rr yo(*E1btxj)he)picr;s( t,r , o | rwg ^esr ,so/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp iw:zc 56oeil_:fs15t ,o:n )ei;enote: nd tin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here e br| en56 ^ a | l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h| : : ^:3278 s: c21 :a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hlnote: c:aoin instantiation of member function 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::_resize_delta' requested here4219u r:n _56tc3278s:o_ | n. s tsa e nnote: ttin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here O_ no e4219 sp | (< )S ; c a l | a i ^r f> ((In file included from sv_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpptar:dle58:u: s:In file included from epi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp)za):ei;10_r d: >::Constant' requested here: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :In file included from :i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coret e:r348a3813t: o327r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h,: 92b: | o29 :o29l:> warning: : p rdefinition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] note: e=in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int>, std::vector, boost::hash>, spp::sparse_hash_map, unsigned int, boost::hash>>::SelectKey, spp::sparse_hash_map, unsigned int, boost::hash>>::SetKey, std::equal_to>, spp::libc_allocator, unsigned int>>>::find_or_insert, unsigned int, boost::hash>>::DefaultValue, std::vector &>' requested heret ur er92p | . i n s enrot_(aosns ib 3813jd) | ;g e n| rm ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cppn t_ o:p971 i:e16 :r anote: tin instantiation of member function 'spp::sparse_hash_set::insert' requested hereov r e & d971 | or(p e r e a)[ 90%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o tt ocd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy=r stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp =u C(r ocn no snr ts eatupnm .tintoe_maps(ssliagtnem. efnitn_do_poerr_aiitrnnoowssresret(&r<))tD;,( e cf| iaot ^ul.l sf/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h(ti:)Vr90,a: s65ltv:u ea)>note: ;l(in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here s) ; | t90 ^ d | :| t: ^f eo/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hmr:pw627l:a10ar:td e>::setConstant' requested heret y p627e | n a mree tTNuurlnl asre>ytOCpo,n sttyapnetn(aSmcea lM(aaktrer(iyx)T1y))p.)es;>e c o| n ^ d ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp : 56 c:| l15 ^a: s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cppsnote: :in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 413 :C 20w56:i | s note: e in instantiation of function template specialization 'spp::sparse_hash_map, unsigned int, boost::hash>>::operator[] &>' requested hereN u l 413l | ac ro yu On pt ;s _ . | se ^eq tc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hlO:an176se:ss10H(:a) s;note: h in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here[ g| e ^176n | e s Vreect]u r+n= D1e;In file included from n s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp e| :B ^1a : sIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp<:D10e: rIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppv:e44d: >In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp::N22u: lIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densea:r1y: EIn file included from x/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corep:r420(: r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ho:w86s:,63 :c owarning: lconverting the enum constant to a boolean [-Wint-in-bool-context]s , 86i | nt ernal: :scalar_consta n tM_oap:V(5ev: caIn file included from tl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hppou:re11i): z)In file included from e;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp := 7 | : b ^In file included from o o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:l:18(327: M:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hi22:g:946h :tnote: 33Vin instantiation of member function 'Eigen::DenseBase>::Constant' requested here:e c warning: t327definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]o | r i 946zr | ee )t u &r &nT wMdoae_yrdLii_vndeeedas(rt)irz ue=c t&Ci&ov neDss_ttHiaatsnDetir(raretocowtrA&s op(erator=(c)on,st Twoc_ dc_destcreucotsliss v(e )| ,_ i ^vIn file included from In file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/DedupUMI.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:el::)195r;: : a607 In file included from In file included from | t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/DedupUMI.hpp::/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp20o:4 ^: 44: note: rIn file included from : in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h& :In file included from o607)627/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp | :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp; :10 8:t: In file included from :note: y22in instantiation of member function 'Eigen::DenseBase>::setConstant' requested herep /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp: e dIn file included from e627 f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense| | ::t ^1y47 : p /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hr ee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hn:a2817mte: :u 946:AIn file included from 40:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core33s:r415s:ni: warning: : note: g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hdefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]:n in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here139m :e14 n946t2817 | T | r s ae : i ttwarning: sdefinition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]T: C w 139:ooP a_c kde n_ | s dt et Tsayfpno ter (DP tSar(cdueekrceictasvTtlteyarrp(ude1c;&)t) ; io v| ip ^e vr e| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he ^:_ i739/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppt::ae5610r_t:oia:rt etnote: r=in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested hereo(r c15 oa739n: | ts t oKre &rnote: niin instantiation of member function 'Eigen::DenseBase>::setOnes' requested hereeM a olt56 t | r ki e= x B arhp ns eel &(cdo teo.srduttEnhtearse)vt;a l_ so.u| rts=a ^t(orrc,uo ec/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hnt ti:sOr90nvse:te 65_cT:bsEe vw(note: ago)lin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required hereu_ ;i da n_ 90t | (od| t) ^e;rs, te rfmupnlca,ut ec , std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested herel_o: c)In file included from a;ls /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppatr: y44| : O ^p_ In file included from , d /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppteyr2948: | 22pi evn/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ha: m :eIn file included from 2817Mea/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense d:( t:)r i)1; x : T y40pIn file included from :_ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core> :| m 420o ^note: : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hin implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required herev /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h e: _862817f: | r: 87963 :o 5:: m ( warning: cnote: mconverting the enum constant to a boolean [-Wint-in-bool-context] olin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heref avoe s r879r | 86s , | (C wh cd e asltlt i_,dsMr auycmtLieienNvinesn_eu_ebaulrlcV_ieakrtyaecOtpteosrs;sart_ow riaz n | iei t ^=t ge/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h=:nd m)h176;e:btn10 :. o| to ^note: ldin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here( eM_s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h lt176oio | :r gu2745 c:prh(26dtse:ti tvu,e rstnr_c note: ,V in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested hereeDb ce gfitn2745ue(n | n co 2))r; warningis sz ; e| e generated ^. ) B& a&s | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :eM< ^Dsa p836/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:y46a:Lreis:re2948i_nv:ee9hd >aa:rs note: hnote: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested herei :in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here tz 836a : | b2948N l eAe u | lst&lsmiag&rp[ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o (y nD scd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isyMstem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp m Eeoxn vp tr>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herer cea s,mFii607n | luanrz__ec _c obtt>o:uyn:scr)upnt;k (ea acn| te ^t_toupa, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested herefr;ue n n| >ac ( ^3278 m | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.he : 2745 ):A26vsa; sl i : g| note: n ^ umin instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :) 804 : 2745e)3 | : ; n t | T ^ r /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h : 327ia:f22i :note: tin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here (snote: _s rp:in instantiation of member function 'Eigen::DenseBase>::Constant' requested heree : s aP327r | i sza804ec_ek | h _ adscehetartaeTblllt_ulytrapasen(s 1ed)eir) iPv eatgdnmmc| (pk)e(e ^Mto T vy=e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hDn :potC_oneon;_s n3813 tt| C:a ^ao 29/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:ln itpa:ynote: s(in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here,739(r:d o*s 10twths,3813( ) | :s,ri cc ,o note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herelfs s ,u( nr)c ,) r;eve739 sa | itl| z )e ^K;e ur/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h_ :t on)782| ;re : ^n3l :| ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hnote: :(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 627 :kr e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hep 10r.782:tn | ee :m 3278cnote: :lpa21in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here(:d l note: lsin instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested herel ta 627t | e_ E 3278vaf sis | arn eildt_uorr u_nagi nsseentmtrCtoE,(i vfia)s ln(uttedr_n:ra:e)fl;oa: t:ors raw| ,ai zr ^sds ifg:d_(e15lko:eptcy< a)note: t,y)p.in instantiation of member function 'Eigen::DenseBase>::setOnes' requested heres e c d56s | ( e1 t) o)n anm. de c | c;o ^ o n | usnt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht ^_s :_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp.3813:Dsc1087s::40e:t29tO na:es:tS:_note: dsce (in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested herera)l note: ; ia 1087 | | r ^, tvin instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned int &>' requested here e In file included from y3813 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppd: | ( 95 ) p: )e ; n ma| In file included from m ^R n /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppa:G44e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h: eIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp :n:S22ee: sr.tIn file included from 879/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densec:i:nu5sr:e:r1n :: note: rIn file included from in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core e:Sptc( .414879: tag | e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.he: mnle Ia rd xpM>a281(c)l)p:;a14 :a twarning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]l | [ ^l _ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hgd: eee 281nfen i]710)ns: | e17d:; _ _ o| ^note: a sin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herer s_ ii gn710nD | sme eern rit tv < D_ee ldfoi&aon utpole(tdVpasltu,er nsarlc:,e:> (rfscuantldl:_:afsosrawcai)tgr;donote: din instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here=e r i836v>(e( | cdk o(e n)yAs,)st s) o.iDtgsehnenemcsre.oenndBted::operator[]' requested here:T y& p225477 e | :oC 20tl: he e note: arin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here n )e d225; , | S r v ce| ,r F ^u t er/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hxeItnnducir>c:e::sr[n48u g:neB34(na:ase ce]tnote: :u in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here:=a _l sDg48esi | ttdt(;e, om t p| hsl ^rea rct),e; < ft u| ny ^c p)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h;: 327e :n| 20 ^a :m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :enote: 804 in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here:D 3e :327 | r note: iin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hererv ee td804u> | r nc lcdaaeslrsli _vMaeasdts(ri)g nim=exn tC_onnos_taalnita(Brsao(swdess (t ),| , ^ s cr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hoc:l,90s :(f65)u:,n cnote: v)ain implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here;l ) ;90| | ^ t e| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hm ^:p 782l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:a:3t627:e: <10note: t:(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)y pnote: ein instantiation of member function 'Eigen::DenseBase>::setConstant' requested here782n | a m627 e | c aN lurlle_ltaausrrsyniO gpsn,em tetCnyotpn(esdntsaatmn,et (sMSraccta,rl iaixrnT(ty1e)r)n;a l :| : ^ap s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpps:i56g:n15_:o pnote: >::setOnes' requested heret y p56e | n> a m e D sct o:u:nSt csa_l.asre,ttOyn ep se (n )a ;m e cS| lra ^cs s: :CIn file included from In file included from w/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/CollapsedCellOptimizer.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppSi:s:51c: : aIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppa:In file included from 10er/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedCellOptimizer.hppN>: u:lIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp(a)13)r:;44: : yIn file included from In file included from O/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp;: | :2217 : ^: In file included from In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h ^:: 1/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h: :710176In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:1710/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:: :note: 8in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here: In file included from 710/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp | : 40 : In file included from note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp : 7i: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herenIn file included from t e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.hr:n34a: l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h:::377c:a42l:l176 _warning: ainline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline]s s i377 | | g: n m 420 ercento: tnu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(srt:t_86ih:tni63 s:-e >rwarning: aDdconverting the enum constant to a boolean [-Wint-in-bool-context]ee rt io86vn | es erB d _(_) ,a as Meo(:e:icuvtesNdoue(ldr))i))l za;pe ap reyn| E= ^dx (c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hop: 225nr:b20(s:rto_ oinote: oin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested herewtl esr, ( a225tcoM | ori gl hse t,n dV_ eoif n_trecerbttnouuarcrlkin:z e:Bteas,)cs aec&l:&a: or_nMs_saceyttoL( niCosnthteaharanerrTti*_) zo;kepe _:t(t327Hv:ya20apsle:uD einote: k)re)in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested herey;e_ sc it327| zA ^ec | c ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.he sr: se327 :t | u| 22 ^ ^: r /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.hnnote: ::in instantiation of member function 'Eigen::DenseBase>::Constant' requested here1318 :607d :e32720r74 | i:v : note: erused here e dt note: u(1318rin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here | )n d = 607e | rC i osv tntedsdy:tp(:a)pe nda=tie( rrCfo i cgeovnmlampslel)(na;tc) Te, _ ri| vm ^aa ip/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hllt)(:;s 627s:: t:d| : ^:Ps10i za/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:ce :knote: _627etin instantiation of member function 'Eigen::DenseBase>::setConstant' requested heret T: i10 b627u | :c knote: yein instantiation of member function 'Eigen::DenseBase>::setConstant' requested here p er t627, | tPy paeencatkrueermtnteT uy rspnae retr;sC eoat nC| s ^t yo_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ha:bnn739sutt:cak10e(t:S: :ncctnote: a(oSncin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested hereaslt _a ir739l(t | 1 a )re(K)r1aet);ro) n;r e| | l ^ ^ kee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppr::nn56de_:olf56(:_db15u:c kse15tt,: E note: vnote: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested hereain instantiation of member function 'Eigen::DenseBase>::setOnes' requested here | l u ^ a 56t | o r56 , | s r cE val uc ao tuconort,u snftu_sn_c..s,se edttsOOtnn.eecsso((n))s;;t _ c| | a ^ ^s tIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppd:e95r: iIn file included from ved()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879::445: note: : In file included from in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp58 : 879:In file included from | 22/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp : : In file included from 10 : In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppa::l441l: _In file included from : d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppIn file included from e:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core22n:: s348In file included from e: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:a:1s92s:: i29In file included from g:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coren m:warning: e420definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]n: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h _:92l86o | :o63 p:( d swarning: t converting the enum constant to a boolean [-Wint-in-bool-context], n so86r_ | ca ,s s fi ugMnncam)ye;n Lt i| _noe ^pa er/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hrV:ae836t:c46o:t ronote: &rin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here i oz pe836e | r= a tbAoosros=li((gcMnoimngeshnttt oD:rs:&tr)Hu;an s( Da| ic ^rte uc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hat:lA90Dc:sc65te:,s snote: s in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required herer c| , ^90 | f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.htu:en607mc:p)20l;:a t note: | ein instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here ^< t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hy607:p | 804e :n 3at:my epnote: ein instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested hereNd ue lf804l | at ry ypcOeapnl,al m_teay spAsesinsgainmgmene mnMetan_ttnrToir_xaaTilytipsae:s>:( Pd as ct k, e ts Tr yc p,ce l faPusanscc k)Ce;wt iT sy| ep ^Ne u;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.hl :l 21a| : ^13 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h r:note: 739yin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here: O10 p:21; | note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here i | n739t | e ^r n Ka/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hel:r:176n::ec10la: l klnote: e_in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herera ns es176ilg | n(m edn stt(rtEhevitasul-ru>nad teDorerin,vs eesdBr(ac)sE,ev afc:ut:n:Nc:u,Cl oldnassttar.nyctEo(xnrpsotwr_s(c(ra)os,wtcs_odlesr(i)v,eodt(h)e)r;) , | i ^n t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he:r879n:a5,:l :note: :in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here m u l879_ | ac s soi lg scna_lo,lp_ n(t)_)l;o o p| ( ^d s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppt:57:15t:e note: ,in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here srr nc57,a | l f: u: n cs) c;a lcao u n| t ^s _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h *= salmonr::836::m46a:t hnote: :in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here: L O836G | _ Assignm_e0c; | n ^o tn(vCalleuaneed),)S;r c, F| u ^n c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: >in instantiation of member function 'Eigen::DenseBase>::Constant' requested here : 327 | : rruent(uarcntIn file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp :a1ld: DIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppt:,10 : sIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppc:,44 : fIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppur:ni22cv: )e;d In file included from ( /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense)| : ^1= : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hIn file included from C:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreo804:n:420s3: t:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ha :nnote: 86tin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here:( 63r :o 804warning: | converting the enum constant to a boolean [-Wint-in-bool-context] c86a | l l _ a wsMssa(iy)gL,ni mnceeonaltrs_V(ne)oc,_t aovlraiiazse( d=s tb,o oslr(cM,i gfhutnVce)c;t o r| i ^z e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h): 21&:&l 13M): ;note: ain instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herey L i21n | e a rin it ez| re ^n a&/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hl&:: 627:D:cs10at:lH lanote: _sin instantiation of member function 'Eigen::DenseBase>::setConstant' requested hereaD si sri627eg | cn tmA ecrncetet(sutshr in s | -s ^>e dt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.heC:r607oi:nv20se:td a(note: n)in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested heret, ( SP607cl | aa i ntOybpjeedcetf:l: Catoryn(ps1et)naa)nmt;e( r o wA| ss ^(s )i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp,g:cn56om:le15sn:(t )Tnote: ,rin instantiation of member function 'Eigen::DenseBase>::setOnes' requested hereoa ti ht56es | r: ): ,P a ic nk tecetoTruynnpatels :_P:.amscueklte_OantseTssyip(ge)n;; _ o| p ^| < ^S/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h c:739:10: anote: lin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested herea r 739, | S c aKlearrne>l (ke)r)nIn file included from ;e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp l: (95| d: ^sIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:E:44v57: a:In file included from l15/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppu::a 22tnote: : oin instantiation of member function 'Eigen::DenseBase>::operator*=' requested hereIn file included from r /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense, : 57s1 | r: cIn file included from E/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core v: a420 : l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.huc:ao86tu:on63rt:,s _warning: f converting the enum constant to a boolean [-Wint-in-bool-context]u* n=c ,86s | ad ls mto .n c:oM:namsatty_hLc:ia:nsLtOe_Gad_re0Vr;ie vc et| do ^( )r)i; | ^ z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5:e note: =in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here b879 | o o l ( Mciaglhlt_Vdeecntsoer_iazses)ig n&m&e nMta_ylLoiop(dst, src, func);n e a| r ^i z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he:836:46: note: &in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here & 836D | In file included from s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppt :HA58as: ssIn file included from Di/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppig:rn10em: ceIn file included from tn/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppAt:c<44cA: ecIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppu:a22l: DIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denset:T1y: pIn file included from se/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoresC: l420 e: | a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h ^n: e86/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hd::,63607S::r 20cwarning: :,converting the enum constant to a boolean [-Wint-in-bool-context] F note: u in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested heren86 | c > 607: | : rM uanty(yLapicneteduaearflV Detscyttp,oe rnsiarzmcee, =Af subsnicgon)om;l e( nM| ti ^Tg rh/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hat:iV728te:sc17:t::o Prnote: aiin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested herecz ke e)728t | T& y& p eM a Py aLicinknteeetarTrnyiapzlee:; : &c &a| l ^Dl s_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hta:Hs739as:si10Dg:in rmnote: eein instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested heren ct _t739n | Ao _c acKleeisrassn( teh il| s ^-k >e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hdr:en607re:il20v(:ed dsnote: (tin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here)E ,v a607o | lt hu eatrt.yodre,pr isvrecedEd(ve)af,l utiayntptoeernr,an mafelu :A:nsacss,is gidngsmnte_.noctpoTe(in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here;) ) ;879| | ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h ^ : 739/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hc::a10278l::l 15_note: :din instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here e note: n in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested heres739 e | _ 278a | sK se ir gn ne ml e nBktaes_el:ro:no_epsl(e(dtds_sttn,Eo vasalrlicua,as t(foourtn,hc )s;r ec E| rv ^a) l;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu :a 836t| :o ^46r :,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :note: f84in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested hereu: n3 c:836, | note: din instantiation of member function 'Eigen::Matrix::Matrix' requested here s At s.84sc | io gn nsGmtCe_Fncrtaa, Eigen::Matrix, Eigen::internal::assign_op>' requested hereae ud l,879tS | ;r c , | F ^u cnacl>l:_:run(daecntsuea_laDsssti,g nsmrecn,t f_ulnoco)p;( d s| t ^ ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpps804:r:1c3: ,:In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppfnote: :uin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here10n : c In file included from )804/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp; | : 4433 : | warningcIn file included from ^sa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp generatedl:. /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hl30:_: 836aIn file included from :s46s:i gnote: nin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested herem e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp n:836t | 13_ : n In file included from oA/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp_s:as24li: igIn file included from an/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpps[ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o m:(e10cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy: nd/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpptstem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentStartPositionDistribution.cpp s<:tA657,:c15 t:s uwarning: radefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]cl ,D s657ft | uT ny cpl)eh;Cs l_ es| ae ^nt et/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hde:,r782S&:r 3co:, Fpnote: ue(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)n rc a>782t | call:_o:arrs=sui(gncn(omanecsnttt(u dasltlh,Ds s_strsc,e t,st reicn,tr &ef urrhnnsac)) l;{ : | :| ^a ^ s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hs/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:i:728g167:n:17_26:o: p note: , Eigen::Matrix, Eigen::internal::assign_op>' requested heretin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here y p 728e167 | n | a m e D s it n: t: eS rc na al la :r :, ct ay lp le _ na am es S r?c :t:sySipcgeanlnmaaermn>et( _)in)to;e _ r| a ^a lt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hi:o710a:rs17:(:: tnote: lhin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested herehi ss _-710s | > e d e triintveerdnta(le:):rc,a llo_tahsesirg_n.mtdeyenptr(etih(vimes_d-m>(de)emr,i v+ie dn((t)i,e ort*hne ra.BdleI:rTi:vSead)(s) s)/i; g Un| B_ ^,o p /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h<:BS225Ic:Ta20Sl:,a rnote: (,in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested hereit y *p225 e | B In Ta Sm ) %er eUOtBtu)hr en r | DB ^ea rs/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppie:v645ed::Sca:l::a22_r:s enote: t>in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here( o(t h)645e) | ;r ) ; | ^| ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h 278: :327 15:g:20c :Bnote: iin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested herenote: t in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested hereA r278 r | 327a | y _ [ ri e] t u= r Bn1a ;sd ee :r| :i ^_ vseed() = Constt_annot(arloiwass(()o, tchoelrs)(;) , | v ^a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp):;84 : | ^ 3/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10:: note: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested herein instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | 84 | r eGtCuFrrn asgeMtoCdoenstant(Scalar(1))l; ( | G ^C F/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15:r anote: gin instantiation of member function 'Eigen::DenseBase>::setOnes' requested here M 56 | o d countes_.selt&Ones(); | ^ &) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVecIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppo:r58i: zIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp :=10 : bIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppo:l44(Migh: tIn file included from V/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppe:c30t: oIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppi:z13e: )In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp&:&24 : MIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppy:L10i: n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppe:a657rize: 15&:& warning: Ddefinition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]s t H657a | s D ilrhesc_tsAectctess | ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:&607 :o20p:e rnote: ain instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested heret o r607= | ( c otnysptedef t ylphenames _Assestitger& rnhs) { | ^ m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppe:n167t:T26r:a inote: tin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required heres : :167P | a c k e t T y p e P a c k e t T y p e ; | ? ^ t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hy:p739e:n10a:m enote: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested herei t e739r | a t oKre:r:nlhesl_ skeetrtneerl_(tdyspteE(vma_lmuIn file included from ea/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppmt: o1+r: ,In file included from (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpps:ir10: In file included from */wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp :B47I: T/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hc:946:33: warning: Edefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] Sv )946a | l u /a t UoTrBw,,o _fBduI_nTdcSe,,s td(rsiut c.*tc ioBvnIesT_tSi_)tc ea%rs atUt_Bod)re &rived() )| o; ^p| e ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h::a645879t:5::o 22note: r:in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here= (note: cin instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here879o | n s 645t | T w o _ cd a_ ld le _s dtgercnuBsciett_Aiarvsresa_iyignment_loop(dst, src, _tf[euirn]ac t)=o; r 1 | ^ ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h& :836o :)| 46; ^: note: | in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here ^ 836 | A s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hsignm:e2817n:t:: note: :in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here r 2817 | u n ( a c tualDst, src, func); | ^ f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ho:804r: (destructive_iterat3o: rnote: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herei t 804 | = hcta.ldle_starssuicgtnimvee_nbte_gnion_(); | ^ a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hl:2948i:a9: snote: (in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested hered s 2948 | _move_from(tm,o vsrc, func); e | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h,: 21h:t13,: mnote: iin instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heren _ b21 | u c kienttsernal::c_awlaln_taesds)i;g nme n| t(this->derived(), Pla ^i nObj/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hect:::2745Co:n26st:a nnote: tin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here(row s(),cols(),other), internal::mul_assign_op( | ) ) ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp : s57pa:r15s:e _note: hin instantiation of member function 'Eigen::DenseBase>::operator*=' requested herea s h57t | a b l e t mcountsp_(Mov eDontC*o=p ysalmon,: :m*ath::LOG_0; | ^ this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86: 63: In file included from warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp converting the enum constant to a boolean [-Wint-in-bool-context]: 58 : 86In file included from r | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppe :t 10u : r In file included from nM/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp a:yr47Le: ip/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h.n:te946ea:mr33pV:le acwarning: ttdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]eo r fi946iz | n ed _ o= r T_bwioono_slde(_rMdtiei_(zisett ed&r:&a: tfDostorHra&swD aiorrpdeeco(crke=es(ysc) o) n.| ss ^t e /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hc:607To:w20no:d_ ;dnote: _in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here d | e607 ^ | s t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp r:tu51yc:pet17dief: typename Assivg nmentTeranote: _iin instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested hereitst::ePracketTay tp eo 51Pra | c k&e toT )y ;pe ; | ^ | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10 ^:b anote: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hrin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here:c 2817o :d739 | 40e: G rnote: Koin implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required hereeurnelp ker[ bnael(drstEvalua ct2817oor | ,d sr ec ]E [va luua tmo ri ,] f ufnc=o, r 1 ds;(t d. ce| os ^nt st_cast_derived()); | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here c 879 | call_dense_assignment_loop(dst, src, func); | ^t In file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:836:46: vnote: :ein instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here1 _: i836 | tIn file included from e Assi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpprg:nment::run946(hactuat:l.33Dst, d:serc s, func); | ^ warning: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hdefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]r: 728u: c17946: tnote: | iin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here v e _ 728 | bT ew g oi _n d(i_)nd;te es rt| nr ^au lc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:t::i2948cv:ae9l_:li _tnote: aein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested heresr sa it2948go | nr m& e no tp _e r na ot__omarol=vi(eac_sof(nrtsohtmi (sTm-wo>ovd_eedrr_,id vehestdt,(r )um,c itoinv_tbehu_ecirkt.edteesrr_aiwtvaoenrd t(&e)od)),;; i | | n ^ ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h::27452817::2640:: note: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested herein implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 27452817 | | t e r n a l : f:soaprsa sr(idsgees_thrauschttiavbenl_ei tte_mrpaot(poM::(921):: )note: note: ;in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested herein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here | 29483278 | | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h : 278 : 15 : _ note: m in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested hereo v e 278_ | f r oi mf ( m( o_ vr eeBrsa,is zehe:t_:,d_ esmleittna__(nb1ou)c)ak le it| as ^s_ (w/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hoa:tn3813ht:ee29rd:)) ;;note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here | | ^ ^3813 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :: 842745 :: 263 :: note: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested herein instantiation of member function 'Eigen::Matrix::Matrix' requested herer e t274584u | | r n Gr Ce Fp r. at gesMmpopadlreaslte(e_G hCfaFisrnhadtg_aMoborld_eei lnt&sm&e)p r(=tM (*stthdi:s:,f orrewsairzde<_KtTo>)(;k e y| ) ^) ./wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hs:e3278c:o21n:d ;note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here | ^3278 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp : 51 : 17 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppnote: :in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 95 : In file included from 51 /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp | : 44 : In file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppbf:a 30r(: c_In file included from or/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppde:es13Gi: rzIn file included from oe/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppu_:pd24[e: blIn file included from at/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppra:c(10o1: d)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppe):] 657[ :u| 15m ^:i ]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hwarning: :definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]=3813 : 129657;: | note: | in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested herel ^ h s3813_ | s e t t e r & orpeetruartno rr=e(pc.otnesmt lhpsl_asteette rf&i nrdhs) { _ | o ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp_:i167n:s26e:r tIn file included from note: ' first required hereD e: f167 | 58a : u In file included from l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppt :V 10a : l In file included from u /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppe :> 47( : s /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht :d 946: :: 33f :o r warning: w definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]a r d 946y (p keTenwyao)m_)ed. _sidetecesortnardtu;oc rt :i| :v ^le h_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppsi:_t51se:er26ta:tt eonote: rrin instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here&_ t oy51pp | eer (am t_o mre =mb( ac+ro cn(osidt e* G rTBoIuTwpSo[)_b da/_r dcUeoBsd,te r]Bu[IcuTtmSii,v] e (_=ii t1*e; r BaItT oS| r) ^ &%o); | U ^B )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2817| : ^40 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp :note: 645in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here: 22 :2817 | note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | f o r ( dgecsBtirtuAcrtriavye__[ii]t e=r a1t;o r | ^i t = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it In file included from = ht.destructive_begin(); /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp :| ^ 84/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:: 9:In file included from note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hppin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here: 7 : 2948In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp : 30 : In file included from _move_/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppf:r13o: m(moveIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp,: 24ht, mi: nIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppucke:ts_wanted); 348 | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: 37in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here: In file included from warning: 2745/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppunused parameter 'p' [-Wunused-parameter] | : 1 : 348 In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp : 10D : e In file included from spra/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppr:s47e: _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hhia:vs946he:tda33b&:l eowarning: pdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]te mr pa946(t | Mo or v= e( DTosnwttodC_:od:pn_yudl,el sp*tttrhr_iutsc ,tp i)rve es{_i iz te| e_ ^rta ot/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp)o:;367 r: &34| : ^ o warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hp:unused parameter 'p' [-Wunused-parameter]e3278 r: a21t367:o | r note: = in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here(b co o3278on | s t lT w o op _e dr a _t do er s= t= r(iusfct td(i:_v:rene_usliilztpeetr_rad_tetol tpra )(& o1{)) ;) | ^| | ^ ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3712817::3813In file included from 40:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FragmentLengthDistribution.cpp::29: 3412:: In file included from note: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppwarning: :unused parameter 'p' [-Wunused-parameter]37 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp371in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here | : note: 73 :in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 50b:2817 | o warning: o3813unused parameter 'version' [-Wunused-parameter] | l In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppo p73:e | r58 av: oIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppif o:r10dre !so=er(r ts: ui(In file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpprda::47n: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:dlr:ne946euis:lt33zrleu:(pcA. pttrwarning: ecdefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]mihv iptvere__l& t946a | pi t tee) rTaawrt oo,{r_ f cido_| int ^dnesds t_trou rc=tui_n vies_hni/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppsg:entr582ie:.d32dt etr:(ip(nceso(rnt)sadt;t: o:T rf| w=oo ^=_ r(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hdws_ad:tr2948edds::t<9r:Ku:nT cu>tnote: l(in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested hereil vp ket2948e | ry_ _) ti) t. les fres ac, to onc_rdom ;no& vso et)| _; ^cf or/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp m:om| 28mo ^:n 14<(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hD:m, Io:,v2817note: e:in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested hereBr40, ,: W28hnote: ,tin implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here | , U m>2817i & | n _ rb hu sc k) e et {d s g_ wfea| sn ^ot[ ersd o)(u;dr ec se| t] ^. ri/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hun:cs2745t:ei26rv:t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp e(note: :_sin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here785 ii :t2745n27ek | :) r ;warning: a unused parameter 'b' [-Wunused-parameter]t o| r ^ 785 i | t s=ip athretsr.ead_tehosarts(rhutcatbilvee _tbmepg(iMno(v)e;D o n| t ^C o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hp:y2948,: 9*:t hnote: iin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested heres , Wr2948*e | s pi ,z e _u tn os )i ;g_ nm eo| dv ^ e _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hf:r3278o:m21(:m onote: vin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested heree rb ,,3278 | hutn,s i mg in ne_ bdu c koe t) s _ w | a ^n te d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp ): ;806i :f 22 | :( ^ _ warning: r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hunused parameter 'b' [-Wunused-parameter]e: s2745 i:806z26 | e: _ dnote: vein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested hereol it da2745 ( | b1 i) t) s ( u| n ^ s i In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hgs/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:np3813:ea:95dr: 29 s:In file included from be/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp )_:note: hin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here47{ : a s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h}3813:h | t946/ a:/ 33b l:N eO warning: O tdefinition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]P m p r946(| eM | ^t o u vr ne/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp DrT:owe845npo:t_.Ctd22o_e:pmd yepwarning: ,lsunused parameter 'b' [-Wunused-parameter] ta *tr tue845h c | itf sii ,vnv deor__ieoidstr e_ibizrinaets_tseot(rorut&)n<; sDo ie pgfe| na ^reua dl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht :otb3278Vr):=a 21l({:cu oe }nnote: > s(in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here/ts / t Td3278Nw: | Oo :_O dfP o_ dr we| sa ^ rt dr t (i kv ee y_i)if)t .e(sr_earcteoosnrid z&;eo _) d;| e ^l t| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppa ^:( 281/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h::142817:: 40note: :)in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here28 | 2817 | ) e d g efso[r s o(udrecsetr]u.citni| svert(s ^ei _n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hikt:)e;r a t| 3813o ^:r 29 :i tnote: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here= h3813t | . d e s t r u c trievteu_breng irne(p).;t e m| p ^l a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht:e2948 :f9:i nnote: din instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here_ o r2948 | _ i n s e r t < D_emfoavuel_tfVraolmu(em>o(vsetrd,: :hfto,r wmairnd<_KbIn file included from Tu>c(kke/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppt:s1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hy:)946):.33s:e cwarning: odefinition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]n d ;946_ | w a nT| wot_ ^d _e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppdd:e)s28;: 14 :| ^note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ht :r2745 :u26c:t inote: v28ein instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here | _ i t 2745e | r a t o re &d g oe psse[prsaaortusorerc_=eh](a.csiohnnssetrtat b(Tlsweio n_tkdm)_p;d( eM so| tv ^re uDcotnitvCeo_piyt,e r*atthoirs ,& roe)s; i | ^ z/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:e40_:t onote: )in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here; 2817| | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 3234 : 9 : fnote: oin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested herer (3234d | e s t r u c t i v_er_eistiezrea_tdoerl tiat( 1=) ;h t . d e s t r u c t i v e _ b e g i n ( ) ;/ / | a ^d d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hi:n2948g: 9a:n note: objin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested heree c t2948, | g r o w i fIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cppn:e58e: dIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppb e: _10 : m| In file included from o ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp :v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h47e: _:f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h4225r:In file included from o946:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cppm67(::: 33m84note: o:: vin instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here In file included from warning: e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]r4225: | 7 , : 946 In file included from | h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp t : s,8 t: dmIn file included from Ti:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppw:n:o_p37_ab: di/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp_udr:ecir ^d&i /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hnsos:epe2745rer:irt26a(a:lP tinote: oz&in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested herere&= (( Ac2745oor | bnc jsh )ti v T ew &o _ ad r_ s, dp {aec srorstnereutc_ustrhitnav esur_henitstpaie.bgrinlnaeestd eot rri mn&ttpo( ()svMt;eo drv s:e| i:D ^ofo non/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h)rt:w C2817a{o:rp 40dy:<, P | note: >* ^(tin implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here oh bi js2817),) ;r e} | s i z| e ^_ t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppo :)28; : 23 | : ^ note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hf:in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here3234o :r 9 28:( | d note: e in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested heres t r 3234u | c t ie d gv ee _s i[ ts_eorruearstcioezr]e ._idinesletrtat ((=1s )ih;ntk .) d; e s | t ^r u c t i v e _ b e g i n (/)/; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:a2948:d9: dnote: iin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here n g2948 | a n o b je c t ,_ mgorvoew_ firfo mn(emeodv ebre, h| t ^, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hm:i4225n:_67b:u cnote: kin instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested heree t s4225_ | w a n t esdt)d;: : p| a ^i r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h<:i2745t:e26r:a tnote: oin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested herer , 2745b | o o l > i n s esrpta(rPs&e&_ hoabsjh)t a b l e t m p{( MroevteuDronn trCeopp.iy,n s*etrhti(ss,t dr:e:sfiozrew_atrod)<;P > (| o ^b j/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h):)3234;:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here } 3234 | | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp : 28 : 23_:r enote: sin instantiation of function template specialization 'spp::sparse_hash_set::insert' requested herei z e28_ | d e l t a ( 1 ) ;e d g e s [ s o u r c e ] . i n s e r t ( s i/n/k )a;d d i| n ^g an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/GZipWriter.cpp.o -MF CMakeFiles/salmon.dir/GZipWriter.cpp.o.d -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(c33o warningnss generatedt. Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_b[ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o egin(cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy)stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here 3813 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp : 92 : In file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hppe:t15u: rIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp :r9e: p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp.:t4e:m32p:l awarning: tunknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]e f4i | n#dp_roarg_mian sGeCrCt n(osrtedd: :f"o-rWwmaarydbn(ikneiyt))i.aslizeedc"o n d| ^ ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:12:14: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 12 | txpIdxMap[ transcripts[i] ] = i; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned int, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; In file included from | In file included from In file included from ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/Alevin.cpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp::12058:93: : 35: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:19:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp92610::: :In file included from 44note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp25: ::in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here40 In file included from warning: : lambda capture 'early_stop' is not used [-Wunused-lambda-capture]In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp35:: | 7926 7: | : In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp: 34: : 17t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h : :x In file included from 377p /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:T :42o 29:&G: el/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hhnawarning: :einline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline]r258 Mg: ea26377ps | :[t t_ warning: io unused parameter 'dst' [-Wunused-parameter]dc c ]c, o n258=s& | te _gai irvdlto;yie _rd sa | tct ^ooo pr, _p_sayt_tarliilbgutnoeec_d_a(_t(rolru,(sAe d&k)d,)s tsa,ip gpcneoenndds_(tkc ,oA n qs&itds_rict,e rsattdo:r: fexanl,ds_eo_ft_ybpuec)k e{t} | | ^ ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh,: :c258563o:n62s:t note: Cin instantiation of function template specialization 'salmon::mapping_utils::pasc::map_read' requested hereh aIn file included from r563T | */wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp: :40k 1:e : y In file included from warning: , /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hppunused parameter 'src' [-Wunused-parameter] : s 10i z e: _258 In file included from t y | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp p : eb47vo : ook/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hlei:y d946_e :s33ac:i rowarning: zlpdefinition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]y ey_, _e946 xai l t| | l ^ =o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.h c : a1318s t:Tao74wl:rom (_onote: Adused heren :_& :dd1318me | ass ptt p,r i ucncsogtnt_idsuvt:te :i_pAli ats&ie:srr:raryc epoeaenmd)spS tlu{ ab}TcS wee o_q| i_, ^md p m_lad(pset_ds:c:tasrciuhzece__tstie vcieob_nuidct,ke erPtaa,ti ortriy np&geoSn)ta;am te u | sa ^:r :r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hU:aN2817yP:_A40bI:uR cEnote: kDin implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required heree_ tR :I2817:G | cH oT n) s; t _ i| t ^ e fr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppoa:rt1730 o:(r10d :ee snnote: tdin instantiation of function template specialization 'process_reads_sc_sketch' requested herer_ uo cf1730t_ | ib vu ec _k ie tt e, r a t p| or ^ro ciets s=_ rheta.ddse_sstcr_usckteitvceh_(b e g| i ^n (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp):;2094 : 5| ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hnote: :in instantiation of function template specialization 'sc_align_read_library' requested here2948 :9 : 2094note: | in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | s c _ a l i g n __rmeoavde__lfirboramr(y(eexrp,e rhitm,e nmti,n _rblu,c kseitdsx_,w atnrtaends)c;r i p| t ^s ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2745 :| 26 ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppnote: :in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here2521 : 232745: | note: in instantiation of function template specialization 'do_sc_align' requested here 2521 | s pbaorosle _mhaapsphitnga_bolke =t mdpo(_Msoc_vaelDiognnte69(s: ei/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hxz:pe241e_:rt36io:m) e;warning: n builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]t ,| ^241s | o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h p t :, :3278 :| s21 ^t:d::i nnote: In file included from tin instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp : 1203278: | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hppe :g 926r : 48 : awarning: llambda capture 'k' is not used [-Wunused-lambda-capture] _ c o926 n | s t a n it f< b (o _o rl&e,ls ai_rzg_eeh_sadtse__lottcarc(i,1v )i&)ae la _r| dl ^ey _s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hst:tr3813ou:pc29,t: o srnote: i(in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested heregT n) e 3813d& | _& r l ,| ^ k ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h : s246ri:eg36tn:ue rdwarning: n_builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins] kr ,e p246q. | it de xm ,p l: a | ts ^et d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hppf::i:927ni:dn10_t:oe rgwarning: _rlambda capture 'verbose' is not used [-Wunused-lambda-capture]ia n ls927_e | cr ot n< sD te af na tu _e(_]sh(taadsu:_t:tofr&oi rvrwiaaawrl_d_hs,(t kraeuuyct)to)o&.r s(peTrc)eo vn&_d&r; e a | d| _ ^ ^p o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hs::,98252 ::a1936u::t onote: warning: &in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested herebuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] m a98252x | | _ a l l o :w e sd t_bdoa:cr:cci,on dt ee| M ^ga rpa[li_]c o=n sit;a n | t ^< bool, __has_trivial_copy(T) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpp:10: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: In file included from definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp 946 | : 93 : In file included from T/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hppw:o55_: dIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/SAMWriter.hppd:e4s: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BinWriter.hppr:u31c:t60iv:e _iwarning: tunqualified call to 'std::move' [-Wunqualified-std-cast-call]e rator &31 | o p era t or = ( c oBnsitn WTrwoi_tde_rd(essttdru:c:tvievcet_oirt &&&o )b; | ^ i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817n:_40d:a tnote: ain implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here) 2817: | _ b i n _ d a t af(or (mdoevset(rbuicnt_idvaet_iterator it = ht.desat)r)u c{t}i;v e_ b| e ^g i n| ( std::) ; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, const std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cpp:105:23: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 105 | trueBarcodeMap[bc] = idx; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:926:25: warning: lambda capture 'early_stop' is not used [-Wunused-lambda-capture] 926 | &largest_occ, &early_stop, signed_rl, k, signed_k, qidx, | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:563:62: note: in instantiation of function template specialization 'salmon::mapping_utils::pasc::map_read' requested here 563 | bool early_eIn file included from x/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cppi:t93 : =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp :s298a:l62m:o nwarning: :lambda capture 'invalidScore' is not used [-Wunused-lambda-capture]: m a298p | p i n g _ u t i l s : : p a s c : :[m&aspc_orreeasd,( rheaarddSFuiblSteeqr,, m&s_ic,a cdheec_oIn file included from sy/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlevinHash.cppeT:ch1o: rnIn file included from ed/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinHash.hpps,: 10hP: oIn file included from al/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppid:r,40i: nIn file included from ig/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hppn:Svt7aa: ltIn file included from iu/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.hds:S:34c: :o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.hUr:Ne377P]:A(42I :R warning: E| inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline] ~~^~~~~~~~~~~~ D _377 | R I G H Tc)o;n s t| _ ^i t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppe:r1730a:t10o:r note: _in instantiation of function template specialization 'process_reads_sc_sketch' requested here_a t t1730r | i b u t e _ _ (p(ruocseeds)s_reads)_ sacp_pseknedt(ccho( n| s ^ t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp_:i2094t:e5r:a note: tin instantiation of function template specialization 'sc_align_read_library' requested here o r2094 | e n d _ osfc__baulcikgent_,r ecaodn_slti bCrhaarT* key, size_type key_size, r y| ^ ,( ebxopIn file included from eo/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpprl:i>103m : ee/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppnm:tp16,l: a3rc:le ,_warning: iexplicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted]sm pi l(stdd::size_t ibuxcket, ,type 16nta | rm ae array_bucket: :connFsstoc_iterrator egnd_eof_butcket, | ^ rtiipntgsM,a s s C| a ^l c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppu:l2521a:t23o:r (note: Fin instantiation of function template specialization 'do_sc_align' requested hereo r g2521e | t t i n gbMoaosls Cmaalpcpuilnagt_oork& &=) do_=s cd_ealfiagunlmove constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructor( e x141p | e r ismtedn:t:,m ustoepxt ,ff Mu t| ex ^_ ; In file included from | ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp :/usr/include/c++/v1/__mutex/mutex.h120:: 30/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp::3926:: 48note: :'mutex' has been explicitly marked deleted here warning: lambda capture 'k' is not used [-Wunused-lambda-capture]30 | 926 | m u t e x ( c o n s&tl amrugteesxt&_)o c c , & e a r l y _ s=t odpe,l estieg;n e| d ^_ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppl:,16 :k58,: snote: ireplace 'default' with 'delete'g n e16d | _ k ,F oqirdgxe,t t i| n ^ gMa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpps:s927Ca:l10c:u lwarning: alambda capture 'verbose' is not used [-Wunused-lambda-capture]t o r927( | F o r g e t t i n gvMearsbsoCsael]c(ualuattoo&r &r&a)w _=h idtesf,a ualutt;o & | p ^~~~~~~r e v| _ deleter e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hppa:d17_:p29o:s ,warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted]a u t17o | & mFaoxr_gaeltltoiwnedg_Mocacs,s C a| l ^c ulator& operator=(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:95: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hpp:47: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, std::string, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, std::string &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cpp:2647:27: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; | ^ 32 warnings generated. In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:[ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o 37: warning: unused parameter 'p' [-Wunused-parameter]cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -MF CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o.d -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cpp 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from 12/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp warning:s30 generated: . In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignore[ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o d "cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy-stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/FASTAParser.cpp.o -MF CMakeFiles/salmon.dir/FASTAParser.cpp.o.d -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp Wmaybe-uninitial/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cppi:z549e:d14": warning: variable 'auxProbSum' set but not used [-Wunused-but-set-variable]| ^ 549 | double auxProbSum{0.0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:824:10: warning: variable 'locRead' set but not used [-Wunused-but-set-variable] 824 | size_t locRead{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:827:12: warning: variable 'localNumAssignedFragments' set but not used [-Wunused-but-set-variable] 827 | uint64_t localNumAssignedFragments{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:1657:10: warning: svariable 'locRead' set but not used [-Wunused-but-set-variable]t d 1657 | size_t locRead{0}; | ^ ::integral_constant::type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: In file included from note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cppin instantiation of member function 'Eigen::DenseBase>::Constant' requested here :4: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ProgramOptionsGenerator.hpp327 | : 5 : rIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13e: tIn file included from ur/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: dbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] e 241 | : strd::integral_constanit>::setConstant' requested here o r627( | T ) r&et&u r n| ^s etConstan/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.ht:(Scal246a:r36(:1 )warning: ); | ^ builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp : 56:15: 246note: | in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | : s t d : counts_.setOnes(); | ^ :In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hppi:7: nIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppe:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:g5: In file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:a1l: _In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:o348: n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:s92:t29a:n twarning: e g r a l _ c o n sctlaansts< bCwiosoeNullaryOp; l ,| ^_ _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hh:a176s:_10t:r inote: vin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herei a l176 | _ creturn DenseBase(:T:)N ullaryExpr&(&r o w| s ^, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hc:o259ls:,17 :inte rwarning: nal::scalabuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]r _ c259o | n s ta nt _op(val u e ) bool, __has_trivia)l_;a | ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327s:i22In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cppg :note: 8in instantiation of member function 'Eigen::DenseBase>::Constant' requested here: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp327: | 35 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppr:e102t:u16r:n warning: dvariable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]e r i102v | e d (cnh)a (r=t y ppCaeodnndasimtnea gnstd::r[etmn(ovre_rboe_wfeprsean(c)d,d icnogl]s;( ) ,| ^~~~~~~~~~v a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppl:)102;: 16 :| ^note: read of non-const variable 'nb_padding' is not allowed in a constant expression/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp627::9510: enote: :in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here <11 :627 | note: T declared here> :r:t ey95pte) & | & u r | ns ^ ssizetConstant(Scalar(e1_)t) ;nb_padd i n| g ^ =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :o56s:.wi15dth(:) - (prefnote: iin instantiation of member function 'Eigen::DenseBase>::setOnes' requested herex .s tr(56) | . s i z e() + cbouufn.tsst_r.(s)e.tsOinzees(()));; | | ^ ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp : 8M: a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hppy:L647i:32: warning: nunused parameter 'k' [-Wunused-parameter] e 647 | mera_rVbecatosrei_zstatei c=( ubnosoilgne(Mighdt Viectnotr ikz,e )c o&n&s t McahyaLri* s) : sunper(k_) e{ | a ^ rize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraiIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ProgramOptionsGenerator.cpp:4: sIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ProgramOptionsGenerator.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: :unused parameter 'p' [-Wunused-parameter]:PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :348739 | : 10: Dnote: ein instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested herer i 739 | vKeerdn&e l kernoelp(edrsattEovraluator, srcEvalua=tor(, sIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonAlevin.cppfd:u:95n:c,n : duIn file included from ls/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlevinUtils.hppl:pt40t.r: _In file included from tc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BarcodeGroup.hpp :p7): In file included from {/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_map.h:o 34 : n| /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.hs: ^t377 _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:c:42a367:s: t34warning: _:inline function 'tsl::detail_array_hash::array_bucket, unsigned short, true>::append' is not defined [-Wundefined-inline]d ewarning: r377unused parameter 'p' [-Wunused-parameter] | i v 367e | c obnosotl_ diotpe(erraattoorr =_=_(astttdr:i:bnuutlel_p_t(r(_)uts epd)) ){ a p| p ^e n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppd:(371c:o34n:s twarning: _unused parameter 'p' [-Wunused-parameter]i t e371r | a t obro oeln )od;p_eoraft_obru!c=k(estt d,::nu l l| pct ^or _nt/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hs :tp879 ):C 5h:{a rnote: Tin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here| * ^ k 879e | y , s iczae/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppl_:lt582_ype k:de32ye_size,:n s warning: e unused parameter 'lfs' [-Wunused-parameter]_ | a ^s582 s | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/tsl/array_hash.hib:go1318no:ml74e :no pnote: teused here_r la ot1318oo | pr (= d= s( tss,tt dds::r::cn,p ufaluir emplacet_im p l l(| std:f: ^size_st ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hib u:ckce836t,o type:nna46mes :artr anote: cyin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested hereo_bu ckme mt836:o | :n consft&_u baurlchkDet, | ^ ss)t T{y p e| C ^ leaned,Src,Func/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp>:785:27: :warning: :unused parameter 'b' [-Wunused-parameter] r u785n | ( aictteuraaltDosrt(,W *s rpc,, ufnusnicg)n;e d | b ^, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu:n804s:i3g:n enote: din instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here o )804 | | ^c al/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppl:_806a:s22s:ig nwarning: munused parameter 'b' [-Wunused-parameter]e n t806_ | n o _vaoid bits(unlsiignaesIn file included from d(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp d:bs9)t: ,{ In file included from }/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpps :r/12c/: , In file included from NfunOc)O; | P ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp ::15| : 3 ^In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppnote: 8:(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)845: :In file included from 22/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:782: | 37warning: : unused parameter 'b' [-Wunused-parameter] /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp c: a73845l: | l50 _: av sowarning: siunused parameter 'version' [-Wunused-parameter]idg n m eb73ni | tt( dss (tvu,on issdi rgscn,eed riinatbernla)l:: a{s is}zi gn_o/pe/< tNyOpO(ePnAa me | D ^s t::Scalrar,tycpheinavmee& Src::Scalar>()); a| ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h,:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710c | o n s internal::call_ats signment(this->deruinvesd(), other.derived()); | ^ i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: gin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested herene d i225n | t v e r si orn)eturn Ba s{e : :| _ ^set(o ther); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, In file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: cIn file included from ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp :f145: u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:n12c: )warning: ;variable 'n' set but not used [-Wunused-but-set-variable] | ^609 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h size_t n:{210}:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here ; 21 | | i ^n ternal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant:cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy:stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/AlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp type) && | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:11: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348 | Derived& operator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:84: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ClusterForest.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] b 657 | lhs_setter& operatoro=(const lhs_setteorl& rohpse)r a{t o r| ! ^In file included from = /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpps::t9167d: ::In file included from 26:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp::n 19unote: : lin implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required hereIn file included from l /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppp :t16717r | : _ In file included from t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh :p 29) : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh{ : 258 :| 26 ^ : warning: unused parameter 'dst' [-Wunused-parameter] 258 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp v o i?d: 582tc:yo32pp:ey n_warning: aaunused parameter 'lfs' [-Wunused-parameter]ml el o582ic | tabetrooart(oAor :&:dlls htos,_p seceotnrtsaettro _Art =y&=ps(ers(ctm,d_ :ms:tnedu:ml: fa+lse_t ylp(epi)t {}r | _ ^ t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh :258:40: lwarning: funused parameter 'src' [-Wunused-parameter] s ,* 258 cBo | In sTtS )cv oom/im doU nBc<,oD p,By _IIn file included from IaT,lS l,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantMerge.cppoB :c(ai 30*: ,tIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hppo Wr:(,BA18I : U TIn file included from &>S/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppd&:s )37tr h,s: )% /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp: {73U c: o50| B:n ^)s t warning: | unused parameter 'version' [-Wunused-parameter]A ^ &73/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpps | :r c645,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp :s785:t:v27do::i :warning: 22df:unused parameter 'b' [-Wunused-parameter]a lnote: s in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested herese785e | _r t i645 a | yi tp leei r)z a et {( }A or r| c (h ^ W ig*vc eBp&i, t aAurnr,sr iacgyon_nesd[t i b]u, n s=iu gnn1se;id g n| ie ^ndt ov)e r s| i ^o n)/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp :{806 : | ^22 : warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buck&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:254:7: note: in instantiation of template class 'phmap::is_trivially_destructible>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool ets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested hereunused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivial 2745 | sparse_hashtable tmp(MoveDontCopy,ly_copy_assignable>' required here 2053 | class optional : private optional_inte *this, resirzneal:_t:o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.ho:3278:21: note: pin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resitional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insze_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ ert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | 29 warningisf generated . (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o = 1; cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy| stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GZipWriter.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ 11 warnings generated. [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void serialize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp:93: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hpp:44: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destrIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/mer_dna.hpp:35: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 102 | char padding[nb_padding]; | ^~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp:117:uctive16:_ note: iin instantiation of function template specialization '__int128_ns::__print<__int128>' requested heret e r117at | o r it = ht. d_e_instt1r2u8c_tnivse:_:be__gpriinn(t()o;s , | x ^) ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h : 2948| : ^9 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp :note: 102in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here: 16 :2948 | note: read of non-const variable 'nb_padding' is not allowed in a constant expression 102 | cha_rm opvaed_dfirnogm[(nmbo_vpeard,d ihntg,] ;m i n| _ ^b u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppc:95:11: note: declared here k e95 | t s _swsainztee_dt); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hnb_padding = os.width() :- (prefix2745.s:tr().siz26e: note: (in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here) +2745 | b u f . s t r().size()) ; spars e _| h ^a shtable tmp(MoveD/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hppo:102:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] n t102C | o p yc,h a*rt hpiasd,d irnegs[inzbe__ptadod)i;n g ]| ; ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h| : ^~~~~~~~~~3278 :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp21::123 :note: 16in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here: note: 3278in instantiation of function template specialization '__int128_ns::__print' requested here | 123 | __int128_ns::__pr i n t ( o s , x ) ; i| f ^ (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp_:r102e:s16i:z enote: _read of non-const variable 'nb_padding' is not allowed in a constant expressiond e 102 | char lpaddintga[(n1b)_)p a d| d ^i n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hg:]3813;: 29 :| note: ^in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/jellyfish/int128.hpp :381395 | : 11 : note: declared here 95r | e ssize_t nbt_uprand drinegp = o.st.ewmidth(p) - (prefix.str().lsaize() + buf.str().size()); | ^ te find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantify.cpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:93:: 8In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonMappingUtils.hppIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp44:: 7In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hppIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: 7In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp13: :In file included from 18/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h23:: 946In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h33::69 : warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hdefinition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]: 241 :94636 | : warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] T241w | o _ d : _std::intdeegsral_constant> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required herea l _2817c | o n s t a n t < bfooorl ,( d_e_hass_ttrruicvitailv_coep_y(iTt) e&r& a | t ^o r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :259:i17t: warning: =builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] h t259. | d e s t r u c t i v eb_oboelg,i n_(_)h;a s _| t ^r i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hv:i2948a:l9_:a snote: sin instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested herei g n2948( | t y p e na m e std:_:rmemoovvee__frreofme(rmeonvceer<,T >h::tt,y pmei)n &_& | ^ buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 3234 139 | Derived& operator=(const MatrixBase& other); | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 9 90 | template class CwiseNullaryOp; | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested herein instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constan t3234(rows( | ), cols(), v a l ); _| r ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10:s inote: zin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here e _627 | d reetlurtna (s1e)t;C on s t a n t ( S c a l a r(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp : 56 : 15 : note: /in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here/ a56d | d i n g a nc ooubntjse_.setOnces(t),In file included from ; /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp g: r8| o: ^wIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hppiIn file included from :f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp7:: 13In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:In file included from 7/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp: :In file included from 5/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp: :In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp30:5: In file included from : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:In file included from 1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h::281:1314: : In file included from warning: n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppdefinition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]: 24 : 281In file included from | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp : 10 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppD:e348r:i37v:e dwarning: &unused parameter 'p' [-Wunused-parameter] o p348e | r a tDoerr=i(vceodn&s to pDeernasteoBra=s(es&t do:t:hneurl)l;p t r| _t p) { | ^ e ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h367::4834::34 :warning: unused parameter 'p' [-Wunused-parameter]note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 367 | 48 | tbeomopll aotpeep tcrl_ats sp )M a{t r i| x ^B a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpps:e371 : 34| : ^ warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hunused parameter 'p' [-Wunused-parameter]: 90 :37165 | : note: bin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required hereo o l90 | otpeemrpaltaotree!, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested herepp ), {4225t | y p| e ^ n asme MatrixType> /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp : 582 : c32l:a sswarning: unused parameter 'lfs' [-Wunused-parameter]C wiseN utl582la | ryOpb;o | o ^ l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h: 176:o10: pnote: ein implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here r 176 | a treturn DenseBase::Nullarryd=E=x(:psrt(dr:o:wnsul,lptr_ t clfosl, scon,st cionmtmeornnn&s trahnst)_ oIn file included from p{p < S| c ^a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cppaa:ir3r>: <(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppIn file included from v:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppa785:l:6u27: e:i) In file included from )t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppwarning: ;e:unused parameter 'b' [-Wunused-parameter] r 23 a: 785| tIn file included from ^ | o /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.hr :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h,i:69 327: tb:e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h22o::241r :oa36note: ltin instantiation of member function 'Eigen::DenseBase>::Constant' requested here:>o rwarning: i(327builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]nW | * s241 erp | re, tt u (u rPnn &s: &id gesontrbeidjd:v) e:bd ,i( n) u t =en sg Cir oagnlsn_e ctd{a o nnors)tet( tra uno| rwt ^ns < (b/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppr):oe,o806p :l.c22,o: il _swarning: _n(unused parameter 'b' [-Wunused-parameter]hs)a es ,r_806 t | tr vi(av sivlta)odl;i: _d: d | efb ^soi ttr/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hsrw:u(a627cur:ntd10os:nTin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here(e) od b 627&jb | &)) ) { ;| r ^ } e}/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h :/t 246/| : u ^36Nr: O n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppwarning: O:builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]sP28 e : t23246| C: | o ^ n note: sin instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp a:: n84528 t: | s(22 t:S d c :warning: a :unused parameter 'b' [-Wunused-parameter]li a n r (t845 1e | eg) dr )ga;vel o_s ic[| dos ^ on bus/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpprit:cta56es:n](15.ut:ni< snbnote: siin instantiation of member function 'Eigen::DenseBase>::setOnes' requested hereoego nlre, d t _(56b_s)h | i a{ns _}k t )r/;i/ v i aNl| _OcOoPn s ^ t| r ^u c t ocro(uTn)t s&_&. s e| t ^ O/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: nwarning: ebuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] s (252) | ; : std::integral_con| stante: :Ntuylplea)r y&O&p , | ^ typename MatrixType> class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: cIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppl:l6_: dIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppn:s24e: _In file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:s10: s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppi:g348n:37: mwarning: eunused parameter 'p' [-Wunused-parameter]n t _348 | l o oDpe(rdisvte,d &s rocp,e rfautnorc=)(;s t d| : ^: n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu:l836l:pt46r:_ tnote: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested herep ) 836{ | | ^ A/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpps:s367i:g34: nwarning: munused parameter 'p' [-Wunused-parameter] e 367 | n t p:): r{u n(actualDst ,| ^ s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppr:c371,: 34f: uwarning: nunused parameter 'p' [-Wunused-parameter]c ) ;371 | | ^b o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ho:l804 :o3p:e rnote: ain instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested heret o r804! | = (s tcdall_assignment_no_a:l:inausl(ldpsttr,_ ts rp)c ,{ f | ^ unc); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp3::582 :note: 32(skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all): warning: unused parameter 'lfs' [-Wunused-parameter]782 | 582 | b ocoall lo_pearsatsoirg==n(msetndt:(:dnsutl,l pstrrc_,t ilnftse,r ncoanls:t: caosmsmonim&e rDhsst): :{ S | ^ calar,typename Src::Sca/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppl:ar>());785 : | 27 ^: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hwarning: :unused parameter 'b' [-Wunused-parameter]710 : 17785: | note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested hereit er a710t | o r ( W * pi,n tuenrsniagln:e:dc b, aulnls_iagsnseidg nom) e| ^ n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppt:(806t:h22i:s -warning: >unused parameter 'b' [-Wunused-parameter]d e r806i | v e dv(o)i,d obtihtesr(.udnesriigvneedd( )b)); { | } ^ //wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h/: 225N:O20O:P note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here| ^ 225 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp : 845r:e22t:u rwarning: nunused parameter 'b' [-Wunused-parameter] B a845s | e : :v_osiedt (boitthse(ru)n;s i g| n ^e d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :b327): 20{: }note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here/ / 327N | O O Pr e t| u ^r n derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:5: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpprize): 8: &In file included from &/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp :M7a: yIn file included from L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hppi:n7e: aIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hppz13:e warning73 s:&50 generated&:. Dwarning: sunused parameter 'version' [-Wunused-parameter]t H a73 | s D ivroeicdt Ascecreisasl i z| e ^( A/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:c607h:i20v:e ¬e: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested herea r ,607 | c o ntsytp eunsigdneefd tiynpte nvaemres iAosns)i g{ n m| e ^n tTraits::PacketType Packe[ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o tTypecd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isy; | ^ stem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCIn file included from F/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: rIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hppg:M15o: dIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppl:&8&: )In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22=: In file included from d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densee:f1a: uIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coret:;415 : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h| : ^139 :14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cppIn file included from r:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/FASTAParser.cpp20::1131c: :In file included from ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13 : warning: In file included from moving a temporary object prevents copy elision [-Wpessimizing-move]f/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp u: n2420c: | )In file included from ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp : 10| t: ^r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp a:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hn657::s83615i::t46 i:warning: o definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]nnote: Pin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here r o657 b | 836 | s L leAhfssts__is[geintm]te enr=t&< Asocpttedura:al:tDosrmt=To(yvcpeoe(nCslte alAnhtesdo_,msSiertcct,MFearut&rn icrx>h<:sd:)or uu{bn l( e| a> ^c( t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppu :a| 167 ^l: D26/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpps::t 20,note: : in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here31s :r c167note: , | remove std::move call here f u 20n | c ) ; t| r ^ a n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h s: i804 t: i3 o: n Pnote: rin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here o b s804?L | e tf ytcp_ae[lnila]_m ae=s sisittgednr:ma:etmnootrv_:en:(olA_htasol_misiaecstM(tadetsrrt_i,tx ynm(c )+ ; | ( ^~~~~~~~~~ i | ^*21 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hB :I 782T :S 3) : / note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)Un Bu ,m782 A | Bl Ii TgcSna,ml el(n_ita Ss*ts aiBtgIenTsmSe()n) t,% ( ndUusBm)tA ,l i| sg ^rn cm/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp,e: n645it:nS22tt:ea rtnote: nein instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested hereas l( :)645:, | a sa sl ip ghna_)o)p;< t y| p ~ e n a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp m: e22 : D32gs:ct B:warning: i:moving a temporary object prevents copy elision [-Wpessimizing-move]tS Ac ra22rl | aa yr_ ,[ ti y]p e=n a1m;e St| r ^rc a:n:sSictailoanr>(P)r)o;b s R| i ^ g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here h 710 | t _ [ i ] =i nsttedr:n:amlo:v:ec(aAltlo_maiscsMiagtnrmiexnderived(),b loet>her.derived()); | ^ (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225: 20 : note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here | 225 | return Base::_set(other); | ^ ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cppin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here : 327 | 22r:e32: tnote: uremove std::move call herer n 22d | e r i v etdr(a)n s=i tCioonnsPtraonbts(Rriogwhst_([)i,] c=ols (s)t,d :v:amlo)v;e ( | ^A t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ho:m627i:c10M:a tnote: rin instantiation of member function 'Eigen::DenseBase>::setConstant' requested herei x <627d | o u brleet>u(r n setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here | 56 | ^~~~~~~~~~ counts_.setOnes(); | ^ 23 | numAlignmentSIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: tIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: tIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpps:8: (In file included from )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp,:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1n: uIn file included from m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoreA:l420: i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: gwarning: nmeconverting the enum constant to a boolean [-Wint-in-bool-context]nt S ta86t | e s ( ) ,M aalpha)); | ~ yLinearVectorize = bool(Mi/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cppg:h96tVe:c33:t owarning: runused parameter 'primary' [-Wunused-parameter]i z e96) | & & MbayaLmi_nseeaqr_itz*e r&e&a dD,s tbHaams_Dsierqe_ctt*A prcicmeasrsy , | T ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.ha:607n:s20: note: cin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested herer i p607t | & rteyfp,e d e| f ^ typename AssignmentTraits:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp::P230a:75: warning: cunused parameter 'primary' [-Wunused-parameter]k e t230 | Tdyopueb lPe AlignmentModealc:k:eltoTgyLpikelihood(const ReadePair& hit, const Read;Pair& primary, Transcript& ref) { | ^ | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel ker/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] n 429 | void AlignmentMeodel::lupdate(const( dRsetaEdvPaaliura&t ohri,t ,s rccoEnvst ReadPair& parliumaatroyr,, f| u ^n c, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: In file included from in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp : 142745: | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant::type) && | ^ 23 warnings generated. [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3 -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/cereal/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/digestpp -I/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++14 -flto=thin -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -stdlib=libc++ -DBOOST_HAS_INT128 -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/BAMUtils.cpp In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] In file included from 73 | void seriali/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppz:e14(: AIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppc:h8i: vIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp& :a30r: ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hppc:o13n: sIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp :u24n: sIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hppg:n10e: d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter] 348i | n t Dveerrisvieodn&) o{ | ^ perator=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter] 367 | bool operator==(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter] 371 | bool operator!=(std::nullptr_t p) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter] 582 | bool operator==(std::nullptr_t lfs, const common& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter] 785 | iterator(W* p, unsigned b, unsigned o) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter] 806 | void bits(unsigned b) { } // NOOP | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter] 845 | void bits(unsigned b) { } // NOOP | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(ScalaIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp(:114): )In file included from ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp : 8| : ^In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp::3756:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp56: | 73 : 50 : warning: unused parameter 'version' [-Wunused-parameter]c ounts_.setOnes(); | ^ 73 | void sIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cppr:i8alize(Archive&: In file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hppr:,7 : cIn file included from o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hppn:s7t: In file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hn:s86i:g63n:e dwarning: converting the enum constant to a boolean [-Wint-in-bool-context]i n t86 | v e r s iMoany)L i{n e a| r ^V ectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.cons/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppt:_17c:a45s:t _warning: dunused parameter 'alpha' [-Wunused-parameter]e r i17v | eOdN(T)A)l;i gn m| e ^n t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hM:o879d:e5l:: :note: Oin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hereN T A879l | i g n m ecnatlMlo_ddeeln(sdeo_uabslsei algpnhma,e nuint32_t readBitns) _ | ^ loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here : 836 | Assignment::run(actu53a:22: lwarning: Dcomparison of integers of different signs: 'int32_t' (aka 'int') and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]s t, 53s | r c, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hi:f(804c:3: note: oin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here u n804 | call_assignment_nto_alias(dst, src,s f.usclinpc)s;( ) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h>:=782 :3:c igarRLen)note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) | ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ 782 | call_assig/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppn:m137:e56: nwarning: tunused parameter 'p' [-Wunused-parameter] ( ds137 | t , s r c , T riannstcreipt& ref, double p, doubler mass) { n al| ^ ::assign/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp_:194:50: warning: ounused parameter 'os' [-Wunused-parameter] p 194 | void ONTAlignme()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedefIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpp:9: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hy:946:33: pwarning: edefinition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]n a m946e | A s s iTgwnom_edn_tdTersatructiivtes_:i:tPearcakteotrT&y poep ePraactkoert=T(ycpoen;s t | T ^w o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h_:d739_:d10e:s tnote: rin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereu c t739i | v e _Kietrenrealt koerrn e&lo()d;s t E| v ^a l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hu:a2817t:o40r:, note: sin implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required herer c E2817v | a l u a t o r , ffourn c(,d edssttr.uccotnisvte__ciatsetr_adteorri vietd (=) )h;t . d| e ^s t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:u879c:t5i:v enote: _in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested hereb e g879i | n ( ) call_de;n s e| _ ^a s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.hs:i2948g:n9m:e nnote: t_loin instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested hereo p(ds t2948, | s r c , f u n_cm)o;v e _| f ^r o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hm:(836m:o46v:e rnote: ,in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here h t836, | m iAns_sbiugcnkmeetnts<_AwactunatleDds)t; | ^ T/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:y2745p:e26:C lnote: ein instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here a 2745 | n e d , Sr c,F u nscp>a:r:sreu_hnas(hatcatbule atlmDps(tM,o vserDco,n tfCuonpcy,) ;* t h| i ^s ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h :r728e:s17i:z enote: _in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested heret o )728; | | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h :i3278n:t21e:r nnote: ain instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested herel : 3278 | : c a l l _ a s s i g n m e n t _inf o(__raesliizaes_(dtehlitsa->(d1e)r) i | v ^e d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h(:)3813,:29: note: oin instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here t h3813e | r . d e r i v e return redp(.)t,e mipnltateer nfal::aisnsdi_gonr_insertc(asltadr:,:tfyoprewnaarmde< KOT>(ktey)).sheceornDde;r i ved::Sc| a ^l a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hppr:>28(:)14):; note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here| ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h28 | : 278 : 15 : note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here e d278g | e s [ s o u r c e]B.aisne::_sets_enrota(lsiiasnk()ot; h | ^ er); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentModel.cpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentModel.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AtomicMatrix.hpp:7: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhsIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/GZipWriter.cpps:e9t: tIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppr:_19t: yIn file included from pe(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hppm:_18mem + (i * BITS) / UB, BITS, : (i * BITS) %/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h UB) | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 946 645 | gcBi:tArray_[i] = 133;: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructiv| e_iterator& operato ^r=(const Two_d_destructive_it erator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h: 139_:move_f14rom(mover, ht, min_buckets_wanted:) ; warning: | ^ definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 139 2745 | | D esparse_hashtable tmp(Morvivede& operator=(const MatrixBase& oDther); | ^ o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:n90t:C65o:p ynote: ,in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here * t90h | its, eresimze_ptloa)t;e < t| y ^ p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.he:3234:9: nnote: ain instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here m 3234 | e _resize_delta(1); N u l l a r y O // adding an object, grow if need be | ^ p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67,: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^t y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: pin instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here e 28 | edges[source].insert(sink); | ^ name MatrixType> class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::5:: NIn file included from u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppl:l5a: rIn file included from y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/DenseE:x1p: rIn file included from (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corer:o415w: s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h,: 139c:o14l:s ,warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]i n t139e | r n a l :D:esrciavleadr&_ coopnesrtaatnotr_=o(pct(rviaxlBuaes)e)&; o t| h ^e r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h):;327 : 22| : ^ note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hin instantiation of member function 'Eigen::DenseBase>::Constant' requested here: 90 :32765 | : note: rin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required heree t u90r | nt edmeprliavteed<(t)y p=e nCaomnes tNaunltl(arroywOsp(,) ,t ycpoelnsa(m)e, Mvaatlr)i;x T y| p ^e >/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h : 627 : 10 : note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here c l627a | s s rCewtiusrenN usleltaCroynOspt;a n t| ( ^S c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ha:l176a:r10(:1 )note: )in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here; 176| | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppr:e56t:u15r:n note: Din instantiation of member function 'Eigen::DenseBase>::setOnes' requested heree n s56e | B a s e < D ecroiuvnetds>_:.:sNeutlOlnaersy(E)x;p r (| r ^o wIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp,: 3c: oIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpps:,8 : iIn file included from n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22t: eIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:n1a: lIn file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core::s414c: a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.hl:a281r:_14: warning: cdefinition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]o n s281t | a n t D_eorpi(va&l uoe)p)e; | ^ r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ha:t327o:r22=:( cnote: oin instantiation of member function 'Eigen::DenseBase>::Constant' requested heren s t327 | D e nrseetBuarsne &d eortihveerd)(;) =| ^C o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.hn:s48t:a34n:t (note: rin implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required hereo w s48( | )t,e mpcloaltse(<)t,y pveanl)a;m e | D ^e r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hi:v627e:d10>: cnote: lin instantiation of member function 'Eigen::DenseBase>::setConstant' requested herea s s627 | M a trreitxuBrans es e t| C ^o n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.hs:t90a:n65t:( Snote: cin implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required herea l a90r | (t1e)m)p;l a t| e ^< t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppy:56p:e15n:a mnote: ein instantiation of member function 'Eigen::DenseBase>::setOnes' requested here N u56l | l a r y O p ,c otuynptesn_a.msee tMOantersi(x)T;y p e| > ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp : 14 : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp :c5l: aIn file included from s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpps: 5C: wIn file included from i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denses:e1N: uIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corel:a414r: y/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.hO:p281;: 14 :| ^warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h : 176281: | 10 : note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required hereD e r176i | v e dr&e touprenr aDteonrs=e(Bcaosness:e:& Noutlhlearr)y;E x p| r ^( r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.ho:w48s:,34 :c onote: lin implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required heres , 48i | ntteemrpnlaalt:e:p a(tvrailxuBea)s)e; | | ^ ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h::90327::6522:: note: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required herein instantiation of member function 'Eigen::DenseBase>::Constant' requested here 90327 | | t e mrpeltautren< tdyepreinvaemde( )N u=l lCaornysOtpa,n tt(yrpoewnsa(m)e, Mcaotlrsi(x)T,y pvea>l ); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h : 627 :c10l:a snote: sin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here C w627i | s e Nrueltluarrny Ospe;t C o| n ^s t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ha:n176t:(10S:c anote: lin implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required herea r (1761 | ) ) ;r e t| u ^r n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :D56e:n15s:e Bnote: ain instantiation of member function 'Eigen::DenseBase>::setOnes' requested heres e <56D | e r i v e d >c:o:uNnutlsl_a.rsyetOnEexsp(r)(;r o w| s ^, In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cppo:l3s: ,In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppi:n8t: eIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hppn:a22l: :In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Denses:c1a: lIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Corer:_348c: o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.hn:s92t:a29n:t _warning: odefinition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy]p < S92c | a l a r >n(ov_aalsusei)g)n;m e | ^ n/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ht:_327o:22p:e rnote: ain instantiation of member function 'Eigen::DenseBase>::Constant' requested heret o r327& | o preertautronr =d(ecroinvsetd (n)o _=a sCsoingsntmaenntt(_roopwesr(a)t,o rc&o)l;s ( )| , ^ v/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:a90l:)65: ;note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here | ^ 90/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h | :t627e:m10p:l anote: tin instantiation of member function 'Eigen::DenseBase>::setConstant' requested heree < t627y | p e nraemteu rNnu lsleatrCyoOnps,t atnytp(eSncaamlar(1)); | ^ e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: Min instantiation of member function 'Eigen::DenseBase>::setOnes' requested herea t r56i | x T y p e > c o u n t s _ . sceltaOsnse sC(w)i;s e N| u ^ lIn file included from l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppa:r14y: OIn file included from p/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp;: 5 : | In file included from ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h5:: 176In file included from :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense10::1 : note: In file included from in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core : 348176: | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h : 92r:e29t:u rwarning: ndefinition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] D e92n | s e B a sneo<_Daesrsiivgendm>e:n:tN_uolplearraytEoxr& operator=p(In file included from cro/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cppn(:sr33to: wIn file included from ns/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppo,:_ 12ac: soIn file included from sl/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hppis:g,15n : miIn file included from en/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppnt:te6_r: onIn file included from pa/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppel:r:23a:: tsIn file included from oc/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.hra:&l69)a: ;r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h _: c241| o: ^n36 s:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.ht :awarning: 90nbuiltin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins]:t 65_ :o241 p | note: < in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required hereS c a 90l: | a trse>tm(dpv:la:alituneet<)et)gy;rp ae ln| _a ^cm oe/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hn :sN327tu:al22nl:ta >::Constant' requested hereop l, , 327 t | _y _p heranesat_muterr niM vaditearrlii_xvdTeeydsp(te)r> u =c t Co or n( sT t) a n&ct&l( ar so| sw ^ s C(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.hw):i,246 :sc36eo:Nl uswarning: l(builtin __has_trivial_constructor is deprecated; use __is_trivially_constructible instead [-Wdeprecated-builtins]l) a, r 246yv | Oa pl ;) ; :| ^| s ^t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h d:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:::627i10:n:10t: e note: gnote: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required hererin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here a l 176_627 | c | o n rsertteautnrutnr< nbD oesonelst,eC Bo_an_sshetaal:r_:(cN1ou)nl)sl;ta rr uy| cE ^tx op/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpprr:((56Tr:)o15 w:&s ,note: & in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here c o | l56 ^s | ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h : i252 n: t36 e:cr onwarning: uabuiltin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins]nl t: s:252_s | .c sa el ta Or:n_ ecssotnds(:t):a;in nt t_| eo ^gp rs(tvaanltu>::Constant' requested here:a 1l : _327In file included from c | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Coreo :p 420yr: (e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hTt:)u86 r:&n63& : d ewarning: | rconverting the enum constant to a boolean [-Wint-in-bool-context] ^i v /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.he86:d | 259( :) 17 := Mwarning: Cabuiltin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins]oy nL si259tn | ae na tr (V re oc wt so (r )i ,zb eoc oo=ll ,sb (o_)o_,lh (avMsai_lgt)hr;ti Vv ei| ca ^lt _o/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.ha:sr627si:i10zg:ne ()note: tin instantiation of member function 'Eigen::DenseBase>::setConstant' requested here y &p e&627n | aM ma eyr Lesittnuder:an:r risezemeto Cv&oe&n_ srDtesaftneHtra(esSnDcciaerlt(:A1:c)tc)ye;ps es ) | ^&| & ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp : /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h56| :: ^60715 ::20 :note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested herenote: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 56 | 607 | t y pceoduenft sIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp_y:.p33se: enIn file included from ta/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hppOm:ne12e : sAIn file included from (s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp)s;i: g15 n: | mIn file included from ^e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp n:t6T: rIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hppi:In file included from t24/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpps: ::In file included from 14:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp: :PIn file included from 10a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp: c:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppk:5e348: t:In file included from T37/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppy::24 p5 warningwarning: e: sunused parameter 'p' [-Wunused-parameter] In file included from generated P/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense . a:348c1 | k: eIn file included from t /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoreT:420y: Dp/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hee:r;86i :v 63e| :d ^ & warning: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hconverting the enum constant to a boolean [-Wint-in-bool-context]o: p739 e:8610 | r: a tnote: oin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here r M= a(739ys | Lt id n:eK:aenrruVnleelclpt tokrr_eitzr epn) e =l{ ( d bs| ot ^oE lv(/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppaM:li367ug:ah34tt:oV rewarning: c,unused parameter 'p' [-Wunused-parameter]t os r367ri | cz Ee v)ba ol&ou&la tMooaprye,Lr iafntueonarcr=,i= z(desst td&.:&c: onDnusslttlH_pactsarDs_ittr_ edpce)tr Ai{cv ce ed| s( ^s) )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp ;:| 371 ^ : | 34/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h ^:: 607/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hwarning: ::unused parameter 'p' [-Wunused-parameter]20879 :: 5371note: : | in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hereb607 o | o 879l | t oy pp ee rdcaeatflo lrt_!yd=pe(ensnstaedm_:ea: snAsusilsglinpgmtnermn_ettn_ tlpTo)ro ap{i( td ss| :t ^:, P ascrkce,t Tfy/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppup:ne582c :)P32;a: c kwarning: | eunused parameter 'lfs' [-Wunused-parameter] ^t T /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hy582:p | 836eb:;o46 o: l | note: ^oin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here p /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he :r836739a | :t 10o :rA =snote: =sin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here(i sg tn739dm | :e :n ntKuE,:v :aBrl,uu naW(t,ao crUt,>u &af lurDnhscst,), d{ss rt c.| ,c ^ o fnusntc_)c; a s| t ^_ d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he:/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hppr804:i785::v273e::d (warning: note: )unused parameter 'b' [-Wunused-parameter]in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here) ; 785804 | | | ^ ic/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hta:el879rl:a_5ta:os rnote: (sin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested hereW i* g 879np | m, e nu tn _scniaogl_nlae_lddi eabns,s( edu_snatss,is gisngrencdm, e onf)tu _n lc| o) ^o; p (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp d:| s806 ^t: ,22/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h ::s 782rwarning: :cunused parameter 'b' [-Wunused-parameter]3, : f806note: u | (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)n c )v782;o | i d | c ^ba il/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.htl:s_836(a:us46ns:si ignote: gnin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested herenm ee dn836 t | b( )d sA{ts ,s} i sg/rn/cm ,eN nOitOnt::s::Sr(cuuannl(saaircg,tntueyadpl eDbns)at m,{e s}Sr rc/c,/: :fNSuOcnOacPl) a; r | > ^(| ) ^) ;/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h : 804| ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:3710:: 17note: :in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here804 | 710 | c a l l _ a sisnitgenrmneanlt:_:ncall_assigon_ment(atlhiiass-(>ddsetrived(),, other.deri vserdc(,) )f;u n c| ^ )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h;:225 :20: | note: ^in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :225782 | : 3 : note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) r e782t | u r nc aBlal_saes:s:i_gsnemte(nott(hdesrt),; s r| c ^, /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hi:n327t:e20r:n anote: lin instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here: : a327s | s i grne_toupra(l)));; | | ^ ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h627::10710:: 17note: :in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here627 | 710r | e t u r n sienttCeornnsatla:n:tc(aSlcla_laasrs(i1g)n)m;e n t| ( ^ t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56h:i15s:- >note: din instantiation of member function 'Eigen::DenseBase>::setOnes' requested heree r i56v | e d ( ) , ocounttsh_.setOnees(); | ^ r.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return In file included from B/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cppa:s3e::_: sIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hppt:(8: oIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpph:22e: rIn file included from )/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense;: 1 : | In file included from ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h420: :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h327:86:63: :warning: 20converting the enum constant to a boolean [-Wint-in-bool-context] : 86note: | in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 MayLinearVe | c t orreitzuer n= dbeoroilv(eMdi(g)h t=V eCcotnosrtiaznet)( r&o&w sM(a)y,L icnoelasr(i)z,e v&a&l )D;s tH a| s ^D i/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.hr:e627c:t10A:c cnote: ein instantiation of member function 'Eigen::DenseBase>::setConstant' requested heres s 627| | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:e607t:u20:r nnote: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested heres e t607C | o n sttyapnetd(eSfc atlyapre(n1a)m)e; A s| s ^i g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppn:m56e:n15t:T rnote: ain instantiation of member function 'Eigen::DenseBase>::setOnes' requested herei t s56: | : P a c k e tcToyupnet sP_a.cskeettOTnyepse(;) ; | ^| ^/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp739 | : 14 : KIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hppr:n5e: lIn file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppk:e5r: nIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densel:(1d: sIn file included from t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/CoreE:v420a: l/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hu:a86t:o63r:, warning: sconverting the enum constant to a boolean [-Wint-in-bool-context]r c E86v | a l u a tor, funcM,a ydLsti.nceoanrsVte_cctaosrti_zdeer i=v ebdo(o)l)(;M i g| h ^t V/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he:c879t:o5r:i znote: ein instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here) &879& | M a y Lcianlela_rdieznes e&_&a sDssitgHnamseDnitr_elcotoApc(cdessts, s| r ^c ,/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :f607u:n20c:) ;note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here | ^ 607/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: | in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836t | y p eAdsesfi gtnympeenntame A::run(act| ualDst, ^sr c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h,: 739f:u10n: cnote: )in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here; 739 | | ^ K/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.he:r804n:e3l: knote: ein instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested herer n e804l | ( d sctaEvalluator,l _sarscsEivganlmueantto_rn,o _faulnica,s (ddsstt.,c osnrsct,_ cfausntc_)d;e r i| v ^e d/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h(:)21):;13 : | note: ^in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :21879 | : 5 :i nnote: tin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested heree r n879a | l : : c aclall_la_sdseingsnem_eansts(itghnimse-n>td_elroiovpe(dd(s)t,, Pslraci,n Ofbujnecc)t;: : Co| nstant(rows(),co ^l s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h(:)836,:o46t:h enote: rin instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here) , 836 | i n tAesrsniagln:m:emnutl<_AacstsuiaglnD_sotpT,(F)u)n;c > :| : ^r u/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppn:(57a:c15t:u anote: lin instantiation of member function 'Eigen::DenseBase>::operator*=' requested hereD s t57, | s r c , fcuonucn)t;s _ | ^ */wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h=: 804s:a3l:m onote: nin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here: : m804a | t h :c:aLlOlG__a0s;s i g| n ^m ent_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), inteIn file included from r/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cpp:3: nIn file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:l8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp::22: :In file included from m/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:u1l: _In file included from a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Cores:s420i: g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hn:_86o:p63<: warning: Sconverting the enum constant to a boolean [-Wint-in-bool-context] c a86 | MayLlianre,aSrcVaelcatro>r(ize) )=; b o| ol ^( M/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppi:g57h:t15V:e ctorizenote: )in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here & &57 | M a y L i n ecaoruinzet s&_& *D=s tsHaalsmDoinr:e:cmtAccesast h | ^ :/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: :in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested hereL O G607_ | 0 ; t y| p ^e def typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cppin instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here : 14879 | : In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp: 5: In file included from c/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hppa:l5: lIn file included from _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Densed:e1n: sIn file included from e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:_420a: s/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:s86i:g63n:m ewarning: nconverting the enum constant to a boolean [-Wint-in-bool-context] t _86l | o o p ( dMsaty,L isnreca,r Vfeucntco)r;i z e| ^ =/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h :836:46: note: bin instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here o 836 | Asosli(MighgtVectorize) && MaynLmiennet::20::r unote: nin instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here( a c607t | u a ltDyspte,d esfr ct,y pfeunnacm)e; A s| s ^i g/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.hn:me728ntTraits:::17P:a cnote: kin instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested heree t T728y | p e P a c kienttTeyrpnea;l : :| ^c a/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:l739l:_10:a snote: sin instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested herei g n739 | m e nKte_rnnoe_alli akse(rtnheils(-d>sdteErviavleuda(t)o,r other,. dserrivedc(E)v,a liunatteorrn,a lf:u:nacs,s idgsnt_.ocpo, Eigen::Matrix, Eigen::internal::assign_op>' requested herel a r879> | ( ) ) ; c a| l ^l _/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.hd:e278n:s15e:_ anote: sin instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested heres i g278n | m e n t _ l o o pB(adsset:,: _ssrect,_ nfouanlci)a;s ( o| t ^h e/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.hr:)836;: 46 :| ^note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp: 84 :3: note: 836in instantiation of member function 'Eigen::Matrix::Matrix' requested here | 84 | A s sGiCgFnrmaegnMto :| : ^r un(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.dIn file included from er/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/AlignmentCommon.cppi:v3e: dIn file included from (/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp):,6 : internal::assign_op()); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp::278:15: note: 24in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here : In file included from 278 | /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp : Base10::_set_noalias(o: t/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:h657er); : | ^ 15/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp::84:3: note: warning: in instantiation of member function 'Eigen::Matrix::Matrix' requested here definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 84 | GCFragModel657( | GCFragModel&&) = default; | ^ lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ 34 warnings generated. In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/ONTAlignmentModel.cpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:30: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonOpts.hpp:13: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:37: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/TranscriptGeneMap.hpp:73:50: warning: unused parameter 'version' [-Wunused-parameter] 73 | void s19e warningrsi generateda. lize(Archive& ar, const unsigned int version) { | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.hpp:145: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/BAMQueue.tpp:609:12: warning: variable 'n' set but not used [-Wunused-but-set-variable] 609 | size_t n{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:17: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/cuckoohash_map.hh:29: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:26: warning: unused parameter 'dst' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/bucket_container.hh:258:40: warning: unused parameter 'src' [-Wunused-parameter] 258 | void copy_allocator(A &dst, const A &src, std::false_type) {} | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:252:36: warning: builtin __has_trivial_copy is deprecated; use __is_trivially_copyable instead [-Wdeprecated-builtins] 252 | : std::integral_constant>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:241:36: warning: builtin __has_trivial_destructor is deprecated; use __is_trivially_destructible instead [-Wdeprecated-builtins] 241 | : std::integral_constant>' requested here 254 | is_trivially_destructible::value> {}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1818:32: note: in instantiation of template class 'phmap::is_trivially_copy_constructible>' requested here 1818 | bool unused = phmap::is_trivially_copy_constructible::value&& | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2053:45: note: in instantiation of default argument for 'optional_data>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:23: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap.h:69: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:259:17: warning: builtin __has_trivial_assign is deprecated; use __is_trivially_assignable instead [-Wdeprecated-builtins] 259 | bool, __has_trivial_assign(typename std::remove_reference::type) && | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:1819:22: note: in instantiation of template class 'phmap::is_trivially_copy_assignable>' requested here 1819 | phmap::is_trivially_copy_assignable>' required here 2053 | class optional : private optional_internal::optional_data, | ^~~~~~~~~~~~~~~~ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2820:37: note: in instantiation of template class 'phmap::optional>' requested here 2820 | phmap::optional alloc_; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/parallel_hashmap/phmap_base.h:2832:28: note: in instantiation of template class 'phmap::priv::node_handle_base>, std::allocator>' requested here 2832 | class node_handle : public node_handle_base | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:125:41: note: in instantiation of template class 'phmap::priv::node_handle, phmap::priv::hash_policy_traits>, std::allocator>' requested here 125 | decoys.insert(header->ref[i].name); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:39: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/MiniBatchInfo.hpp:28:12: warning: variable 'ng' set but not used [-Wunused-but-set-variable] 28 | size_t ng{0}; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:49: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/CollapsedEMOptimizer.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadExperiment.hpp:14: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonIndex.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/PufferfishIndex.hpp:9: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option] 4 | #pragma GCC diagnostic ignored "-Wmaybe-uninitialized" | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:52: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:3: warning: explicitly defaulted move constructor is implicitly deleted [-Wdefaulted-function-deleted] 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move constructor of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move constructor 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:30:3: note: 'mutex' has been explicitly marked deleted here 30 | mutex(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:16:58: note: replace 'default' with 'delete' 16 | ForgettingMassCalculator(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:29: warning: explicitly defaulted move assignment operator is implicitly deleted [-Wdefaulted-function-deleted] 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:141:14: note: move assignment operator of 'ForgettingMassCalculator' is implicitly deleted because field 'ffMutex_' has a deleted move assignment operator 141 | std::mutex ffMutex_; | ^ /usr/include/c++/v1/__mutex/mutex.h:31:10: note: 'operator=' has been explicitly marked deleted here 31 | mutex& operator=(const mutex&) = delete; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ForgettingMassCalculator.hpp:17:69: note: replace 'default' with 'delete' 17 | ForgettingMassCalculator& operator=(ForgettingMassCalculator&&) = default; | ^~~~~~~ | delete /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:403:11: warning: variable 'sidx' set but not used [-Wunused-but-set-variable] 403 | int sidx{0}; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:577:14: warning: variable 'auxProbSum' set but not used [-Wunused-but-set-variable] 577 | double auxProbSum{0.0}; | ^ 30 warnings generated. In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:415: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:139:14: warning: definition of implicit copy constructor for 'MatrixBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 139 | Derived& operator=(const MatrixBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:414: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/DenseBase.h:281:14: warning: definition of implicit copy constructor for 'DenseBase, Eigen::Matrix>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 281 | Derived& operator=(const DenseBase& other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: note: in implicit copy constructor for 'Eigen::DenseBase, Eigen::Matrix>>' first required here 48 | template class MatrixBase | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::MatrixBase, Eigen::Matrix>>' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:348: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/XprHelper.h:92:29: warning: definition of implicit copy constructor for 'no_assignment_operator' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 92 | no_assignment_operator& operator=(const no_assignment_operator&); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/util/ForwardDeclarations.h:90:65: note: in implicit copy constructor for 'Eigen::internal::no_assignment_operator' first required here 90 | template class CwiseNullaryOp; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:176:10: note: in implicit copy constructor for 'Eigen::CwiseNullaryOp, Eigen::Matrix>' first required here 176 | return DenseBase::NullaryExpr(rows, cols, internal::scalar_constant_op(value)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:22: note: in instantiation of member function 'Eigen::DenseBase>::Constant' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:782:3: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) 782 | call_assignment(dst, src, internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:710:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>>' requested here 710 | internal::call_assignment(this->derived(), other.derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:225:20: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set, Eigen::Matrix>>' requested here 225 | return Base::_set(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:327:20: note: in instantiation of function template specialization 'Eigen::Matrix::operator=, Eigen::Matrix>>' requested here 327 | return derived() = Constant(rows(), cols(), val); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:627:10: note: in instantiation of member function 'Eigen::DenseBase>::setConstant' requested here 627 | return setConstant(Scalar(1)); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:56:15: note: in instantiation of member function 'Eigen::DenseBase>::setOnes' requested here 56 | counts_.setOnes(); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator, Eigen::Matrix>>, Eigen::internal::mul_assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:804:3: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 804 | call_assignment_no_alias(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:21:13: note: in instantiation of function template specialization 'Eigen::internal::call_assignment, Eigen::CwiseNullaryOp, Eigen::Matrix>, Eigen::internal::mul_assign_op>' requested here 21 | internal::call_assignment(this->derived(), PlainObject::Constant(rows(),cols(),other), internal::mul_assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:57:15: note: in instantiation of member function 'Eigen::DenseBase>::operator*=' requested here 57 | counts_ *= salmon::math::LOG_0; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:8: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/SalmonUtils.hpp:22: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Dense:1: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/Core:420: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:86:63: warning: converting the enum constant to a boolean [-Wint-in-bool-context] 86 | MayLinearVectorize = bool(MightVectorize) && MayLinearize && DstHasDirectAccess | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:607:20: note: in instantiation of template class 'Eigen::internal::copy_using_evaluator_traits>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 607 | typedef typename AssignmentTraits::PacketType PacketType; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:739:10: note: in instantiation of template class 'Eigen::internal::generic_dense_assignment_kernel>, Eigen::internal::evaluator>, Eigen::internal::assign_op>' requested here 739 | Kernel kernel(dstEvaluator, srcEvaluator, func, dst.const_cast_derived()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:879:5: note: in instantiation of function template specialization 'Eigen::internal::call_dense_assignment_loop, Eigen::Matrix, Eigen::internal::assign_op>' requested here 879 | call_dense_assignment_loop(dst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/AssignEvaluator.h:836:46: note: in instantiation of member function 'Eigen::internal::Assignment, Eigen::Matrix, Eigen::internal::assign_op>::run' requested here 836 | Assignment::run(actualDst, src, func); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/PlainObjectBase.h:728:17: note: in instantiation of function template specialization 'Eigen::internal::call_assignment_no_alias, Eigen::Matrix, Eigen::internal::assign_op>' requested here 728 | internal::call_assignment_no_alias(this->derived(), other.derived(), internal::assign_op()); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/eigen3/Eigen/src/Core/Matrix.h:278:15: note: in instantiation of function template specialization 'Eigen::PlainObjectBase>::_set_noalias>' requested here 278 | Base::_set_noalias(other); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/GCFragModel.hpp:84:3: note: in instantiation of member function 'Eigen::Matrix::Matrix' requested here 84 | GCFragModel(GCFragModel&&) = default; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:12: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentGroup.hpp:15: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/ReadPair.hpp:6: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/Util.hpp:24: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:10: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 657 | lhs_setter& operator=(const lhs_setter& rhs) { | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:167:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter' first required here 167 | ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Transcript.hpp:645:22: note: in instantiation of member function 'compact::vector_imp::vector, unsigned long, 1, unsigned long, std::allocator, 64, false>::operator[]' requested here 645 | gcBitArray_[i] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_dest46r warnings generatedu. ctive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:17: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator>> *, std::pair *, std::input_iterator_tag, spp::libc_allocator>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable, unsigned long, spp::spp_hash, spp::sparse_hash_map::SelectKey, spp::sparse_hash_map::SetKey, std::equal_to, spp::libc_allocator>>::find_or_insert::DefaultValue, unsigned long &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:51:26: note: in instantiation of function template specialization 'spp::sparse_hash_map::operator[]' requested here 51 | barcodeGroup[barcode][umi] = 1; | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator>, spp::sparsegroup>, spp::libc_allocator>>> *, std::pair> *, std::input_iterator_tag, spp::libc_allocator>>>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3278:21: note: in instantiation of member function 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::_resize_delta' requested here 3278 | if (_resize_delta(1)) | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3813:29: note: in instantiation of function template specialization 'spp::sparse_hashtable>, unsigned int, spp::spp_hash, spp::sparse_hash_map>::SelectKey, spp::sparse_hash_map>::SetKey, std::equal_to, spp::libc_allocator>>>::find_or_insert>::DefaultValue, unsigned int &>' requested here 3813 | return rep.template find_or_insert(std::forward(key)).second; | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:14: note: in instantiation of function template specialization 'spp::sparse_hash_map>::operator[]' requested here 28 | edges[source].insert(sink); | ^ In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/src/SalmonQuantifyAlignments.cpp:33: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/AlignmentLibrary.hpp:19: In file included from /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/EquivalenceClassBuilder.hpp:18: /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2817:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator> *, unsigned int *, std::input_iterator_tag, spp::libc_allocator>' first required here 2817 | for (destructive_iterator it = ht.destructive_begin(); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2948:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_move_from' requested here 2948 | _move_from(mover, ht, min_buckets_wanted); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:2745:26: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::sparse_hashtable' requested here 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:3234:9: note: in instantiation of member function 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::_resize_delta' requested here 3234 | _resize_delta(1); // adding an object, grow if need be | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/include/pufferfish/sparsepp/spp.h:4225:67: note: in instantiation of function template specialization 'spp::sparse_hashtable, spp::sparse_hash_set::Identity, spp::sparse_hash_set::SetKey, std::equal_to, spp::libc_allocator>::insert' requested here 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ^ /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/include/Graph.hpp:28:23: note: in instantiation of function template specialization 'spp::sparse_hash_set::insert' requested here 28 | edges[source].insert(sink); | ^ 35 warnings generated. [100%] Linking CXX executable salmon cd /wrkdirs/usr/ports/biology/salmon/work/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -flto=thin -lpthread -fstack-protector-strong -Xlinker --dependency-file=CMakeFiles/salmon.dir/link.d CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/lib -L/wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib -L/usr/local/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib:/usr/local/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff /usr/local/lib/libboost_iostreams.a /usr/local/lib/libboost_system.a /usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_timer.a /usr/local/lib/libboost_chrono.a /usr/local/lib/libboost_program_options.a /usr/local/lib/libboost_regex.a /usr/local/lib/libcurl.a /usr/lib/libz.a -lm /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libstaden-read.a /wrkdirs/usr/ports/biology/salmon/work/salmon-1.10.2/external/install/lib/libhtscodecs.a /usr/lib/liblzma.a /usr/lib/libmd.a /usr/lib/libbz2.a -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -lc /usr/local/lib/libtbb.so.12.14 /usr/local/lib/libtbbmalloc.so.2.14 -lrt gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' [100%] Built target salmon gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/salmon/work/.build' /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/salmon/work/.build/CMakeFiles 0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for salmon-1.10.2_7 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/salmon/work/.build/src/salmon /wrkdirs/usr/ports/biology/salmon/work/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-05T03:55:31+0000' 'PKG_NOTE_ports_top_git_hash=57a50b106b87' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e7219' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for salmon-1.10.2_7 ===> Building salmon-1.10.2_7 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for salmon-1.10.2_7 build of biology/salmon | salmon-1.10.2_7 ended at Mon May 5 00:04:55 EDT 2025 build time: 00:09:26