=>> Building biology/velvet build started at Sun May 4 20:03:50 EDT 2025 port directory: /usr/ports/biology/velvet package name: velvet-1.2.10_2 building for: FreeBSD 13amd64-weekly-desktop-job-02 13.4-RELEASE-p4 FreeBSD 13.4-RELEASE-p4 amd64 maintained by: mzaki@m.u-tokyo.ac.jp Makefile datestamp: -rw-r--r-- 1 root wheel 2559 Feb 24 2024 /usr/ports/biology/velvet/Makefile Ports top last git commit: 57a50b106b87 Ports top unclean checkout: yes Port dir last git commit: d9c7e0b18ad0 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1304000 Job Id: 02 ---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/02/.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--- ===> The following configuration options are available for velvet-1.2.10_2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mzaki@m.u-tokyo.ac.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/velvet/work/.cache HOME=/wrkdirs/usr/ports/biology/velvet/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/velvet/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/velvet/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- MAXKMERLENGTH=31 CATEGORIES=2 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/velvet/work/.cache HOME=/wrkdirs/usr/ports/biology/velvet/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/velvet/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/velvet/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/velvet" EXAMPLESDIR="share/examples/velvet" DATADIR="share/velvet" WWWDIR="www/velvet" ETCDIR="etc/velvet" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/velvet DOCSDIR=/usr/local/share/doc/velvet EXAMPLESDIR=/usr/local/share/examples/velvet WWWDIR=/usr/local/www/velvet ETCDIR=/usr/local/etc/velvet --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 ===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [13amd64-weekly-desktop-job-02] Installing pkg-2.0.6... [13amd64-weekly-desktop-job-02] Extracting pkg-2.0.6: .......... done ===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of velvet-1.2.10_2 =========================================================================== =================================================== ===== 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 velvet-1.2.10_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by velvet-1.2.10_2 for building => SHA256 Checksum OK for velvet_1.2.10.tgz. =========================================================================== =================================================== ===== 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 velvet-1.2.10_2 for building ===> Extracting for velvet-1.2.10_2 => SHA256 Checksum OK for velvet_1.2.10.tgz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for velvet-1.2.10_2 ===> Applying FreeBSD patches for velvet-1.2.10_2 from /usr/ports/biology/velvet/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> velvet-1.2.10_2 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [13amd64-weekly-desktop-job-02] Installing gmake-4.4.1... [13amd64-weekly-desktop-job-02] `-- Installing gettext-runtime-0.23.1... [13amd64-weekly-desktop-job-02] | `-- Installing indexinfo-0.3.1_1... [13amd64-weekly-desktop-job-02] | `-- Extracting indexinfo-0.3.1_1: . done [13amd64-weekly-desktop-job-02] `-- Extracting gettext-runtime-0.23.1: .......... done [13amd64-weekly-desktop-job-02] Extracting gmake-4.4.1: .......... done ===> velvet-1.2.10_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of velvet-1.2.10_2 ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.11.pkg [13amd64-weekly-desktop-job-02] Installing python311-3.11.11... [13amd64-weekly-desktop-job-02] `-- Installing libffi-3.4.6... [13amd64-weekly-desktop-job-02] `-- Extracting libffi-3.4.6: .......... done [13amd64-weekly-desktop-job-02] `-- Installing mpdecimal-4.0.0... [13amd64-weekly-desktop-job-02] `-- Extracting mpdecimal-4.0.0: .......... done [13amd64-weekly-desktop-job-02] `-- Installing readline-8.2.13_2... [13amd64-weekly-desktop-job-02] `-- Extracting readline-8.2.13_2: .......... done [13amd64-weekly-desktop-job-02] Extracting python311-3.11.11: .......... done ===== Message from python311-3.11.11: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of velvet-1.2.10_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for velvet-1.2.10_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for velvet-1.2.10_2 rm obj/*.o obj/dbg/*.o rm: obj/*.o: No such file or directory rm: obj/dbg/*.o: No such file or directory gmake: [Makefile:51: cleanobj] Error 1 (ignored) mkdir -p obj cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.c:31: In file included from src/run.h:35: src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 21 | #ifndef _SSCAFFOLD_H_ | ^~~~~~~~~~~~~ src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'? 22 | #define _SCAFFOLD_H_ | ^~~~~~~~~~~~ | _SSCAFFOLD_H_ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run2.c:26: In file included from src/run.h:35: src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 21 | #ifndef _SSCAFFOLD_H_ | ^~~~~~~~~~~~~ src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'? 22 | #define _SCAFFOLD_H_ | ^~~~~~~~~~~~ | _SSCAFFOLD_H_ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/concatenatedGraph.c:56:14: note: used here 56 | position = getShortReadMarkerPosition(marker); | ^ In file included from src/concatenatedGraph.c:25: src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not defined [-Wundefined-inline] 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^ src/concatenatedGraph.c:59:4: note: used here 59 | setShortReadMarkerPosition(marker, position); | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o src/passageMarker.c:50:1: warning: unused function 'PM_I2P' [-Wunused-function] 50 | DECLARE_FAST_ACCESSORS (PM, PassageMarker, markerMemory) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/allocArray.h:69:21: note: expanded from macro 'DECLARE_FAST_ACCESSORS' 69 | static inline type* name##_I2P(ArrayIdx idx) \ | ^~~~~~~~~~ :27:1: note: expanded from here 27 | PM_I2P | ^~~~~~ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/graphStats.c:848:19: note: used here 848 | starts[index] = getShortReadMarkerPosition(marker); | ^ In file included from src/graphStats.c:28: src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' is not defined [-Wundefined-inline] 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^ src/graphStats.c:849:34: note: used here 849 | stops[index] = starts[index] - getShortReadMarkerOffset(marker) + readLengths[getShortReadMarkerID(marker) - 1] - 1; | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/correctedGraph.c:776:15: note: used here 776 | position = getShortReadMarkerPosition(shortMarker); | ^ In file included from src/correctedGraph.c:26: src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not defined [-Wundefined-inline] 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^ src/correctedGraph.c:799:4: note: used here 799 | setShortReadMarkerPosition(shortMarker, position); | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c:641:21: warning: incompatible pointer types assigning to 'gzFile' (aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ ~~~~~~~~~~~~~~~~~~~~ src/readSet.c:680:22: warning: incompatible pointer types assigning to 'gzFile' (aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ ~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:681:22: warning: incompatible pointer types assigning to 'gzFile' (aka 'struct gzFile_s *') from 'AutoFile *' [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ ~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:632:1: warning: unused function 'kseq_rewind' [-Wunused-function] 632 | KSEQ_INIT(FileGZOrAuto, fileGZOrAuto_read) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/kseq.h:220:2: note: expanded from macro 'KSEQ_INIT' 220 | __KSEQ_BASIC(type_t) \ | ^~~~~~~~~~~~~~~~~~~~ src/kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC' 152 | static inline void kseq_rewind(kseq_t *ks) \ | ^~~~~~~~~~~ 4 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c:248:13: warning: variable 'totalLength' set but not used [-Wunused-but-set-variable] 248 | Coordinate totalLength = 0; | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:34: src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 21 | #ifndef _SSCAFFOLD_H_ | ^~~~~~~~~~~~~ src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'? 22 | #define _SCAFFOLD_H_ | ^~~~~~~~~~~~ | _SSCAFFOLD_H_ src/shortReadPairs.c:191:8: warning: variable 'counter' set but not used [-Wunused-but-set-variable] 191 | IDnum counter = 0; | ^ In file included from src/shortReadPairs.c:27: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/shortReadPairs.c:590:14: note: used here 590 | position = getShortReadMarkerPosition(marker); | ^ In file included from src/shortReadPairs.c:27: src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not defined [-Wundefined-inline] 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^ src/shortReadPairs.c:593:4: note: used here 593 | setShortReadMarkerPosition(marker, position); | ^ 4 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c:1244:13: warning: variable 'index' set but not used [-Wunused-but-set-variable] 1244 | Coordinate index = 0; | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/preGraph.c:35: In file included from src/run.h:35: src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 21 | #ifndef _SSCAFFOLD_H_ | ^~~~~~~~~~~~~ src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'? 22 | #define _SCAFFOLD_H_ | ^~~~~~~~~~~~ | _SSCAFFOLD_H_ src/preGraph.c:165:17: warning: taking address of packed member 'preArcRight' of class or structure 'preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:17: warning: taking address of packed member 'preArcLeft' of class or structure 'preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~ src/preGraph.c:285:17: warning: taking address of packed member 'preArcRight' of class or structure 'preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:17: warning: taking address of packed member 'preArcLeft' of class or structure 'preNode_st' may result in an unaligned pointer value [-Waddress-of-packed-member] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~ src/preGraph.c:520:27: warning: unused function 'mergeDescriptors_pg' [-Wunused-function] 520 | static inline Descriptor *mergeDescriptors_pg(Descriptor * descr, | ^~~~~~~~~~~~~~~~~~~ src/preGraph.c:635:27: warning: unused function 'mergeDescriptorsH2H_pg' [-Wunused-function] 635 | static inline Descriptor *mergeDescriptorsH2H_pg(Descriptor * descr, | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:760:27: warning: unused function 'mergeDescriptorsF2F_pg' [-Wunused-function] 760 | static inline Descriptor *mergeDescriptorsF2F_pg(Descriptor * descr, | ^~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c:416:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 416 | seqReadInfo->m_pFile = file; | ^ src/preGraphConstruction.c:414:2: note: previous statement is here 414 | if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/readCoherentGraph.c:367:14: note: used here 367 | position = getShortReadMarkerPosition(marker); | ^ In file included from src/readCoherentGraph.c:25: src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' is not defined [-Wundefined-inline] 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^ src/readCoherentGraph.c:369:3: note: used here 369 | setShortReadMarkerPosition(marker, position); | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c:28:23: warning: unused variable 'longLongLeftFilter' [-Wunused-const-variable] 28 | static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; | ^~~~~~~~~~~~~~~~~~ src/kmer.c:29:23: warning: unused variable 'longLeftFilter' [-Wunused-const-variable] 29 | static const uint32_t longLeftFilter = (uint32_t) 3 << 30; | ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: unused variable 'intLeftFilter' [-Wunused-const-variable] 30 | static const uint16_t intLeftFilter = (uint16_t) 3 << 14; | ^~~~~~~~~~~~~ src/kmer.c:31:22: warning: unused variable 'charLeftFilter' [-Wunused-const-variable] 31 | static const uint8_t charLeftFilter = (uint8_t) 3 << 6; | ^~~~~~~~~~~~~~ 4 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:39: src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard] 21 | #ifndef _SSCAFFOLD_H_ | ^~~~~~~~~~~~~ src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'? 22 | #define _SCAFFOLD_H_ | ^~~~~~~~~~~~ | _SSCAFFOLD_H_ In file included from src/scaffold.c:32: src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' is not defined [-Wundefined-inline] 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^ src/scaffold.c:455:7: note: used here 455 | getShortReadMarkerPosition(shortMarker); | ^ In file included from src/scaffold.c:32: src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' is not defined [-Wundefined-inline] 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^ src/scaffold.c:457:7: note: used here 457 | getShortReadMarkerOffset(shortMarker); | ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c:49:6: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int rc, status; | ^ src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] 56 | static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -fstack-protector-strong -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -fstack-protector-strong -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.11 - found ===> velvet-1.2.10_2 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_2.pkg [13amd64-weekly-desktop-job-02] Installing perl5-5.36.3_2... [13amd64-weekly-desktop-job-02] Extracting perl5-5.36.3_2: .......... done ===> velvet-1.2.10_2 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of velvet-1.2.10_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for velvet-1.2.10_2 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/velvetg /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin install -s -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/velveth /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/shuffleSequences_fasta.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/shuffleSequences_fastq.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/VelvetOptimiser.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/afg_handling/asmbly_splitter.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/asmbly_splitter.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/afg_handling/snp_view.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/snp_view.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/columbus_scripts/enlarge_exons.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/enlarge_exons.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/columbus_scripts/gff2fasta.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/gff2fasta.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/columbus_scripts/merge_gtf_exons.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/merge_gtf_exons.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/velvet-estimate-exp_cov.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/extractContigReads/extractContigReads.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/extractContigReads.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/fasta2agp/fasta2agp.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/fasta2agp.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/observed-insert-length.pl/observed-insert-length.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/observed-insert-length.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/read_prepare/pe_read_prepare.0.1.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/pe_read_prepare.0.1.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/select_paired/select_paired.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/select_paired.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/show_repeats/show_repeats.pl /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/show_repeats.pl install -m 555 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/bin/AssemblyAssembler1.3.py /bin/mkdir -p /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/lib/perl5/site_perl/VelvetOpt install -m 0644 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/Assembly.pm /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/lib/perl5/site_perl/VelvetOpt/Assembly.pm install -m 0644 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/Utils.pm /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/lib/perl5/site_perl/VelvetOpt/Utils.pm install -m 0644 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/gwrap.pm /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/lib/perl5/site_perl/VelvetOpt/gwrap.pm install -m 0644 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/hwrap.pm /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/lib/perl5/site_perl/VelvetOpt/hwrap.pm install -m 0644 /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/ChangeLog /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/Manual.pdf /wrkdirs/usr/ports/biology/velvet/work/velvet_1.2.10/Columbus_manual.pdf /wrkdirs/usr/ports/biology/velvet/work/stage/usr/local/share/doc/velvet ====> 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=2025-05-05T00:03:50+0000' 'PKG_NOTE_ports_top_git_hash=57a50b106b87' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=d9c7e0b18ad0' '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 velvet-1.2.10_2 ===> Building velvet-1.2.10_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for velvet-1.2.10_2 build of biology/velvet | velvet-1.2.10_2 ended at Sun May 4 20:04:07 EDT 2025 build time: 00:00:18