=>> Building biology/bedtools build started at Fri Jan 23 10:11:30 EST 2026 port directory: /usr/ports/biology/bedtools package name: bedtools-2.31.1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 614 Aug 27 2024 /usr/ports/biology/bedtools/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 1e46f94e3f92 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/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 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bedtools/work/.cache HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bedtools/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bedtools/work/.cache HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bedtools/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=" " 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-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/bedtools" EXAMPLESDIR="share/examples/bedtools" DATADIR="share/bedtools" WWWDIR="www/bedtools" ETCDIR="etc/bedtools" --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_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bedtools DOCSDIR=/usr/local/share/doc/bedtools EXAMPLESDIR=/usr/local/share/examples/bedtools WWWDIR=/usr/local/www/bedtools ETCDIR=/usr/local/etc/bedtools --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bedtools-2.31.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> bedtools-2.31.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bedtools-2.31.1 =========================================================================== =================================================== ===== 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 bedtools-2.31.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bedtools-2.31.1 for building => SHA256 Checksum OK for arq5x-bedtools2-v2.31.1_GH0.tar.gz. =========================================================================== =================================================== ===== 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 bedtools-2.31.1 for building ===> Extracting for bedtools-2.31.1 => SHA256 Checksum OK for arq5x-bedtools2-v2.31.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for bedtools-2.31.1 ===> Applying FreeBSD patches for bedtools-2.31.1 from /usr/ports/biology/bedtools/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bedtools-2.31.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> bedtools-2.31.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of bedtools-2.31.1 ===> bedtools-2.31.1 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [pkg.DaveG.ca] Installing python311-3.11.14... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] `-- Installing readline-8.3.3... [pkg.DaveG.ca] `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- 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 ===> bedtools-2.31.1 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of bedtools-2.31.1 ===> bedtools-2.31.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> bedtools-2.31.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of bedtools-2.31.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bedtools-2.31.1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bedtools-2.31.1 Building BEDTools: cd src/utils/htslib && /usr/local/bin/gmake config.h DETECTED_VERSION = v2.31.1 CURRENT_VERSION = Updating version file. ========================================================= gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.31.1/src/utils/htslib' * compiling src/htsutil.cpp CXXFLAGS is [-g -Wall -O2 -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing ] * compiling src/bedtools.cpp * compiling src/annotateBed/annotateBed.cpp * compiling src/annotateBed/annotateMain.cpp * compiling src/bamToBed/bamToBed.cpp * compiling src/bamToFastq/bamToFastqMain.cpp * compiling src/bamToFastq/bamToFastq.cpp * compiling src/bedToBam/bedToBam.cpp * compiling src/bedpeToBam/bedpeToBam.cpp * compiling src/bedToIgv/bedToIgv.cpp * compiling src/bed12ToBed6/bed12ToBed6.cpp echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h * compiling src/closestFile/closestHelp.cpp * compiling src/closestFile/closestFile.cpp * compiling src/clusterBed/clusterMain.cpp * compiling src/clusterBed/clusterBed.cpp * compiling src/complementFile/complementHelp.cpp echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.31.1/src/utils/htslib' * compiling src/coverageFile/coverageHelp.cpp * compiling src/coverageFile/coverageFile.cpp * compiling src/complementFile/complementFile.cpp * compiling src/expand/expand.cpp * compiling src/fastaFromBed/fastaFromBedMain.cpp * compiling src/flankBed/flankBedMain.cpp * compiling src/fastaFromBed/fastaFromBed.cpp * compiling src/flankBed/flankBed.cpp * compiling src/genomeCoverageBed/genomeCoverageMain.cpp * compiling src/genomeCoverageBed/genomeCoverageBed.cpp * compiling src/getOverlap/getOverlap.cpp * compiling src/groupBy/groupByHelp.cpp * compiling src/groupBy/groupBy.cpp * compiling src/intersectFile/intersectHelp.cpp * compiling src/intersectFile/intersectFile.cpp * compiling src/fisher/fisherHelp.cpp * compiling src/jaccard/jaccardHelp.cpp * compiling src/fisher/fisher.cpp * compiling src/fisher/kfunc.cpp * compiling src/linksBed/linksMain.cpp * compiling src/linksBed/linksBed.cpp * compiling src/jaccard/jaccard.cpp * compiling src/maskFastaFromBed/maskFastaFromBedMain.cpp * compiling src/maskFastaFromBed/maskFastaFromBed.cpp * compiling src/mapFile/mapHelp.cpp * compiling src/mapFile/mapFile.cpp * compiling src/mergeFile/mergeHelp.cpp * compiling src/mergeFile/mergeFile.cpp * compiling src/multiBamCov/multiBamCovMain.cpp * compiling src/multiBamCov/multiBamCov.cpp * compiling src/multiIntersectBed/multiIntersectBedMain.cpp * compiling src/multiIntersectBed/multiIntersectBed.cpp * compiling src/nucBed/nucBedMain.cpp * compiling src/nucBed/nucBed.cpp * compiling src/pairToBed/pairToBedMain.cpp * compiling src/pairToBed/pairToBed.cpp * compiling src/pairToPair/pairToPairMain.cpp * compiling src/pairToPair/pairToPair.cpp * compiling src/randomBed/randomBedMain.cpp * compiling src/randomBed/randomBed.cpp src/bamToFastq/bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable] 38 | bool haveFastq2 = false; | ^ 1 warning generated. src/clusterBed/clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable] 38 | bool haveMaxDistance = false; | ^ 1 warning generated. src/getOverlap/getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable] 44 | bool haveColumns = false; | ^ 1 warning generated. * compiling src/regressTest/regressTestMain.cpp * compiling src/regressTest/RegressTest.cpp * compiling src/reldist/reldistMain.cpp * compiling src/reldist/reldist.cpp * compiling src/sampleFile/sampleHelp.cpp src/bedToBam/bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] 60 | bool haveMapQual = false; | ^ 1 warning generated. * compiling src/sampleFile/sampleFile.cpp * compiling src/shiftBed/shiftBedMain.cpp * compiling src/shuffleBed/shuffleBedMain.cpp * compiling src/shiftBed/shiftBed.cpp * compiling src/shuffleBed/shuffleBed.cpp * compiling src/slopBed/slopBedMain.cpp * compiling src/slopBed/slopBed.cpp * compiling src/sortBed/sortMain.cpp src/annotateBed/annotateBed.cpp:158:28: warning: variable 'totalLength' set but not used [-Wunused-but-set-variable] 158 | CHRPOS totalLength = 0; | ^ 1 warning generated. * compiling src/sortBed/sortBed.cpp * compiling src/spacingFile/spacingHelp.cpp * compiling src/spacingFile/spacingFile.cpp src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] 45 | bool haveFiles = false; | ^ src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] 47 | bool haveGenome = false; | ^ src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] 48 | bool haveFiller = true; | ^ 3 warnings generated. src/bedpeToBam/bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable] 61 | bool haveMapQual = false; | ^ 1 warning generated. * compiling src/split/splitBedMain.cpp * compiling src/split/splitBed.cpp * compiling src/subtractFile/subtractHelp.cpp src/pairToBed/pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 43 | bool haveFraction = false; | ^ 1 warning generated. * compiling src/subtractFile/subtractFile.cpp * compiling src/summaryFile/summaryHelp.cpp * compiling src/summaryFile/summaryFile.cpp * compiling src/tagBam/tagBamMain.cpp * compiling src/tagBam/tagBam.cpp * compiling src/unionBedGraphs/unionBedGraphsMain.cpp * compiling src/unionBedGraphs/unionBedGraphs.cpp * compiling src/windowBed/windowMain.cpp * compiling src/windowBed/windowBed.cpp * compiling src/windowMaker/windowMakerMain.cpp * compiling src/windowMaker/windowMaker.cpp src/pairToPair/pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 44 | bool haveFraction = false; | ^ 1 warning generated. * compiling src/utils/FileRecordTools/FileRecordMgr.cpp * compiling src/utils/FileRecordTools/FileRecordMergeMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/FileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BamFileReader.cpp * compiling src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp * compiling src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp src/bamToBed/bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable] 88 | bool useAlignmentScore = false; | ^ 1 warning generated. * compiling src/utils/FileRecordTools/Records/Record.cpp * compiling src/utils/FileRecordTools/Records/EmptyRecord.cpp * compiling src/utils/FileRecordTools/Records/Bed3Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed4Interval.cpp src/multiBamCov/multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable] 38 | bool haveBed = false; | ^ src/multiBamCov/multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable] 39 | bool haveBams = false; | ^ src/multiBamCov/multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable] 47 | bool haveFraction = false; | ^ 3 warnings generated. * compiling src/utils/FileRecordTools/Records/BedGraphInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed5Interval.cpp * compiling src/utils/FileRecordTools/Records/Bed6Interval.cpp * compiling src/utils/FileRecordTools/Records/PlusFields.cpp * compiling src/utils/FileRecordTools/Records/GffRecord.cpp * compiling src/utils/FileRecordTools/Records/GffPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp * compiling src/utils/FileRecordTools/Records/BedPlusInterval.cpp * compiling src/utils/FileRecordTools/Records/Bed12Interval.cpp * compiling src/utils/FileRecordTools/Records/BamRecord.cpp * compiling src/utils/FileRecordTools/Records/VcfRecord.cpp * compiling src/utils/FileRecordTools/Records/StrandQueue.cpp * compiling src/utils/FileRecordTools/Records/RecordMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordList.cpp * compiling src/utils/FileRecordTools/Records/BlockMgr.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyList.cpp * compiling src/utils/FileRecordTools/Records/RecordKeyVector.cpp * compiling src/utils/bedFile/bedFile.cpp * compiling src/utils/BinTree/BinTree.cpp src/pairToPair/pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable] 112 | bool found1 = false; | ^ src/pairToPair/pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable] 113 | bool found2 = false; | ^ 2 warnings generated. * compiling src/utils/version/version.cpp src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable] 46 | bool haveFiles = false; | ^ src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable] 48 | bool haveGenome = false; | ^ src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable] 49 | bool haveFiller = true; | ^ 3 warnings generated. * compiling src/utils/bedGraphFile/bedGraphFile.cpp * compiling src/utils/chromsweep/chromsweep.cpp * compiling src/utils/Contexts/ContextBase.cpp * compiling src/utils/Contexts/ContextIntersect.cpp * compiling src/utils/Contexts/ContextFisher.cpp * compiling src/utils/Contexts/ContextMap.cpp * compiling src/utils/Contexts/ContextSample.cpp * compiling src/utils/Contexts/ContextSpacing.cpp * compiling src/utils/Contexts/ContextMerge.cpp * compiling src/utils/Contexts/ContextJaccard.cpp * compiling src/utils/Contexts/ContextClosest.cpp * compiling src/utils/Contexts/ContextSubtract.cpp * compiling src/utils/Contexts/ContextCoverage.cpp * compiling src/utils/Contexts/ContextComplement.cpp * compiling src/utils/Contexts/ContextGroupBy.cpp * compiling src/utils/Contexts/ContextSummary.cpp * compiling src/utils/general/ParseTools.cpp * compiling src/utils/general/PushBackStreamBuf.cpp * compiling src/utils/general/CompressionTools.cpp * compiling src/utils/general/Tokenizer.cpp * compiling src/utils/general/CommonHelp.cpp c++ -g -Wall -O2 -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Isrc/utils/gzstream -c -o obj/gzstream.o src/utils/gzstream/gzstream.C * compiling src/utils/general/Random.cpp * compiling src/utils/fileType/fileType.cpp * compiling src/utils/general/ErrorMsg.cpp src/pairToBed/pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] 257 | CHRPOS spanLength = 0; | ^ src/pairToBed/pairToBed.cpp:310:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable] 310 | CHRPOS spanLength = 0; | ^ 2 warnings generated. * compiling src/utils/fileType/FileRecordTypeChecker.cpp src/split/splitBed.cpp:180:5: warning: implicit conversion from 'long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] 180 | REPORT_CHUNK(filename, bedItems->nbases,bedItems->items.size()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/split/splitBed.cpp:33:19: note: expanded from macro 'REPORT_CHUNK' 33 | if( NBASES >= LONG_MAX) \ | ~~ ^~~~~~~~ /usr/include/sys/limits.h:62:18: note: expanded from macro 'LONG_MAX' 62 | #define LONG_MAX __LONG_MAX /* max for a long */ | ^~~~~~~~~~ /usr/include/x86/_limits.h:63:20: note: expanded from macro '__LONG_MAX' 63 | #define __LONG_MAX 0x7fffffffffffffff /* max for a long */ | ^~~~~~~~~~~~~~~~~~ src/split/splitBed.cpp:250:13: warning: implicit conversion from 'long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] 250 | REPORT_CHUNK(info->filename, info->nbases,info->count); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/split/splitBed.cpp:33:19: note: expanded from macro 'REPORT_CHUNK' 33 | if( NBASES >= LONG_MAX) \ | ~~ ^~~~~~~~ /usr/include/sys/limits.h:62:18: note: expanded from macro 'LONG_MAX' 62 | #define LONG_MAX __LONG_MAX /* max for a long */ | ^~~~~~~~~~ /usr/include/x86/_limits.h:63:20: note: expanded from macro '__LONG_MAX' 63 | #define __LONG_MAX 0x7fffffffffffffff /* max for a long */ | ^~~~~~~~~~~~~~~~~~ 2 warnings generated. * compiling src/utils/bedFilePE/bedFilePE.cpp * compiling src/utils/KeyListOps/KeyListOps.cpp * compiling src/utils/KeyListOps/KeyListOpsMethods.cpp * compiling src/utils/NewChromsweep/NewChromsweep.cpp * compiling src/utils/NewChromsweep/CloseSweep.cpp * compiling src/utils/sequenceUtilities/sequenceUtils.cpp * compiling src/utils/tabFile/tabFile.cpp * compiling src/utils/BamTools-Ancillary/BamAncillary.cpp * compiling src/utils/BlockedIntervals/BlockedIntervals.cpp * compiling src/utils/Fasta/Fasta.cpp * compiling src/utils/Fasta/split.cpp * compiling src/utils/VectorOps/VectorOps.cpp * compiling src/utils/GenomeFile/NewGenomeFile.cpp * compiling src/utils/GenomeFile/GenomeFile.cpp * compiling src/utils/RecordOutputMgr/RecordOutputMgr.cpp * compiling src/utils/ToolBase/ToolBase.cpp cd src/utils/htslib && /usr/local/bin/gmake lib-static * compiling src/utils/driver/BedtoolsDriver.cpp - Creating executables for old CLI. gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.31.1/src/utils/htslib' done. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o kfunc.o kfunc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o knetfile.o knetfile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o kstring.o kstring.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o bcf_sr_sort.o bcf_sr_sort.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o bgzf.o bgzf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o errmod.o errmod.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o faidx.o faidx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o hfile.o hfile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o hts_os.o hts_os.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o md5.o md5.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o multipart.o multipart.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o probaln.o probaln.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o realn.o realn.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o regidx.o regidx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o sam.o sam.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o synced_bcf_reader.o synced_bcf_reader.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o vcf_sweep.o vcf_sweep.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o tbx.o tbx.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o textutils.o textutils.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o thread_pool.o thread_pool.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o vcf.o vcf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o vcfutils.o vcfutils.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_codecs.o cram/cram_codecs.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_decode.o cram/cram_decode.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_encode.o cram/cram_encode.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_external.o cram/cram_external.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_index.o cram/cram_index.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_io.o cram/cram_io.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_samtools.o cram/cram_samtools.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/cram_stats.o cram/cram_stats.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/files.o cram/files.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/mFILE.o cram/mFILE.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/open_trace_file.o cram/open_trace_file.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/rANS_static.o cram/rANS_static.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/sam_header.o cram/sam_header.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o cram/string_alloc.o cram/string_alloc.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I. -c -o hts.o hts.c src/utils/Fasta/split.cpp:19:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 19 | char cchars [s.size()+1]; | ^~~~~~~~~~ src/utils/Fasta/split.cpp:19:18: note: function parameter 's' with unknown value cannot be used in a constant expression src/utils/Fasta/split.cpp:17:52: note: declared here 17 | std::vector &split(const std::string &s, const std::string& delims, std::vector &elems) { | ^ 1 warning generated. src/utils/BamTools-Ancillary/BamAncillary.cpp:34:50: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl] 34 | vector::const_iterator cigItr = ((vector)bam.CigarData).begin(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/utils/BamTools-Ancillary/BamAncillary.cpp:35:50: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl] 35 | vector::const_iterator cigEnd = ((vector)bam.CigarData).end(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. src/utils/GenomeFile/GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable] 60 | long c2; | ^ 1 warning generated. ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.31.1/src/utils/htslib' - Building main bedtools binary. done. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bedtools-2.31.1 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bedtools-2.31.1 ===> Generating temporary packing list Building BEDTools: ========================================================= CXXFLAGS is [-g -Wall -O2 -std=c++11 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing ] DETECTED_VERSION = v2.31.1 CURRENT_VERSION = v2.31.1 - Building main bedtools binary. done. mkdir -p /wrkdirs/usr/ports/biology/bedtools/work/stage/usr/local/bin for file in bin/* ; do \ cp -f $file /wrkdirs/usr/ports/biology/bedtools/work/stage/usr/local/bin; \ done /usr/bin/strip /wrkdirs/usr/ports/biology/bedtools/work/stage/usr/local/bin/bedtools ====> 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=2026-01-23T15:11:30+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=1e46f94e3f92' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for bedtools-2.31.1 ===> Building bedtools-2.31.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bedtools-2.31.1 build of biology/bedtools | bedtools-2.31.1 ended at Fri Jan 23 10:12:07 EST 2026 build time: 00:00:38