=>> Building biology/star build started at Fri May 2 10:02:38 BST 2025 port directory: /usr/ports/biology/star package name: rna-STAR-2.7.11.a_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1430 Dec 29 14:16 /usr/ports/biology/star/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: 1a35b19e6d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE 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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/star/work/.cache HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/star/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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/star/work/.cache HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/star/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc13" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp13" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib " LIBS="" CXX="g++13" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -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-- OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/STAR" EXAMPLESDIR="share/examples/STAR" DATADIR="share/STAR" WWWDIR="www/STAR" ETCDIR="etc/STAR" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/STAR DOCSDIR=/usr/local/share/doc/STAR EXAMPLESDIR=/usr/local/share/examples/STAR WWWDIR=/usr/local/www/STAR ETCDIR=/usr/local/etc/STAR --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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 pipebuf (-y) 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 ===> rna-STAR-2.7.11.a_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> rna-STAR-2.7.11.a_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-STAR-2.7.11.a_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 rna-STAR-2.7.11.a_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by rna-STAR-2.7.11.a_1 for building => SHA256 Checksum OK for alexdobin-STAR-2.7.11a_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 rna-STAR-2.7.11.a_1 for building ===> Extracting for rna-STAR-2.7.11.a_1 => SHA256 Checksum OK for alexdobin-STAR-2.7.11a_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 rna-STAR-2.7.11.a_1 ===> Applying FreeBSD patches for rna-STAR-2.7.11.a_1 from /usr/ports/biology/star/files /usr/bin/sed -i.bak -e 's|"htslib/htslib/sam.h"||g' -e 's|"htslib/htslib/kstring.h"||g' -e 's|"htslib/htslib/bgzf.h"||g' /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/BAMfunctions.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/IncludeDefine.h /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/STAR.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/bamRemoveDuplicates.cpp /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/bam_cat.c /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/bam_cat.h /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/signalFromBAM.h =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-STAR-2.7.11.a_1 depends on executable: xxd - not found ===> Installing existing package /packages/All/xxd-9.1.1265.pkg [pkg-builder.dan.net.uk] Installing xxd-9.1.1265... [pkg-builder.dan.net.uk] Extracting xxd-9.1.1265: .. done ===> rna-STAR-2.7.11.a_1 depends on executable: xxd - found ===> Returning to build of rna-STAR-2.7.11.a_1 ===> rna-STAR-2.7.11.a_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> rna-STAR-2.7.11.a_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of rna-STAR-2.7.11.a_1 ===> rna-STAR-2.7.11.a_1 depends on executable: gcc13 - not found ===> Installing existing package /packages/All/gcc13-13.3.0_2.pkg [pkg-builder.dan.net.uk] Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] Extracting gcc13-13.3.0_2: .......... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> rna-STAR-2.7.11.a_1 depends on executable: gcc13 - found ===> Returning to build of rna-STAR-2.7.11.a_1 ===> rna-STAR-2.7.11.a_1 depends on file: /usr/local/bin/as - found ===> rna-STAR-2.7.11.a_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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 gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (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. ===> rna-STAR-2.7.11.a_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of rna-STAR-2.7.11.a_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-STAR-2.7.11.a_1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> rna-STAR-2.7.11.a_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of rna-STAR-2.7.11.a_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for rna-STAR-2.7.11.a_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for rna-STAR-2.7.11.a_1 xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list g++13 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:37+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++13: warning: parametersDefault.xxd: linker input file unused because linking not done gmake: Nothing to be done for 'Makefile'. 'rm' -f STAR.o Parameters.o g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include systemFunctions.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include funPrimaryAlignMark.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_collapseUMI_Graph.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_collapseUMIall.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ParametersClip_initialize.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ClipMate_clip.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ClipCR4.cpp cd opal && \ g++13 -c -I./ -std=c++11 -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include opal.cpp In file included from opal.cpp:10: ./simde_avx2.h: In function 'simde__m256i simde__m256i_from_private(simde__m256i_private)': ./simde_avx2.h:26437:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 26437 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ClipMate_clipChunk.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ClipMate_initialize.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_loadRawMatrix.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_emptyDrops_CR.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include soloInputFeatureUMI.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_countSmartSeq.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_redistributeReadsByCB.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_quantTranscript.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_sumThreads.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_countVelocyto.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_countCBgeneUMI.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome_classifyAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_cellFiltering.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_statsOutput.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include bamSortByCoordinate.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloBarcode.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ParametersSolo.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloRead.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloRead_record.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloReadBarcode.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloReadBarcode_getCBandUMI.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloBarcode_extractBarcode.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloReadFeature.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloReadFeature_record.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloReadFeature_inputRecords.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Solo.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_outputResults.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_processRecords.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SoloFeature_addBAMtags.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_transformGenome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome_transformGenome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript_convertGenomeCigar.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include twoPassRunPass1.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include samHeaders.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome_genomeLoad.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome_genomeOutLoad.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript_transformGenome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_outputSpliceGraphSAM.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_mapOneReadSpliceGraph.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SpliceGraph.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SpliceGraph_swScoreSpliced.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SpliceGraph_swTraceBack.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SpliceGraph_findSuperTr.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjAlignSplit.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include GTF.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include GTF_transcriptGeneSJ.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include GTF_superTranscript.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SuperTranscriptome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_outputAlignments.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include STAR.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:225:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:230:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 230 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SharedMemory.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include PackedArray.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SuffixArrayFuns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Parameters.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Parameters_samAttributes.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include InOutStreams.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include SequenceFuns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ParametersGenome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Stats.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript_alignScore.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript_generateCigarP.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Chain.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcript_variationAdjust.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Variation.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_waspMap.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_storeAligns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_stitchPieces.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_multMapSelect.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_mapOneRead.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include readLoad.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlignChunk.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlignChunk_processChunks.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlignChunk_mapChunk.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include OutSJ.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include outputSJ.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include blocksOverlap.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ThreadControl.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sysRemoveDir.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_maxMappableLength2strands.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include binarySearch2.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_outputTranscriptSAM.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_outputTranscriptSJ.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_outputTranscriptCIGARp.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_createExtendWindowsWithAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_assignAlignToWindow.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_oneRead.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_stitchWindowSeeds.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_peOverlapMergeMap.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_mappedFilter.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ParametersChimeric_initialize.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_chimericDetection.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_chimericDetectionOld.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_chimericDetectionOldOutput.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ChimericDetection.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ChimericDetection_chimericDetectionMult.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_chimericDetectionPEmerged.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include stitchWindowAligns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include extendAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include stitchAlignToTranscript.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ChimericAlign_chimericJunctionOutput.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ChimericAlign_chimericBAMoutput.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ChimericAlign_chimericStitching.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome_genomeGenerate.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include genomeParametersWrite.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include genomeScanFastaFiles.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include genomeSAindex.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Genome_insertSequences.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include insertSeqSA.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include funCompareUintAndSuffixes.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include funCompareUintAndSuffixesMemcmp.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include TimeFunctions.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ErrorWarning.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include streamFuns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include stringSubstituteAll.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome_quantAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome_geneFullAlignOverlap.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_quantTranscriptome.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Quantifications.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Transcriptome_geneCountsAddAlign.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjdbLoadFromFiles.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjdbLoadFromStream.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjdbPrepare.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjdbBuildIndex.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include sjdbInsertJunctions.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include mapThreadsSpawn.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Parameters_readFilesInit.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include Parameters_readSAMheader.cpp g++13 -c -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include -fno-strict-aliasing bam_cat.c bam_cat.c: In function 'int bam_cat(int, char* const*, const bam_hdr_t*, const char*)': bam_cat.c:80:25: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of 'ssize_t bgzf_raw_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include serviceFuns.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include BAMoutput.cpp BAMoutput.cpp: In member function 'void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)': BAMoutput.cpp:59:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function 'void BAMoutput::unsortedFlush()': BAMoutput.cpp:72:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include BAMfunctions.cpp BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const std::string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:78:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:80:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:83:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 87 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:88:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:91:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include ReadAlign_alignBAM.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function 'void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include signalFromBAM.cpp g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::string, std::string, Parameters&)': bamRemoveDuplicates.cpp:130:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 130 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:157:27: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 157 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:268:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 268 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:269:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 269 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ g++13 -c -isystem /usr/local/include -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function 'void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)': BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ g++13 -o STAR -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2025-05-02T09:03:48+00:00 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -Wl,-rpath=/usr/local/lib/gcc13 -isystem /usr/local/include systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -lhts -lz -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> rna-STAR-2.7.11.a_1 depends on executable: gcc13 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for rna-STAR-2.7.11.a_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/star/work/STAR-2.7.11a/source/STAR /wrkdirs/usr/ports/biology/star/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=2025-05-02T09:02:38+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=1a35b19e6d' '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 rna-STAR-2.7.11.a_1 ===> Building rna-STAR-2.7.11.a_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for rna-STAR-2.7.11.a_1 build of biology/star | rna-STAR-2.7.11.a_1 ended at Fri May 2 10:07:46 BST 2025 build time: 00:05:08