Diff of the two buildlogs: -- --- b1/build.log 2024-01-11 16:16:46.278684338 +0000 +++ b2/build.log 2024-01-11 16:34:45.669086428 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 11 03:56:59 -12 2024 -I: pbuilder-time-stamp: 1704988619 +I: Current time: Thu Feb 13 12:39:50 +14 2025 +I: pbuilder-time-stamp: 1739399990 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -33,49 +33,81 @@ dpkg-source: info: applying packaged_simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2569962/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 12 22:39 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='1cb79a0c1acc43829acb5f3ca0b1b9f2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2569962' - PS1='# ' - PS2='> ' + INVOCATION_ID=70cfe482b6af4467a0bea364184a5873 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2264282 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/pbuilderrc_B5CN --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/b1 --logfile b1/build.log rna-star_2.7.10b+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/pbuilderrc_fNKm --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jf0d30nd/b2 --logfile b2/build.log rna-star_2.7.10b+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -133,15 +165,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 12 22:39 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -161,7 +193,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2569962/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -254,7 +286,7 @@ Get: 47 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 xxd amd64 2:9.0.1378-2 [83.7 kB] -Fetched 24.4 MB in 1s (17.9 MB/s) +Fetched 24.4 MB in 1s (31.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18148 files and directories currently installed.) @@ -465,7 +497,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rna-star-2.7.10b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rna-star_2.7.10b+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rna-star-2.7.10b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rna-star_2.7.10b+dfsg-2_source.changes dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.10b+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -492,11 +528,11 @@ make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' mkdir --parents /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin dh_auto_clean ; dh_auto_build -- SFX=-avx2 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 && dh_auto_clean ; dh_auto_build -- SFX=-avx CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx && dh_auto_clean ; dh_auto_build -- SFX=-sse4.1 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 && dh_auto_clean ; dh_auto_build -- SFX=-ssse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 && dh_auto_clean ; dh_auto_build -- SFX=-sse3 CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CXXFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 && true - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-avx2 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx2 STARlong-avx2 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -549,11 +585,11 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp @@ -575,6 +611,7 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; @@ -599,11 +636,6 @@ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); @@ -611,6 +643,10 @@ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp @@ -709,14 +745,14 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.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] @@ -781,11 +817,11 @@ g++ -o STAR-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx2 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-avx "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-avx STARlong-avx make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -840,11 +876,11 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp @@ -863,15 +899,9 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp -STAR.cpp: In function 'int main(int, char**)': -STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 194 | bgzf_flush(P.inOut->outQuantBAMfile); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; @@ -896,7 +926,13 @@ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp +STAR.cpp: In function 'int main(int, char**)': +STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 194 | bgzf_flush(P.inOut->outQuantBAMfile); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp @@ -970,6 +1006,7 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); @@ -995,18 +1032,17 @@ 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++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp -Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': -Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | system(com1.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp +Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': +Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | system(com1.c_str()); + | ~~~~~~^~~~~~~~~~~~~~ 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); @@ -1040,6 +1076,13 @@ 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); | ~~~~~~~~~~^~~~ +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); + | ~~~~~~~~~~^~~~~~~~~ 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); @@ -1053,13 +1096,6 @@ 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); | ~~~~~~~~~~^~~~~~~~~ -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); - | ~~~~~~~~~~^~~~~~~~~ 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); @@ -1070,11 +1106,11 @@ g++ -o STAR-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-avx -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mavx systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-sse4.1 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse4.1 STARlong-sse4.1 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -1134,15 +1170,15 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp -SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': -SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 51 | getcwd(cwd,4096); - | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swScoreSpliced.cpp +SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': +SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] + 51 | getcwd(cwd,4096); + | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp @@ -1159,6 +1195,8 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; @@ -1183,7 +1221,8 @@ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); @@ -1191,9 +1230,6 @@ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp @@ -1265,11 +1301,11 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); | ~~~~~~~~~~~~~^~~~~~~ +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); | ~~~~~~~~~~~~~^~~~~~~~~ @@ -1295,13 +1331,12 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.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); @@ -1327,6 +1362,7 @@ 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++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.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); @@ -1348,13 +1384,6 @@ 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); | ~~~~~~~~~~^~~~~~~~~ -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); - | ~~~~~~~~~~^~~~~~~~~ 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); @@ -1362,14 +1391,21 @@ 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); | ~~~~~~~~~~^~~~~~~~~ +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++ -o STAR-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse4.1 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse4.1 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-ssse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-ssse3 STARlong-ssse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -1393,14 +1429,14 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp @@ -1427,13 +1463,13 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph.cpp @@ -1454,7 +1490,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_samAttributes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; @@ -1479,6 +1514,11 @@ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); @@ -1486,10 +1526,6 @@ STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] 194 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Chain.cpp @@ -1560,7 +1596,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); @@ -1586,6 +1621,7 @@ 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++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp @@ -1597,6 +1633,14 @@ | ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.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); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -1622,14 +1666,13 @@ 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); | ~~~~~~~~~~^~~~ -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); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~~~~~^~~~~~~~~ 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); @@ -1643,13 +1686,6 @@ 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); | ~~~~~~~~~~^~~~~~~~~ -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); - | ~~~~~~~~~~^~~~~~~~~ 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); @@ -1660,11 +1696,11 @@ g++ -o STAR-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-ssse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -mssse3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-sse3 "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-sse3 STARlong-sse3 make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -1688,13 +1724,13 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countSmartSeq.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp @@ -1722,11 +1758,11 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_convertGenomeCigar.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' twoPassRunPass1.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 51 | getcwd(cwd,4096); | ~~~~~~^~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp @@ -1751,14 +1787,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp -STAR.cpp: In function 'int main(int, char**)': -STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 194 | bgzf_flush(P.inOut->outQuantBAMfile); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ SuffixArrayFuns.cpp: In function 'long long unsigned int compareSeqToGenome(Genome&, char**, long long unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, bool, bool&)': SuffixArrayFuns.cpp:18:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 18 | register int64 ii; @@ -1783,6 +1811,14 @@ SuffixArrayFuns.cpp:382:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 382 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ +STAR.cpp: In function 'int main(int, char**)': +STAR.cpp:190:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 190 | bgzf_flush(P.inOut->outBAMfileUnsorted); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +STAR.cpp:194:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 194 | bgzf_flush(P.inOut->outQuantBAMfile); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ParametersGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_alignScore.cpp @@ -1855,7 +1891,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); @@ -1881,17 +1916,18 @@ 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++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortByCoordinate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bamRemoveDuplicates.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::string, std::vector >)': Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMbinSortUnmapped.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); @@ -1917,14 +1953,6 @@ 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); | ~~~~~~~~~~^~~~ -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); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -1938,13 +1966,14 @@ 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); | ~~~~~~~~~~^~~~~~~~~ -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); - | ~~~~~~~~~~^~~~~~~~~ +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); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -1952,15 +1981,22 @@ 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); | ~~~~~~~~~~^~~~~~~~~ +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++ -o STAR-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-sse3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -msse3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' dh_auto_clean ; dh_auto_build -- SFX=-plain CCFLAGS_common_add="-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain - cd source && make -j15 clean + cd source && make -j16 clean make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 'rm' -f *.o opal/opal.o STAR STARstatic STARlong Depend.list parametersDefault.xxd make[2]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' - cd source && make -j15 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain + cd source && make -j16 "INSTALL=install --strip-program=true" SFX=-plain "CCFLAGS_common_add=-flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" STAR-plain STARlong-plain make[2]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg/source' 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 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 @@ -1985,15 +2021,15 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_redistributeReadsByCB.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_quantTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_sumThreads.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp +g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp In file included from /usr/include/simde/x86/avx2.h:33, from opal.cpp:10: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:274:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 274 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countVelocyto.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_countCBgeneUMI.cpp -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_classifyAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_cellFiltering.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SoloFeature_statsOutput.cpp @@ -2020,10 +2056,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' samHeaders.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Genome_genomeOutLoad.cpp -SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': -SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 51 | getcwd(cwd,4096); - | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Transcript_transformGenome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_outputSpliceGraphSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_mapOneReadSpliceGraph.cpp @@ -2032,6 +2064,10 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_swTraceBack.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' SpliceGraph_findSuperTr.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' sjAlignSplit.cpp +SoloFeature_outputResults.cpp: In member function 'void SoloFeature::outputResults(bool, std::string)': +SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of 'char* getcwd(char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] + 51 | getcwd(cwd,4096); + | ~~~~~~^~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_transcriptGeneSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' GTF_superTranscript.cpp @@ -2127,7 +2163,6 @@ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readFilesInit.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' Parameters_readSAMheader.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' bam_cat.c -g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp 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); @@ -2153,6 +2188,7 @@ 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++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMoutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' BAMfunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' ReadAlign_alignBAM.cpp @@ -2189,6 +2225,14 @@ 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); | ~~~~~~~~~~^~~~ +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); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -2202,14 +2246,6 @@ 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); | ~~~~~~~~~~^~~~~~~~~ -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); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -2226,6 +2262,8 @@ | ~~~~~~~~~~^~~~~~~~~ g++ -o STAR-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now g++ -o STARlong-plain -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2023-01-22T14:33:29+00:00 "' -flto -flto -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -D'COMPILE_FOR_LONG_READS' -g -O2 -ffile-prefix-map=/build/reproducible-path/rna-star-2.7.10b+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 systemFunctions.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 -Bdynamic -lz -Wl,-z,relro -Wl,-z,now +In function 'min': +lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] Transcript.h:10:7: warning: type 'struct Transcript' violates the C++ One Definition Rule [-Wodr] 10 | class Transcript { | ^ @@ -2264,8 +2302,6 @@ | ^ In function 'min': lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] -In function 'min': -lto1: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] lto-wrapper: warning: using serial compilation of 24 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information lto-wrapper: warning: using serial compilation of 24 LTRANS jobs @@ -2279,6 +2315,15 @@ opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ +In function 'searchDatabase_', + inlined from 'searchDatabase' at opal/opal.cpp:1013:21, + inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, + inlined from 'opalAlign' at ClipCR4.cpp:77:23, + inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, + inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: +opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] + 756 | minF = SIMD::min(minF, F); // For overflow detection + | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, @@ -2290,15 +2335,6 @@ /usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ -In function 'searchDatabase_', - inlined from 'searchDatabase' at opal/opal.cpp:1013:21, - inlined from 'opalSearchDatabase' at opal/opal.cpp:1465:46, - inlined from 'opalAlign' at ClipCR4.cpp:77:23, - inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, - inlined from 'mapChunk' at ReadAlignChunk_mapChunk.cpp:10:39: -opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] - 756 | minF = SIMD::min(minF, F); // For overflow detection - | ^ In function 'opalSearchDatabase', inlined from 'opalAlign' at ClipCR4.cpp:77:23, inlined from 'clipChunk' at ClipMate_clipChunk.cpp:41:23, @@ -2333,10 +2369,10 @@ 44 | string* sigOutFileName=new string[sigN]; | ^ opal/opal.cpp: In function 'min': +opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ -opal/opal.cpp: In function 'min': opal/opal.cpp:756:29: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 756 | minF = SIMD::min(minF, F); // For overflow detection | ^ @@ -2349,173 +2385,24 @@ if lscpu | grep -q ${SIMD} ; then \ debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-${SIMD} ; \ fi ; done - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-avx --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:40 ..... started STAR run -Jan 11 16:13:40 ... starting to generate Genome files -Jan 11 16:13:40 ..... processing annotations GTF -!!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 -Jan 11 16:13:40 ... starting to sort Suffix Array. This may take a long time... -Jan 11 16:13:40 ... sorting Suffix Array chunks and saving them to disk... -Jan 11 16:13:40 ... loading chunks from disk, packing SA... -Jan 11 16:13:40 ... finished generating suffix array -Jan 11 16:13:40 ... generating Suffix Array index -Jan 11 16:13:40 ... completed Suffix Array index -Jan 11 16:13:40 ... writing Genome to disk ... -Jan 11 16:13:40 ... writing Suffix Array to disk ... -Jan 11 16:13:40 ... writing SAindex to disk -Jan 11 16:13:40 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-avx --runThreadN 1 --genomeDir . --readFilesIn reads.fastq - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:40 ..... started STAR run -Jan 11 16:13:40 ..... loading genome -Jan 11 16:13:40 ..... started mapping -Jan 11 16:13:41 ..... finished mapping -Jan 11 16:13:41 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse4.1 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:41 ..... started STAR run -Jan 11 16:13:41 ... starting to generate Genome files -Jan 11 16:13:41 ..... processing annotations GTF -!!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 -Jan 11 16:13:41 ... starting to sort Suffix Array. This may take a long time... -Jan 11 16:13:41 ... sorting Suffix Array chunks and saving them to disk... -Jan 11 16:13:41 ... loading chunks from disk, packing SA... -Jan 11 16:13:41 ... finished generating suffix array -Jan 11 16:13:41 ... generating Suffix Array index -Jan 11 16:13:41 ... completed Suffix Array index -Jan 11 16:13:41 ... writing Genome to disk ... -Jan 11 16:13:41 ... writing Suffix Array to disk ... -Jan 11 16:13:41 ... writing SAindex to disk -Jan 11 16:13:41 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse4.1 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:41 ..... started STAR run -Jan 11 16:13:41 ..... loading genome -Jan 11 16:13:41 ..... started mapping -Jan 11 16:13:42 ..... finished mapping -Jan 11 16:13:42 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-ssse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:42 ..... started STAR run -Jan 11 16:13:42 ... starting to generate Genome files -Jan 11 16:13:42 ..... processing annotations GTF -!!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 -Jan 11 16:13:42 ... starting to sort Suffix Array. This may take a long time... -Jan 11 16:13:42 ... sorting Suffix Array chunks and saving them to disk... -Jan 11 16:13:42 ... loading chunks from disk, packing SA... -Jan 11 16:13:42 ... finished generating suffix array -Jan 11 16:13:42 ... generating Suffix Array index -Jan 11 16:13:42 ... completed Suffix Array index -Jan 11 16:13:42 ... writing Genome to disk ... -Jan 11 16:13:42 ... writing Suffix Array to disk ... -Jan 11 16:13:42 ... writing SAindex to disk -Jan 11 16:13:42 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-ssse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:42 ..... started STAR run -Jan 11 16:13:42 ..... loading genome -Jan 11 16:13:42 ..... started mapping -Jan 11 16:13:43 ..... finished mapping -Jan 11 16:13:43 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse3 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:43 ..... started STAR run -Jan 11 16:13:43 ... starting to generate Genome files -Jan 11 16:13:43 ..... processing annotations GTF -!!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 -Jan 11 16:13:43 ... starting to sort Suffix Array. This may take a long time... -Jan 11 16:13:43 ... sorting Suffix Array chunks and saving them to disk... -Jan 11 16:13:43 ... loading chunks from disk, packing SA... -Jan 11 16:13:43 ... finished generating suffix array -Jan 11 16:13:43 ... generating Suffix Array index -Jan 11 16:13:43 ... completed Suffix Array index -Jan 11 16:13:43 ... writing Genome to disk ... -Jan 11 16:13:43 ... writing Suffix Array to disk ... -Jan 11 16:13:43 ... writing SAindex to disk -Jan 11 16:13:43 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/source/STAR-sse3 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:43 ..... started STAR run -Jan 11 16:13:43 ..... loading genome -Jan 11 16:13:43 ..... started mapping -Jan 11 16:13:44 ..... finished mapping -Jan 11 16:13:44 ..... finished successfully -debian/tests/run_test.sh /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain - /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/tests/foo.gtf - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:44 ..... started STAR run -Jan 11 16:13:44 ... starting to generate Genome files -Jan 11 16:13:44 ..... processing annotations GTF -!!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 -Jan 11 16:13:44 ... starting to sort Suffix Array. This may take a long time... -Jan 11 16:13:44 ... sorting Suffix Array chunks and saving them to disk... -Jan 11 16:13:44 ... loading chunks from disk, packing SA... -Jan 11 16:13:44 ... finished generating suffix array -Jan 11 16:13:44 ... generating Suffix Array index -Jan 11 16:13:44 ... completed Suffix Array index -Jan 11 16:13:44 ... writing Genome to disk ... -Jan 11 16:13:44 ... writing Suffix Array to disk ... -Jan 11 16:13:44 ... writing SAindex to disk -Jan 11 16:13:44 ..... finished successfully - /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/lib/rna-star/bin/STAR-plain --runThreadN 1 --genomeDir . --readFilesIn reads.fastq - STAR version: 2.7.10b compiled: 2023-01-22T14:33:29+00:00 -Jan 11 16:13:44 ..... started STAR run -Jan 11 16:13:44 ..... loading genome -Jan 11 16:13:44 ..... started mapping -Jan 11 16:13:44 ..... finished mapping -Jan 11 16:13:44 ..... finished successfully -make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' - create-stamp debian/debhelper-build-stamp - dh_testroot -O--sourcedirectory=source - dh_prep -O--sourcedirectory=source - debian/rules override_dh_auto_install -make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' -mkdir --parents /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/bin -dh_install source/STAR-avx2 source/STARlong-avx2 /usr/lib/rna-star/bin && dh_install source/STAR-avx source/STARlong-avx /usr/lib/rna-star/bin && dh_install source/STAR-sse4.1 source/STARlong-sse4.1 /usr/lib/rna-star/bin && dh_install source/STAR-ssse3 source/STARlong-ssse3 /usr/lib/rna-star/bin && dh_install source/STAR-sse3 source/STARlong-sse3 /usr/lib/rna-star/bin && dh_install source/STAR-plain source/STARlong-plain /usr/lib/rna-star/bin && true -dh_install debian/bin/simd-dispatch /usr/lib/rna-star/ -set -e && cd /build/reproducible-path/rna-star-2.7.10b+dfsg/debian/rna-star/usr/bin && for prog in STAR STARlong ; do ln -s \ - ../lib/rna-star/simd-dispatch ${prog} ; done -make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' - dh_installdocs -O--sourcedirectory=source - dh_installchangelogs -O--sourcedirectory=source - dh_installman -O--sourcedirectory=source - dh_installsystemduser -O--sourcedirectory=source - dh_perl -O--sourcedirectory=source - dh_link -O--sourcedirectory=source - dh_strip_nondeterminism -O--sourcedirectory=source - debian/rules override_dh_compress -make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' -dh_compress --exclude=.pdf -make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' - dh_fixperms -O--sourcedirectory=source - dh_missing -O--sourcedirectory=source - dh_dwz -a -O--sourcedirectory=source - dh_strip -a -O--sourcedirectory=source - dh_makeshlibs -a -O--sourcedirectory=source - dh_shlibdeps -a -O--sourcedirectory=source - dh_installdeb -O--sourcedirectory=source - debian/rules override_dh_gencontrol -make[1]: Entering directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' -dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " +/bin/sh: line 1: set: -i: invalid option +set: usage: set [-abefhkmnptuvxBCEHPT] [-o option-name] [--] [-] [arg ...] +make[1]: *** [debian/rules:53: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/rna-star-2.7.10b+dfsg' - dh_md5sums -O--sourcedirectory=source - dh_builddeb -O--sourcedirectory=source -dpkg-deb: building package 'rna-star' in '../rna-star_2.7.10b+dfsg-2_amd64.deb'. -dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.10b+dfsg-2_amd64.deb'. - dpkg-genbuildinfo --build=binary -O../rna-star_2.7.10b+dfsg-2_amd64.buildinfo - dpkg-genchanges --build=binary -O../rna-star_2.7.10b+dfsg-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +make: *** [debian/rules:21: binary] Error 2 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Wed Feb 12 22:57:45 UTC 2025 +Filesystem Size Used Avail Use% Mounted on +tmpfs 32G 0 32G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/2264282/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2569962 and its subdirectories -I: Current time: Thu Jan 11 04:16:45 -12 2024 -I: pbuilder-time-stamp: 1704989805 +I: removing directory /srv/workspace/pbuilder/2264282 and its subdirectories