Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 12:27:20.567154698 +0000 +++ b2/build.log 2024-01-07 12:39:35.381643943 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 8 06:48:41 -12 2025 -I: pbuilder-time-stamp: 1739040521 +I: Current time: Mon Jan 8 02:27:26 +14 2024 +I: pbuilder-time-stamp: 1704630446 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./libstatgen_1.0.14-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.3o7W985o/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.n1Kg0emI/trustedkeys.kbx': General error gpgv: Signature made Mon Aug 3 20:38:42 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -32,49 +32,80 @@ dpkg-source: info: applying Remove_erroneous_deletes_in_Chromosome_constructor.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1912302/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Jan 7 12:28 /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/964465/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/964465/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,-fixfilepath parallel=16 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6e8b1ec2f3584842835ec80e1b4fbfe8' - 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='1912302' - PS1='# ' - PS2='> ' + INVOCATION_ID=cc83173c7ca24eeea2f1c7da3822b936 + 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=964465 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.u0ODuzyT/pbuilderrc_EP6u --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u0ODuzyT/b1 --logfile b1/build.log libstatgen_1.0.14-7.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.u0ODuzyT/pbuilderrc_y7bK --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u0ODuzyT/b2 --logfile b2/build.log libstatgen_1.0.14-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 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 + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash @@ -134,7 +165,7 @@ -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 8 15:47 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 7 12:28 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su @@ -160,7 +191,7 @@ -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/1912302/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -246,7 +277,7 @@ Get: 40 http://deb.debian.org/debian bullseye/main amd64 doxygen amd64 1.9.1-1 [4232 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libssl-dev amd64 1.1.1w-0+deb11u1 [1820 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 64.8 MB in 1s (71.3 MB/s) +Fetched 64.8 MB in 5s (14.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) @@ -430,7 +461,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libstatgen-1.0.14/ && 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 > ../libstatgen_1.0.14-7_source.changes +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libstatgen-1.0.14/ && 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 > ../libstatgen_1.0.14-7_source.changes dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.14-7 dpkg-buildpackage: info: source distribution unstable @@ -440,7 +475,7 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean + make -j15 clean make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' rm -f ../include/bgzf.h ../include/knetfile.h ../include/khash.h ../include/bam.h @@ -464,14 +499,14 @@ ar d ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ -rm -rf obj cigarRollerTest *~ results/* rm -rf obj inputFileTest *~ results/* -rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj stringTest *~ results/* -rm -rf obj referenceSequenceTest *~ results/* -rm -rf obj packedVectorTest *~ results/* +rm -rf obj cigarRollerTest *~ results/* rm -rf obj trimSequence *~ results/* +rm -rf obj packedVectorTest *~ results/* +rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj baseUtilitiesTest *~ results/* +rm -rf obj referenceSequenceTest *~ results/* rm -rf obj nonOverlapRegionsTest *~ results/* rm -rf obj reusableVectorTest *~ results/* # clean current directory @@ -479,49 +514,49 @@ rm -f phiX-bs.umfa phiX-cs.umfa gtest make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/general' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/bam' -make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/glf' -make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' -rm -f ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h -rm -f ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h rm -f ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h -ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o -ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o +make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' +make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ar d ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o -ranlib ../libStatGen.a -ranlib ../libStatGen.a -ranlib ../libStatGen.a rm -f ../include/SamFileHeader.h ../include/SamFile.h ../include/GenericSamInterface.h ../include/SamInterface.h ../include/BamInterface.h ../include/SamRecord.h ../include/BamIndex.h ../include/SamHeaderHD.h ../include/SamHeaderPG.h ../include/SamHeaderRecord.h ../include/SamHeaderSQ.h ../include/SamHeaderRG.h ../include/SamHeaderTag.h ../include/SamValidation.h ../include/SamStatistics.h ../include/SamQuerySeqWithRefHelper.h ../include/SamFilter.h ../include/PileupElement.h ../include/PileupElementBaseQual.h ../include/SamReferenceInfo.h ../include/SamTags.h ../include/PosList.h ../include/CigarHelper.h ../include/SamRecordPool.h ../include/SamCoordOutput.h ../include/SamRecordHelper.h ../include/Pileup.h ../include/SamHelper.h ../include/SamFlag.h ../include/SamStatus.h -ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o -ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o -ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ar d ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o -ranlib ../libStatGen_debug.a +ranlib ../libStatGen.a +ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ranlib ../libStatGen_debug.a ranlib ../libStatGen.a -ar d ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o -ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +rm -f ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h +ar d ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o +rm -f ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h ar d ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o -ranlib ../libStatGen_debug.a -ranlib ../libStatGen_profile.a +ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ranlib ../libStatGen_profile.a ranlib ../libStatGen_debug.a -ar d ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o -rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +ranlib ../libStatGen.a +ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ar d ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o +ranlib ../libStatGen.a ranlib ../libStatGen_profile.a +ranlib ../libStatGen_debug.a +ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o +rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +ranlib ../libStatGen_debug.a +ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ranlib ../libStatGen_profile.a +ar d ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +rm -rf obj samTest *~ results/* +rm -rf obj glfTest *~ results/* +make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' +make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' rm -rf obj fastqTest *~ results/* rm -rf obj vcfTest *~ results/* make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/vcf' -rm -rf obj glfTest *~ results/* -rm -rf obj samTest *~ results/* -make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' -make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a @@ -535,7 +570,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' ln -s ../samtools/bgzf.h ../include/bgzf.h @@ -691,70 +726,68 @@ make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ln -s ../fastq/FastQFile.h ../include/FastQFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h -ln -s ../glf/GlfException.h ../include/GlfException.h -ln -s ../vcf/VcfFile.h ../include/VcfFile.h ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h -ln -s ../glf/GlfFile.h ../include/GlfFile.h -ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h -ln -s ../glf/GlfHeader.h ../include/GlfHeader.h -ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h +ln -s ../glf/GlfException.h ../include/GlfException.h +ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h mkdir -p obj -ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h -ln -s ../glf/GlfRecord.h ../include/GlfRecord.h -ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h -ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h -ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h -ln -s ../glf/GlfStatus.h ../include/GlfStatus.h -ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h -mkdir -p obj -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" -ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h -ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h -ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h -ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamFile.h ../include/SamFile.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" -mkdir -p obj ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h +ln -s ../vcf/VcfFile.h ../include/VcfFile.h +ln -s ../glf/GlfFile.h ../include/GlfFile.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamInterface.h ../include/SamInterface.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" +ln -s ../glf/GlfHeader.h ../include/GlfHeader.h +ln -s ../glf/GlfRecord.h ../include/GlfRecord.h ln -s ../bam/BamInterface.h ../include/BamInterface.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamRecord.h ../include/SamRecord.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h +ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/BamIndex.h ../include/BamIndex.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h +ln -s ../glf/GlfStatus.h ../include/GlfStatus.h ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h +mkdir -p obj +ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h +ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h +ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../bam/SamValidation.h ../include/SamValidation.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h +ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h +ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h ln -s ../bam/SamFilter.h ../include/SamFilter.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" +ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h ln -s ../bam/PileupElement.h ../include/PileupElement.h +ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h +mkdir -p obj ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h ln -s ../bam/SamTags.h ../include/SamTags.h ln -s ../bam/PosList.h ../include/PosList.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/CigarHelper.h ../include/CigarHelper.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h @@ -763,38 +796,40 @@ ln -s ../bam/SamFlag.h ../include/SamFlag.h ln -s ../bam/SamStatus.h ../include/SamStatus.h mkdir -p obj +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o -ar: `u' modifier ignored since `D' is the default (see `U') g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" -make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o -ar: `u' modifier ignored since `D' is the default (see `U') -make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o +ar: `u' modifier ignored since `D' is the default (see `U') g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" +make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o +ar: `u' modifier ignored since `D' is the default (see `U') g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" +make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" @@ -1978,80 +2013,60 @@ Generating docs for compound SamValidationErrors... Generating docs for compound SamValidator... Generating docs for compound SetParameter... -Generating docs for compound Ssh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found +Generating docs for compound Ssh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found hiftIndelsTest... Generating docs for compound SmithWaterman... Generating docs for nested compound SmithWaterman::weight... @@ -2107,7 +2122,7 @@ writing tag file... Running plantuml with JAVA... Running dot... -Generating dot graphs using 17 parallel threads... +Generating dot graphs using 16 parallel threads... Running dot for graph 1/285 Running dot for graph 2/285 Running dot for graph 3/285 @@ -2171,121 +2186,145 @@ Running dot for graph 61/285 Running dot for graph 62/285 Running dot for graph 63/285 -Running dot for graph 64sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found +Running dot for graph 64sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found /285 Running dot for graph 65/285 Running dot for graph 66/285 @@ -2424,102 +2463,98 @@ Running dot for graph 199/285 Running dot for graph 200/285 Running dot for graph 201/285 -Running dot for sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: sh: 1: dot: not founddot: not found - -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: sh: 1: dot: not found -dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found +Running dot for sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found +sh: line 1: dot: command not found graph 202/285 Running dot for graph 203/285 Running dot for graph 204/285 @@ -2706,20 +2741,20 @@ finished... make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' dh_auto_test - make -j16 test + make -j15 test make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o mkdir -p obj/debug -mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') +mkdir -p obj/profile gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/bgzf.o -c bgzf.c gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/knetfile.o -c knetfile.c gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/bgzf.o -c bgzf.c gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/knetfile.o -c knetfile.c ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o -ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') +ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/samtools' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/general' @@ -2853,33 +2888,37 @@ ar: `u' modifier ignored since `D' is the default (see `U') mkdir obj mkdir obj -mkdir obj +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRollerTest.o -c CigarRollerTest.cpp -DVERSION="\"0.0.1\"" +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PackedVectorTest.o -c PackedVectorTest.cpp -DVERSION="\"0.0.1\"" mkdir obj mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringTest.o -c StringTest.cpp -DVERSION="\"0.0.1\"" +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFileTest.o -c InputFileTest.cpp -DVERSION="\"0.0.1\"" mkdir obj +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArrayTest.o -c MemoryMapArrayTest.cpp -DVERSION="\"0.0.1\"" mkdir obj +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequenceTest.o -c ReferenceSequenceTest.cpp -DVERSION="\"0.0.1\"" mkdir obj -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArrayTest.o -c MemoryMapArrayTest.cpp -DVERSION="\"0.0.1\"" mkdir obj -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRollerTest.o -c CigarRollerTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PackedVectorTest.o -c PackedVectorTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFileTest.o -c InputFileTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegionsTest.o -c NonOverlapRegionsTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TrimSequence.o -c TrimSequence.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilitiesTest.o -c BaseUtilitiesTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReusableVectorTest.o -c ReusableVectorTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequenceTest.o -c ReferenceSequenceTest.cpp -DVERSION="\"0.0.1\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o baseUtilitiesTest obj/BaseUtilitiesTest.o ../../../libStatGen_debug.a -lm -lz -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o trimSequence obj/TrimSequence.o ../../../libStatGen_debug.a -lm -lz +mkdir obj +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TrimSequence.o -c TrimSequence.cpp -DVERSION="\"0.0.1\"" +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegionsTest.o -c NonOverlapRegionsTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o stringTest obj/StringTest.o ../../../libStatGen_debug.a -lm -lz -./baseUtilitiesTest g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o reusableVectorTest obj/ReusableVectorTest.o ../../../libStatGen_debug.a -lm -lz -./trimSequence -mkdir -p results && ./stringTest +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o nonOverlapRegionsTest obj/NonOverlapRegionsTest.o ../../../libStatGen_debug.a -lm -lz +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o baseUtilitiesTest obj/BaseUtilitiesTest.o ../../../libStatGen_debug.a -lm -lz ./reusableVectorTest +mkdir -p results && ./stringTest +./baseUtilitiesTest +./nonOverlapRegionsTest 2> results/NonOverlapRegionsTest.txt && diff results/NonOverlapRegionsTest.txt expectedNonOverlapRegionsTest.txt +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o trimSequence obj/TrimSequence.o ../../../libStatGen_debug.a -lm -lz +./trimSequence g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o packedVectorTest obj/PackedVectorTest.o ../../../libStatGen_debug.a -lm -lz +./packedVectorTest +PackedArrayTest PASS: 46 FAIL: 0 In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../include/InputFile.h:23, @@ -2891,22 +2930,18 @@ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' forming offset [65546, 196609] is out of the bounds [0, 65546] [-Warray-bounds] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -./packedVectorTest -PackedArrayTest PASS: 46 FAIL: 0 -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o nonOverlapRegionsTest obj/NonOverlapRegionsTest.o ../../../libStatGen_debug.a -lm -lz -./nonOverlapRegionsTest 2> results/NonOverlapRegionsTest.txt && diff results/NonOverlapRegionsTest.txt expectedNonOverlapRegionsTest.txt g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o cigarRollerTest obj/CigarRollerTest.o ../../../libStatGen_debug.a -lm -lz mkdir -p results; ./cigarRollerTest CigarRoller PASS: 646 FAIL: 0 -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o referenceSequenceTest obj/ReferenceSequenceTest.o ../../../libStatGen_debug.a -lm -lz g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o memoryMapArrayTest obj/MemoryMapArrayTest.o ../../../libStatGen_debug.a -lm -lz +mkdir -p results; ./memoryMapArrayTest +MemoryMapArrayTest PASS: 108 FAIL: 0 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o referenceSequenceTest obj/ReferenceSequenceTest.o ../../../libStatGen_debug.a -lm -lz ./referenceSequenceTest test2 sequence utilization is 6.25% - expect around 6.25% phiX reference utilization is 96.8357% - expect around 96.8% ReferenceSequenceTest PASS: 13 FAIL: 0 -mkdir -p results; ./memoryMapArrayTest -MemoryMapArrayTest PASS: 108 FAIL: 0 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o inputFileTest obj/InputFileTest.o ../../../libStatGen_debug.a -lm -lz mkdir -p results && ./inputFileTest > results/results.log && diff data/InputFileTest.bam results/bgzfFile.glf && diff data/InputFileTest.txt results/defaultFile.glf && diff data/InputFileTest.gz results/defaultFile.gz && diff data/InputFileTest.gz results/gzipFile.glf && diff data/InputFileTest.txt results/InputFileTest.glf && diff data/InputFileTest.txt results/uncompressedFile.glf && diff data/textFile.gz results/textFile.gz && diff data/textFile.gz results/textFile1.gz && diff results/results.log expected/results.log make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/general' @@ -2914,115 +2949,79 @@ make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/glf' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' -ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o -mkdir -p obj/debug ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o -mkdir -p obj/profile +ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o mkdir -p obj/debug -ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') -mkdir -p obj/profile mkdir -p obj/debug -ar: g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" -`u' modifier ignored since `D' is the default (see `U') mkdir -p obj/profile -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" ar: `u' modifier ignored since `D' is the default (see `U') -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" +mkdir -p obj/profile +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" +mkdir -p obj/debug +ar: `u' modifier ignored since `D' is the default (see `U') g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o +ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" +mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/debug mkdir -p obj/profile +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o -ar: `u' modifier ignored since `D' is the default (see `U') -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ar: `u' modifier ignored since `D' is the default (see `U') +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o -ar: `u' modifier ignored since `D' is the default (see `U') -mkdir obj -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReadFiles.o -c ReadFiles.cpp -DVERSION="\"0.0.1\"" -ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o -ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" -mkdir obj -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFileTest.o -c FastQFileTest.cpp -DVERSION="\"0.0.1\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o +ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" -ReadFiles.cpp: In function 'void testReadGlf()': -ReadFiles.cpp:45:24: warning: catching polymorphic type 'class GlfException' by value [-Wcatch-value=] - 45 | catch(GlfException e) - | ^ -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Validate.o -c Validate.cpp -DVERSION="\"0.0.1\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" +mkdir obj +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFileTest.o -c FastQFileTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WriteFiles.o -c WriteFiles.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o -ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" +ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o +ar: `u' modifier ignored since `D' is the default (see `U') +mkdir obj +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReadFiles.o -c ReadFiles.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" @@ -3030,47 +3029,75 @@ g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o glfTest obj/ReadFiles.o obj/Validate.o obj/WriteFiles.o obj/Main.o ../../libStatGen_debug.a -lm -lz g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o fastqTest obj/FastQFileTest.o ../../libStatGen_debug.a -lm -lz +ReadFiles.cpp: In function 'void testReadGlf()': +ReadFiles.cpp:45:24: warning: catching polymorphic type 'class GlfException' by value [-Wcatch-value=] + 45 | catch(GlfException e) + | ^ g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" -./glfTest -make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" -mkdir -p results; ./FastQValidatorTest.sh +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Validate.o -c Validate.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" -make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" -ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o -ar: `u' modifier ignored since `D' is the default (see `U') g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WriteFiles.o -c WriteFiles.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" -mkdir obj g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileTest.o -c VcfFileTest.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o fastqTest obj/FastQFileTest.o ../../libStatGen_debug.a -lm -lz g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" +mkdir -p results; ./FastQValidatorTest.sh +make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeaderTest.o -c VcfHeaderTest.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" ar -cru ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o glfTest obj/ReadFiles.o obj/Validate.o obj/WriteFiles.o obj/Main.o ../../libStatGen_debug.a -lm -lz +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" +./glfTest +make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" mkdir obj g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WriteFiles.o -c WriteFiles.cpp -DVERSION="\"0.0.1\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ValidationTest.o -c ValidationTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReadFiles.o -c ReadFiles.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndexTest.o -c BamIndexTest.cpp -DVERSION="\"0.0.1\"" @@ -3079,6 +3106,8 @@ g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileTest.o -c SamFileTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestValidate.o -c TestValidate.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestEquals.o -c TestEquals.cpp -DVERSION="\"0.0.1\"" +ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o +ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestFilter.o -c TestFilter.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ShiftIndels.o -c ShiftIndels.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestPileup.o -c TestPileup.cpp -DVERSION="\"0.0.1\"" @@ -3088,6 +3117,12 @@ g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestSamCoordOutput.o -c TestSamCoordOutput.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestSamRecordHelper.o -c TestSamRecordHelper.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" +ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o +ar: `u' modifier ignored since `D' is the default (see `U') +mkdir obj +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileTest.o -c VcfFileTest.cpp -DVERSION="\"0.0.1\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeaderTest.o -c VcfHeaderTest.cpp -DVERSION="\"0.0.1\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o samTest obj/WriteFiles.o obj/ValidationTest.o obj/ReadFiles.o obj/BamIndexTest.o obj/ModifyVar.o obj/Modify.o obj/SamFileTest.o obj/TestValidate.o obj/TestEquals.o obj/TestFilter.o obj/ShiftIndels.o obj/TestPileup.o obj/TestPosList.o obj/TestCigarHelper.o obj/TestSamRecordPool.o obj/TestSamCoordOutput.o obj/TestSamRecordHelper.o obj/Main.o ../../libStatGen_debug.a -lm -lz ./test.sh make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' @@ -3130,16 +3165,16 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzeof used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzclose used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit2_ used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gztell64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzseek64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzopen64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol crc32 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gztell64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzrewind used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzdopen used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol deflate used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzwrite used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzopen64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol inflate used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol @@ -3156,12 +3191,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/964465/tmp/hooks/B01_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/1912302 and its subdirectories -I: Current time: Sat Feb 8 06:50:24 -12 2025 -I: pbuilder-time-stamp: 1739040624 +I: removing directory /srv/workspace/pbuilder/964465 and its subdirectories +I: Current time: Mon Jan 8 02:39:33 +14 2024 +I: pbuilder-time-stamp: 1704631173