Diff of the two buildlogs: -- --- b1/build.log 2025-09-10 07:14:17.001032714 +0000 +++ b2/build.log 2025-09-10 07:18:06.297322599 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 9 19:11:31 -12 2025 -I: pbuilder-time-stamp: 1757488291 +I: Current time: Wed Oct 14 03:37:18 +14 2026 +I: pbuilder-time-stamp: 1791898638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying 0006-Make-vcflib-smithwaterman-and-fastahack-external-inc.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3297150/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Oct 13 13:37 /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/2921075/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='51d578f7b767427fbb3209581c7c63de' - 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='3297150' - PS1='# ' - PS2='> ' + INVOCATION_ID=8d3a648c338b4b52acdcf5a9b082d46b + 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=2921075 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.ErQZNnkD/pbuilderrc_6UhR --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ErQZNnkD/b1 --logfile b1/build.log freebayes_1.3.9-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.ErQZNnkD/pbuilderrc_AsvA --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ErQZNnkD/b2 --logfile b2/build.log freebayes_1.3.9-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3297150/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -381,7 +413,7 @@ Get: 244 http://deb.debian.org/debian forky/main amd64 sysstat amd64 12.7.5-2 [623 kB] Get: 245 http://deb.debian.org/debian forky/main amd64 parallel all 20240222+ds-2 [2163 kB] Get: 246 http://deb.debian.org/debian forky/main amd64 samtools amd64 1.22.1-1 [697 kB] -Fetched 138 MB in 3s (48.2 MB/s) +Fetched 138 MB in 2s (56.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19898 files and directories currently installed.) @@ -1189,8 +1221,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Sep 10 07:12:39 UTC 2025. -Universal Time is now: Wed Sep 10 07:12:39 UTC 2025. +Local time is now: Tue Oct 13 13:39:32 UTC 2026. +Universal Time is now: Tue Oct 13 13:39:32 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-15) ... @@ -1414,7 +1446,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/freebayes-1.3.9/ && 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 > ../freebayes_1.3.9-1_source.changes +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/freebayes-1.3.9/ && 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 > ../freebayes_1.3.9-1_source.changes dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.9-1 dpkg-buildpackage: info: source distribution unstable @@ -1487,14 +1523,17 @@ Found ninja-1.12.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson -O--builddir=build - cd build && LC_ALL=C.UTF-8 ninja -j12 -v + cd build && LC_ALL=C.UTF-8 ninja -j16 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp -[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp -[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp -[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp -[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp -[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp -[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp +[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp +[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp +[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp +[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp +[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp +[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp +[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp +[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp +[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp In file included from ../src/BedReader.cpp:14: /usr/include/SeqLib/IntervalTree.h:85:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 85 | ~TIntervalTree() { @@ -1512,10 +1551,9 @@ 124 | intervalVector& ivals, | ^~~~~~~~~~~~~~ /usr/include/SeqLib/IntervalTree.h:124:13: note: remove the ‘< >’ -[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp -[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp -[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp -[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp +[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp +[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp +[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp ../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSequence(std::string)’: ../src/FBFasta.cpp:273:20: warning: pointer ‘pbegin’ used after ‘void free(void*)’ [-Wuse-after-free] 273 | s.resize((pend - pbegin)/sizeof(char)); @@ -1530,17 +1568,16 @@ ../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here 315 | free(seq); | ~~~~^~~~~ -[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp -[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp -[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp +[16/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp -[18/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp -[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp -[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp -[21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp -[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp +[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp +[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp +[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp +[21/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp +[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp +[23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp In file included from ../src/Genotype.cpp:3: ../contrib/multichoose/multipermute.h:47:19: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 47 | ListElement() { } @@ -1554,7 +1591,6 @@ 64 | ~ListElement() { | ^ ../contrib/multichoose/multipermute.h:64:5: note: remove the ‘< >’ -[23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp [24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp [25/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -I/usr/include/fastahack -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libvcflib.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libtabixpp.so -Wl,--end-group @@ -1566,25 +1602,25 @@ mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /build/reproducible-path/freebayes-1.3.9/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 - cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=12 meson test --verbose -v --timeout-multiplier 100 + cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=16 meson test --verbose -v --timeout-multiplier 100 ninja: Entering directory `/build/reproducible-path/freebayes-1.3.9/build' ninja: no work to do. 1/5 T00 RUNNING ->>> MESON_TEST_ITERATION=1 MALLOC_PERTURB_=50 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t +>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=217 MESON_TEST_ITERATION=1 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t 2/5 T01 RUNNING ->>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=60 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01_call_variants.t +>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=76 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 /usr/bin/prove -e bash -v t/01_call_variants.t 3/5 T01b RUNNING ->>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=98 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01b_call_variants.t +>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=201 MESON_TEST_ITERATION=1 /usr/bin/prove -e bash -v t/01b_call_variants.t 4/5 T02 RUNNING ->>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=194 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/02_multi_bam.t +>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=7 MESON_TEST_ITERATION=1 /usr/bin/prove -e bash -v t/02_multi_bam.t 5/5 T03 RUNNING ->>> MESON_TEST_ITERATION=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=222 /usr/bin/prove -e bash -v t/03_reference_bases.t +>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MALLOC_PERTURB_=3 MESON_TEST_ITERATION=1 /usr/bin/prove -e bash -v t/03_reference_bases.t -5/5 T03 OK 0.24s +5/5 T03 OK 0.70s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/03_reference_bases.t .. 1..3 @@ -1593,11 +1629,11 @@ ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. -Files=1, Tests=3, 0 wallclock secs ( 0.01 usr 0.01 sys + 0.03 cusr 0.03 csys = 0.08 CPU) +Files=1, Tests=3, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.04 cusr 0.03 csys = 0.10 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -1/5 T00 OK 0.32s +1/5 T00 OK 0.77s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/00_region_and_target_handling.t .. 1..12 @@ -1615,11 +1651,11 @@ ok 12 - region outside of bounds error ok All tests successful. -Files=1, Tests=12, 0 wallclock secs ( 0.01 usr 0.00 sys + 0.09 cusr 0.07 csys = 0.17 CPU) +Files=1, Tests=12, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.11 csys = 0.25 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -4/5 T02 OK 0.94s +4/5 T02 OK 1.71s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 @@ -1632,11 +1668,11 @@ ok 7 - freebayes rejects two BAMs with the same name ok All tests successful. -Files=1, Tests=7, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.11 cusr 0.10 csys = 0.23 CPU) +Files=1, Tests=7, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.13 csys = 0.27 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -3/5 T01b OK 2.75s +3/5 T01b OK 3.52s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/01b_call_variants.t .. 1..10 @@ -1652,11 +1688,11 @@ ok 10 - freebayes correctly uses CNV map with multiple entries ok All tests successful. -Files=1, Tests=10, 2 wallclock secs ( 0.01 usr 0.01 sys + 2.37 cusr 0.36 csys = 2.75 CPU) +Files=1, Tests=10, 3 wallclock secs ( 0.03 usr 0.00 sys + 3.36 cusr 0.61 csys = 4.00 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― -2/5 T01 OK 7.23s +2/5 T01 OK 9.51s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01_call_variants.t .. @@ -1679,13 +1715,13 @@ ok 16 - ! ok All tests successful. -Files=1, Tests=16, 7 wallclock secs ( 0.03 usr 0.00 sys + 4.20 cusr 5.96 csys = 10.19 CPU) +Files=1, Tests=16, 9 wallclock secs ( 0.02 usr 0.02 sys + 6.05 cusr 6.77 csys = 12.86 CPU) Result: PASS stderr: [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 -t/01_call_variants.t: line 108: 3312135 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null +t/01_call_variants.t: line 108: 2953794 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― @@ -1735,12 +1771,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2921075/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2921075/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/3297150 and its subdirectories -I: Current time: Tue Sep 9 19:14:16 -12 2025 -I: pbuilder-time-stamp: 1757488456 +I: removing directory /srv/workspace/pbuilder/2921075 and its subdirectories +I: Current time: Wed Oct 14 03:41:05 +14 2026 +I: pbuilder-time-stamp: 1791898865