Diff of the two buildlogs: -- --- b1/build.log 2024-12-30 11:55:45.237372092 +0000 +++ b2/build.log 2024-12-30 11:57:27.396685147 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 29 23:53:12 -12 2024 -I: pbuilder-time-stamp: 1735559592 +I: Current time: Tue Dec 31 01:55:48 +14 2024 +I: pbuilder-time-stamp: 1735559748 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3084293/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2470371/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +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 Dec 30 11:55 /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/2470371/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2470371/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b5978febcb4b478e87a94bb89b3b8bd3' - 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='3084293' - PS1='# ' - PS2='> ' + INVOCATION_ID=fcab757dc3a74538b00f1eaaab238ec4 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2470371 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.TyQp492v/pbuilderrc_NzpJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TyQp492v/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.TyQp492v/pbuilderrc_rh8N --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TyQp492v/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3084293/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2470371/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -250,7 +282,7 @@ Get: 124 http://deb.debian.org/debian unstable/main arm64 libjsoncpp-dev arm64 1.9.6-3 [25.0 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b2 [37.9 kB] -Fetched 74.2 MB in 0s (176 MB/s) +Fetched 74.2 MB in 0s (220 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:arm64. (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 ... 19975 files and directories currently installed.) @@ -774,7 +806,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2470371/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2470371/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -812,7 +848,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2' --- Configuring done (1.7s) +-- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -836,61 +872,67 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' -cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build -make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' -[ 1%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp -[ 3%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -[ 4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -[ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -[ 7%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' +[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o +[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o +[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o +[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o +[ 7%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -MF CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o.d -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o +/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -MF CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o.d -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp [ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp [ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o @@ -1377,9 +1413,6 @@ 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 -2: Recalibration was detected from comment lines in bam file(s): -2: 1 unique blocks of recalibration info detected. -2: Loading systematic error contexts. 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1534,9 +1567,6 @@ 3: SampleManager: Found 1 read group(s) and 1 sample(s). 3: SampleManager: Primary sample "85" (default) present in 1 read group(s) 3: TVC found a total of 1 different flow orders of max flow lengths: 500 -3: Recalibration was detected from comment lines in bam file(s): -3: 1 unique blocks of recalibration info detected. -3: Loading systematic error contexts. 4: 4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 4: @@ -1581,6 +1611,10 @@ 6: --merged-plain-bed FILE output a valid plain merged BED [none] 6: --effective-bed FILE output a valid effective BED [none] 6: +1/8 Test #1: tvc_call ......................................... Passed 0.02 sec +2/8 Test #4: tvcutils_call .................................... Passed 0.02 sec +3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec +4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec 7: Parameter novel-tvc-vcf is required and empty. 7: 7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. @@ -1599,6 +1633,7 @@ 7: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 7: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 7: +5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec 8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 8: 8: Usage: tvcassembly [options] @@ -1625,27 +1660,28 @@ 8: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 8: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 8: -1/8 Test #1: tvc_call ......................................... Passed 0.15 sec -2/8 Test #4: tvcutils_call .................................... Passed 0.10 sec -3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.08 sec -4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.07 sec -5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.05 sec -6/8 Test #8: tvcassembly_call ................................. Passed 0.04 sec +6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec +2: Recalibration was detected from comment lines in bam file(s): +2: 1 unique blocks of recalibration info detected. +2: Loading systematic error contexts. +3: Recalibration was detected from comment lines in bam file(s): +3: 1 unique blocks of recalibration info detected. +3: Loading systematic error contexts. 2: Loaded. +3: Loaded. 2: Recalibration model: suppressed 2: 2: -2: [tvc] Normal termination. Processing time: 1 seconds. -7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 0.82 sec -3: Loaded. +2: [tvc] Normal termination. Processing time: 0 seconds. 3: 3: -3: [tvc] Normal termination. Processing time: 1 seconds. -8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.13 sec +3: [tvc] Normal termination. Processing time: 0 seconds. +7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 0.79 sec +8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 0.86 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 1.17 sec +Total Test time (real) = 0.87 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -1713,8 +1749,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_arm64.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.deb'. +dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1722,12 +1758,14 @@ 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/2470371/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2470371/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/3084293 and its subdirectories -I: Current time: Sun Dec 29 23:55:44 -12 2024 -I: pbuilder-time-stamp: 1735559744 +I: removing directory /srv/workspace/pbuilder/2470371 and its subdirectories +I: Current time: Tue Dec 31 01:57:26 +14 2024 +I: pbuilder-time-stamp: 1735559846