Diff of the two buildlogs: -- --- b1/build.log 2025-02-03 15:25:21.306034450 +0000 +++ b2/build.log 2025-02-03 15:35:15.215249844 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 3 03:18:34 -12 2025 -I: pbuilder-time-stamp: 1738595914 +I: Current time: Tue Feb 4 05:26:01 +14 2025 +I: pbuilder-time-stamp: 1738596361 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/14613/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14007/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 3 15:26 /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/14007/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14007/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='819eca82d09b4079983c614fb4b58b89' - 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='14613' - PS1='# ' - PS2='> ' + INVOCATION_ID=c59aa1202ecf44aba9d5f33ff39ef17e + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=14007 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.ncHYB6gd/pbuilderrc_0FzR --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.ncHYB6gd/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.ncHYB6gd/pbuilderrc_eJqx --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.ncHYB6gd/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) 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/14613/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/14007/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 armhf libjsoncpp-dev armhf 1.9.6-3 [25.0 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12+b2 [31.9 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12+b2 [37.2 kB] -Fetched 66.8 MB in 3s (20.8 MB/s) +Fetched 66.8 MB in 3s (23.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:armhf. (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 ... 19565 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/14007/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/14007/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 @@ -829,7 +865,7 @@ -- Build files have been written to: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -846,21 +882,23 @@ cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' -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-arm-linux-gnueabihf' -make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build +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-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build +[ 1%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -[ 3%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -[ 4%] 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/tvcutils.cpp -/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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp +[ 3%] 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -[ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o +[ 4%] Building CXX object 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-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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned 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-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 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-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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c [ 82%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o @@ -1059,10 +1095,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' dh_auto_test - cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 + cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j3 +/usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf @@ -1091,6 +1127,12 @@ 3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 3: Test timeout computed to be: 10000000 +test 4 + Start 4: tvcutils_call + +4: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils +4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf +4: Test timeout computed to be: 10000000 1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 1: 1: Usage: tvc [options] @@ -1369,6 +1411,18 @@ 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 +1/8 Test #1: tvc_call ......................................... Passed 0.08 sec +4: +4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. +4: +4: Usage: tvcutils [options] +4: +4: Commands: +4: prepare_hotspots Convert BED or VCF file into a valid hotspot file +4: validate_bed Validate targets or hotspots file +4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) +4: +2/8 Test #4: tvcutils_call .................................... Passed 0.05 sec 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1523,36 +1577,18 @@ 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 -1/8 Test #1: tvc_call ......................................... Passed 0.03 sec -test 4 - Start 4: tvcutils_call - -4: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils -4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf -4: Test timeout computed to be: 10000000 -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. -4: -4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. -4: -4: Usage: tvcutils [options] -4: -4: Commands: -4: prepare_hotspots Convert BED or VCF file into a valid hotspot file -4: validate_bed Validate targets or hotspots file -4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) -4: -2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec test 5 Start 5: tvcutils_prepare_hotspots_call 5: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots" 5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 5: Test timeout computed to be: 10000000 +test 6 + Start 6: tvcutils_validate_bed_call + +6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed" +6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf +6: Test timeout computed to be: 10000000 5: 5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 5: @@ -1568,13 +1604,16 @@ 5: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] 5: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) 5: -3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec -test 6 - Start 6: tvcutils_validate_bed_call +3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.03 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. +test 7 + Start 7: tvcutils_unify_vcf_call -6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed" -6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf -6: Test timeout computed to be: 10000000 +7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf" +7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf +7: Test timeout computed to be: 10000000 6: 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 6: @@ -1594,13 +1633,16 @@ 6: --merged-plain-bed FILE output a valid plain merged BED [none] 6: --effective-bed FILE output a valid effective BED [none] 6: -4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec -test 7 - Start 7: tvcutils_unify_vcf_call +3: Recalibration was detected from comment lines in bam file(s): +3: 1 unique blocks of recalibration info detected. +3: Loading systematic error contexts. +4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.03 sec +test 8 + Start 8: tvcassembly_call -7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf" -7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf -7: Test timeout computed to be: 10000000 +8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly +8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf +8: Test timeout computed to be: 10000000 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. @@ -1619,13 +1661,7 @@ 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 -test 8 - Start 8: tvcassembly_call - -8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly -8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf -8: Test timeout computed to be: 10000000 +5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.03 sec 8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 8: 8: Usage: tvcassembly [options] @@ -1652,7 +1688,7 @@ 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: -6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec +6/8 Test #8: tvcassembly_call ................................. Passed 0.03 sec 3: Loaded. 2: Loaded. 2: Recalibration model: suppressed @@ -1662,17 +1698,17 @@ 3: 3: 3: [tvc] Normal termination. Processing time: 2 seconds. -7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.02 sec -8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.08 sec +7/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.75 sec +8/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.79 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 2.10 sec +Total Test time (real) = 2.80 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1688,29 +1724,29 @@ -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' dh_installdocs @@ -1730,13 +1766,13 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. +dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1744,12 +1780,14 @@ 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/14007/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14007/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/14613 and its subdirectories -I: Current time: Mon Feb 3 03:25:17 -12 2025 -I: pbuilder-time-stamp: 1738596317 +I: removing directory /srv/workspace/pbuilder/14007 and its subdirectories +I: Current time: Tue Feb 4 05:35:06 +14 2025 +I: pbuilder-time-stamp: 1738596906