Diff of the two buildlogs: -- --- b1/build.log 2024-05-23 02:22:29.376980375 +0000 +++ b2/build.log 2024-05-23 02:31:10.618787959 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 24 20:44:24 -12 2025 -I: pbuilder-time-stamp: 1750841064 +I: Current time: Thu May 23 16:22:34 +14 2024 +I: pbuilder-time-stamp: 1716430954 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1230600/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2657758/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 May 23 02:23 /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/2657758/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2657758/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=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='09cea39432b741ec9033ca736b1317af' - 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='1230600' - PS1='# ' - PS2='> ' + INVOCATION_ID=2bd8996b23104fb5aff9f8d2f0aa78ea + 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=2657758 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.CrmGQxB4/pbuilderrc_imqR --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.CrmGQxB4/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.CrmGQxB4/pbuilderrc_uyTF --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.CrmGQxB4/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 24 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1230600/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 21 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2657758/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +258,7 @@ Get: 96 http://deb.debian.org/debian unstable/main amd64 libjsoncpp-dev amd64 1.9.5-6+b2 [24.8 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB] -Fetched 66.3 MB in 1s (107 MB/s) +Fetched 66.3 MB in 11s (6187 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19718 files and directories currently installed.) @@ -638,7 +670,11 @@ 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/2657758/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2657758/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 @@ -675,8 +711,8 @@ -- 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' --- Configuring done (0.8s) --- Generating done (0.0s) +-- Configuring done (5.4s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -692,7 +728,7 @@ -- Build files have been written to: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /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-x86_64-linux-gnu --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-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -700,196 +736,196 @@ make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend -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-x86_64-linux-gnu' +cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.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-x86_64-linux-gnu' +[ 3%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o +[ 1%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu' +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp +[ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build +[ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.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 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CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SkewGenerator.cpp +In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = long unsigned int]': +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3: required from 'void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] + 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { + | ~~~^~~~~~~~~ +In file included from /usr/include/c++/13/string:48, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: +/usr/include/c++/13/bits/stl_iterator.h:462:5: note: declared here + 462 | operator!=(const reverse_iterator<_Iterator>& __x, + | ^~~~~~~~ +[ 53%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.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 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/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp +[ 55%] Building C object CMakeFiles/tvcutils.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 -fcf-protection -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/external/vcflib/tabixpp/index.c: In function 'ti_index_core': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ +[ 56%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o +[ 58%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.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 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-ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_util.c.o -MF CMakeFiles/tvc.dir/file-io/ion_util.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_util.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_util.c -[ 90%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o +[ 93%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.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 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-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -MF CMakeFiles/tvc.dir/realignment/Realigner.cpp.o.d 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-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/IonVersion.cpp.o -MF CMakeFiles/tvc.dir/IonVersion.cpp.o.d -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c 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-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp -In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = long unsigned int]': -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3: required from 'void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] - 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { - | ~~~^~~~~~~~~ -In file included from /usr/include/c++/13/string:48, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: -/usr/include/c++/13/bits/stl_iterator.h:462:5: note: declared here - 462 | operator!=(const reverse_iterator<_Iterator>& __x, - | ^~~~~~~~ -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] - 36 | arma::set_stream_err1(null_ostream); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from /usr/include/armadillo:405, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: -/usr/include/armadillo_bits/debug.hpp:83:1: note: declared here - 83 | set_stream_err1(const std::ostream&) - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] - 37 | arma::set_stream_err2(null_ostream); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here - 92 | set_stream_err2(const std::ostream&) - | ^~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable tvcassembly -/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 -/usr/bin/c++ -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp -make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target tvcassembly [ 98%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/c++ -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder @@ -904,10 +940,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu @@ -1255,6 +1291,9 @@ 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 @@ -1409,6 +1448,9 @@ 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: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 4: 4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1563,6 +1605,9 @@ 4: SampleManager: Found 1 read group(s) and 1 sample(s). 4: SampleManager: Primary sample "85" (default) present in 1 read group(s) 4: TVC found a total of 1 different flow orders of max flow lengths: 500 +4: Recalibration was detected from comment lines in bam file(s): +4: 1 unique blocks of recalibration info detected. +4: Loading systematic error contexts. 5: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 5: 5: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1717,6 +1762,9 @@ 5: SampleManager: Found 1 read group(s) and 1 sample(s). 5: SampleManager: Primary sample "85" (default) present in 1 read group(s) 5: TVC found a total of 1 different flow orders of max flow lengths: 500 +5: Recalibration was detected from comment lines in bam file(s): +5: 1 unique blocks of recalibration info detected. +5: Loading systematic error contexts. 6: 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 6: @@ -1779,23 +1827,11 @@ 9: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 9: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 9: - 1/10 Test #1: tvc_call ......................................... Passed 0.02 sec - 2/10 Test #6: tvcutils_call .................................... Passed 0.01 sec - 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec - 4/10 Test #8: tvcutils_validate_bed_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. -4: Recalibration was detected from comment lines in bam file(s): -4: 1 unique blocks of recalibration info detected. -4: Loading systematic error contexts. -5: Recalibration was detected from comment lines in bam file(s): -5: 1 unique blocks of recalibration info detected. -5: Loading systematic error contexts. - 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.01 sec + 1/10 Test #1: tvc_call ......................................... Passed 0.14 sec + 2/10 Test #6: tvcutils_call .................................... Passed 0.08 sec + 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.05 sec + 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.04 sec + 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.02 sec 10: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 10: 10: Usage: tvcassembly [options] @@ -1822,38 +1858,38 @@ 10: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 10: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 10: - 6/10 Test #10: tvcassembly_call ................................. Passed 0.01 sec + 6/10 Test #10: tvcassembly_call ................................. Passed 0.03 sec 4: Loaded. -2: Loaded. -5: Loaded. -3: Loaded. 4: 4: -4: [tvc] Normal termination. Processing time: 0 seconds. -2: Recalibration model: suppressed -2: -2: -2: [tvc] Normal termination. Processing time: 0 seconds. +4: [tvc] Normal termination. Processing time: 1 seconds. +5: Loaded. + 7/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 2.07 sec 5: 5: -5: [tvc] Normal termination. Processing time: 0 seconds. +5: [tvc] Normal termination. Processing time: 2 seconds. + 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.66 sec +3: Loaded. +2: Loaded. 3: Recalibration model: suppressed 3: 3: -3: [tvc] Normal termination. Processing time: 0 seconds. - 7/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 0.70 sec - 8/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 0.71 sec - 9/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 0.71 sec -10/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 0.72 sec +3: [tvc] Normal termination. Processing time: 3 seconds. +2: Recalibration model: suppressed +2: +2: +2: [tvc] Normal termination. Processing time: 3 seconds. + 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 3.86 sec +10/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 4.35 sec 100% tests passed, 0 tests failed out of 10 -Total Test time (real) = 0.72 sec +Total Test time (real) = 4.36 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ - cd obj-x86_64-linux-gnu && make -j42 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-x86_64-linux-gnu && make -j20 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-x86_64-linux-gnu' /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-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1869,30 +1905,30 @@ -- 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/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/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_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_somatic_lowstringency_pgm_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/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/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_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/ampliseq_somatic_lowstringency_pgm_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/test.bam.bai +-- 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/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.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/test.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/reference.dict --- 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.bam -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta --- 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.bai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs @@ -1907,7 +1943,7 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -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 @@ -1921,12 +1957,14 @@ 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/2657758/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2657758/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/1230600 and its subdirectories -I: Current time: Tue Jun 24 20:45:28 -12 2025 -I: pbuilder-time-stamp: 1750841128 +I: removing directory /srv/workspace/pbuilder/2657758 and its subdirectories +I: Current time: Thu May 23 16:31:08 +14 2024 +I: pbuilder-time-stamp: 1716431468