Diff of the two buildlogs: -- --- b1/build.log 2024-01-13 05:38:45.305465629 +0000 +++ b2/build.log 2024-01-13 05:42:26.752927812 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Feb 13 23:57:55 -12 2025 -I: pbuilder-time-stamp: 1739534275 +I: Current time: Sat Jan 13 19:38:48 +14 2024 +I: pbuilder-time-stamp: 1705124328 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.qSk4hyq5/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.vsNY18uW/trustedkeys.kbx': General error gpgv: Signature made Sun Mar 1 05:51:37 2020 gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7 gpgv: issuer "stuart@debian.org" @@ -37,51 +37,82 @@ dpkg-source: info: applying python3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/90722/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13131/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 13 05:39 /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/13131/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13131/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='cb4fe5db46e24e9ca8ab1ccc7f895f74' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='90722' - PS1='# ' - PS2='> ' + INVOCATION_ID=b03b8c7bd86a432ea423b486b5ede9e1 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=13131 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.Bj9DcwbB/pbuilderrc_UW4b --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Bj9DcwbB/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Bj9DcwbB/pbuilderrc_H0dI --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Bj9DcwbB/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash @@ -141,7 +172,7 @@ -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 8 15:47 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 13 05:39 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su @@ -167,7 +198,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/90722/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/13131/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -302,7 +333,7 @@ Get: 85 http://deb.debian.org/debian bullseye/main i386 libjsoncpp-dev i386 1.9.4-4 [25.4 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-11 [38.6 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-11 [42.2 kB] -Fetched 54.0 MB in 20s (2694 kB/s) +Fetched 54.0 MB in 5s (10.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17763 files and directories currently installed.) @@ -671,7 +702,11 @@ 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-3_source.changes +I: user script /srv/workspace/pbuilder/13131/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/13131/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-3_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -699,7 +734,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- CMAKE_CXX_FLAGS: '-g -O2 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' +-- CMAKE_CXX_FLAGS: '-g -O2 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done -- Generating done CMake Warning: @@ -715,18 +750,18 @@ -- Build files have been written to: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j7 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-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-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend -make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend -make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= @@ -734,60 +769,38 @@ Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/depend.internal". Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". -Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/depend.internal". -Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/depend.internal". Scanning dependencies of target tvcassembly make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/depend.internal". +Dependee "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/depend.internal". make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -[ 4%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp -[ 7%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -[ 9%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o 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CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp -[ 52%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.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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-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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp: In member function 'void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)': -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Reader' is deprecated: Use CharReader and CharReaderBuilder instead. [-Wdeprecated-declarations] - 240 | Json::Reader recal_reader; - | ^~~~~~~~~~~~ -In file included from /usr/include/jsoncpp/json/json.h:11, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: -/usr/include/jsoncpp/json/reader.h:37:63: note: declared here - 37 | "Use CharReader and CharReaderBuilder instead.") JSON_API Reader { - | ^~~~~~ -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Json::Reader::Reader()' is deprecated: Use CharReader and CharReaderBuilder instead [-Wdeprecated-declarations] - 240 | Json::Reader recal_reader; - | ^~~~~~~~~~~~ -In file included from /usr/include/jsoncpp/json/json.h:11, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: -/usr/include/jsoncpp/json/reader.h:56:3: note: declared here - 56 | Reader(); - | ^~~~~~ +[ 15%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o +/usr/bin/c++ 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TheSilenceOfTheArmadillos(std::ofstream&)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); @@ -894,12 +854,92 @@ /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ -[ 55%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.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 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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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp: In member function 'void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)': +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Reader' is deprecated: Use CharReader and CharReaderBuilder instead. [-Wdeprecated-declarations] + 240 | Json::Reader recal_reader; + | ^~~~~~~~~~~~ +In file included from /usr/include/jsoncpp/json/json.h:11, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: +/usr/include/jsoncpp/json/reader.h:37:63: note: declared here + 37 | "Use CharReader and CharReaderBuilder instead.") JSON_API Reader { + | ^~~~~~ +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Json::Reader::Reader()' is deprecated: Use CharReader and CharReaderBuilder instead [-Wdeprecated-declarations] + 240 | Json::Reader recal_reader; + | ^~~~~~~~~~~~ +In file included from /usr/include/jsoncpp/json/json.h:11, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: +/usr/include/jsoncpp/json/reader.h:56:3: note: declared here + 56 | Reader(); + | ^~~~~~ +[ 39%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o 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-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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp +[ 40%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.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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/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp +[ 43%] 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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-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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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:336:35: 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; + | ^~~~~~~~ +[ 46%] 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 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value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 678 | fread(buf, 1, 28, fp->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.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/VariantCaller/Splice/LocalContext.cpp +[ 54%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.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/VariantCaller/Filter/VariantAssist.cpp +[ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.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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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 int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); @@ -922,55 +962,55 @@ | | std::vector::size_type {aka unsigned int} | long unsigned int | %u -[ 60%] 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 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+[ 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 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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; + | ^~~~~~~~ +[ 82%] Building C object CMakeFiles/tvc.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 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-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 -fdebug-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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:336:35: 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; - | ^~~~~~~~ -[ 83%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o CMakeFiles/tvc.dir/file-io/ion_util.c.o CMakeFiles/tvc.dir/file-io/ion_error.c.o CMakeFiles/tvc.dir/IonVersion.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_auto_test - cd obj-i686-linux-gnu && make -j16 test ARGS\+=-j16 + cd obj-i686-linux-gnu && make -j7 test ARGS\+=-j7 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process -j16 +/usr/bin/ctest --force-new-ctest-process -j7 Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu - Start 1: tvc_call - Start 2: tvc_test_1_thread_sse_on - Start 3: tvc_test_1_thread_sse_off - Start 4: tvc_test_4_threads_sse_on_with_parameter_file - Start 5: tvc_test_4_threads_sse_off_with_parameter_file - Start 6: tvcutils_call - Start 7: tvcutils_prepare_hotspots_call - Start 8: tvcutils_validate_bed_call - Start 9: tvcutils_unify_vcf_call - Start 10: tvcassembly_call - 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 - 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.01 sec - 6/10 Test #10: tvcassembly_call ................................. Passed 0.01 sec - 7/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.09 sec - 8/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.19 sec - 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.19 sec -10/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.25 sec + Start 1: tvc_call + Start 2: tvc_test_1_thread_sse_off + Start 3: tvc_test_4_threads_sse_off_with_parameter_file + Start 4: tvcutils_call + Start 5: tvcutils_prepare_hotspots_call + Start 6: tvcutils_validate_bed_call + Start 7: tvcutils_unify_vcf_call +1/8 Test #1: tvc_call ......................................... Passed 0.13 sec + Start 8: tvcassembly_call +2/8 Test #4: tvcutils_call .................................... Passed 0.10 sec +3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.08 sec +4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.06 sec +5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.04 sec +6/8 Test #8: tvcassembly_call ................................. Passed 0.03 sec +7/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.51 sec +8/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.69 sec -100% tests passed, 0 tests failed out of 10 +100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 1.26 sec +Total Test time (real) = 2.71 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-i686-linux-gnu && make -j16 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-i686-linux-gnu && make -j7 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-i686-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-i686-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-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build -make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build +make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build -[ 10%] Built target tvcassembly -[ 30%] Built target tvcutils make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' +[ 20%] Built target tvcutils +[ 31%] Built target tvcassembly [100%] Built target tvc make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 @@ -1089,30 +1118,30 @@ -- 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/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/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/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/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/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/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/sse/ampliseqexome_germline_p1_hiq_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_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/reference.fasta -- 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.bam.bai +-- 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_merged_plain.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.fasta.fai -- 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/small_variants.vcf -- 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/reference.fasta.fai +-- 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_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.bai +-- 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-i686-linux-gnu' dh_installdocs dh_installchangelogs @@ -1127,13 +1156,13 @@ dh_strip dh_makeshlibs dh_shlibdeps -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) +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) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_i386.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-3_i386.deb'. +dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tvc_5.0.3+git20151221.80e144e+dfsg-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1141,12 +1170,14 @@ 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/13131/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13131/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/90722 and its subdirectories -I: Current time: Fri Feb 14 00:01:39 -12 2025 -I: pbuilder-time-stamp: 1739534499 +I: removing directory /srv/workspace/pbuilder/13131 and its subdirectories +I: Current time: Sat Jan 13 19:42:26 +14 2024 +I: pbuilder-time-stamp: 1705124546