Diff of the two buildlogs: -- --- b1/build.log 2024-12-08 13:25:32.267903446 +0000 +++ b2/build.log 2024-12-08 13:30:05.619453468 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 8 01:18:36 -12 2024 -I: pbuilder-time-stamp: 1733663916 +I: Current time: Mon Dec 9 03:25:41 +14 2024 +I: pbuilder-time-stamp: 1733664341 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17149/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/663/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 8 13:25 /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/663/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/663/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='8db114f6199b470d93c8668cd129a158' - 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='17149' - PS1='# ' - PS2='> ' + INVOCATION_ID=ce83e77946774b8ca276aeb6fe4b2aad + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=663 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.PDLUdIV2/pbuilderrc_PJtO --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PDLUdIV2/b1 --logfile b1/build.log bitseq_0.7.5+dfsg-6.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PDLUdIV2/pbuilderrc_dH2a --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PDLUdIV2/b2 --logfile b2/build.log bitseq_0.7.5+dfsg-6.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/17149/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/663/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -195,7 +227,7 @@ Get: 67 http://deb.debian.org/debian trixie/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 75.2.0-1 [213 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB] -Fetched 43.7 MB in 4s (10.8 MB/s) +Fetched 43.7 MB in 1s (43.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19685 files and directories currently installed.) @@ -437,8 +469,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 8 13:20:21 UTC 2024. -Universal Time is now: Sun Dec 8 13:20:21 UTC 2024. +Local time is now: Sun Dec 8 13:26:44 UTC 2024. +Universal Time is now: Sun Dec 8 13:26:44 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -502,7 +534,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bitseq-0.7.5+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 > ../bitseq_0.7.5+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/663/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/663/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bitseq-0.7.5+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 > ../bitseq_0.7.5+dfsg-6_source.changes dpkg-buildpackage: info: source package bitseq dpkg-buildpackage: info: source version 0.7.5+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -512,7 +548,7 @@ debian/rules clean dh clean dh_auto_clean - make -j5 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/bitseq-0.7.5+dfsg' rm -f *.o convertSamples estimateDE estimateExpression estimateHyperPar estimateVBExpression extractSamples getFoldChange getGeneExpression getPPLR getVariance getWithinGeneExpression parseAlignment transposeLargeFile make[1]: Leaving directory '/build/reproducible-path/bitseq-0.7.5+dfsg' @@ -523,7 +559,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j5 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bitseq-0.7.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.cpp @@ -531,38 +567,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp -In file included from TranscriptInfo.cpp:6: -TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::vector >&)': -TranscriptInfo.cpp:228:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 228 | warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ - | | - | std::vector >::size_type {aka unsigned int} -common.h:32:67: note: in definition of macro 'warning' - 32 | #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} - | ^~~~~~~~~~~ -TranscriptInfo.cpp:228:64: note: format string is defined here - 228 | warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); - | ~~^ - | | - | long int - | %d -TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::map, std::__cxx11::basic_string >&)': -TranscriptInfo.cpp:241:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::map, std::__cxx11::basic_string >::size_type' {aka 'unsigned int'} [-Wformat=] - 241 | warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ - | | - | std::map, std::__cxx11::basic_string >::size_type {aka unsigned int} -common.h:32:67: note: in definition of macro 'warning' - 32 | #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} - | ^~~~~~~~~~~ -TranscriptInfo.cpp:241:65: note: format string is defined here - 241 | warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); - | ~~^ - | | - | long int - | %d In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from misc.cpp:1: @@ -600,6 +604,37 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from TranscriptInfo.cpp:6: +TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::vector >&)': +TranscriptInfo.cpp:228:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 228 | warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ + | | + | std::vector >::size_type {aka unsigned int} +common.h:32:67: note: in definition of macro 'warning' + 32 | #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} + | ^~~~~~~~~~~ +TranscriptInfo.cpp:228:64: note: format string is defined here + 228 | warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); + | ~~^ + | | + | long int + | %d +TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::map, std::__cxx11::basic_string >&)': +TranscriptInfo.cpp:241:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::map, std::__cxx11::basic_string >::size_type' {aka 'unsigned int'} [-Wformat=] + 241 | warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ + | | + | std::map, std::__cxx11::basic_string >::size_type {aka unsigned int} +common.h:32:67: note: in definition of macro 'warning' + 32 | #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} + | ^~~~~~~~~~~ +TranscriptInfo.cpp:241:65: note: format string is defined here + 241 | warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); + | ~~^ + | | + | long int + | %d In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void ns_misc::computeCI(double, std::vector*, double*, double*)' at misc.cpp:89:8: @@ -620,6 +655,7 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'bool ns_params::readParams(const std::string&, std::vector*, std::ofstream*)' at misc.cpp:236:8: @@ -642,21 +678,21 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp In file included from CollapsedSampler.h:3, from CollapsedSampler.cpp:5: Sampler.h: In member function 'pairD Sampler::getSumNorms() const': Sampler.h:83:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 83 | pairD getSumNorms() const { return sumNorm; } | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp In file included from GibbsSampler.h:2, from GibbsSampler.cpp:5: Sampler.h: In member function 'pairD Sampler::getSumNorms() const': Sampler.h:83:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 83 | pairD getSumNorms() const { return sumNorm; } | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp In file included from Sampler.cpp:5: Sampler.h: In member function 'pairD Sampler::getSumNorms() const': @@ -666,7 +702,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from lowess.cpp:17: @@ -687,7 +722,7 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void lowess(const std::vector&, const std::vector&, double, long int, double, std::vector&, std::vector&, std::vector&)' at lowess.cpp:92:11: @@ -708,6 +743,7 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from TranscriptExpression.cpp:1: @@ -724,7 +760,6 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -753,7 +788,13 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)': ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 265 | (! frag->second->core.flag & BAM_FREVERSE))){ @@ -766,7 +807,8 @@ ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 687 | (! frag->second->core.flag & BAM_FREVERSE))){ | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples In file included from /usr/include/c++/14/map:62, from ReadDistribution.h:5, from ReadDistribution.cpp:7: @@ -774,7 +816,7 @@ /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE In file included from /usr/include/c++/14/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)' at ReadDistribution.cpp:846:33: @@ -794,7 +836,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression In file included from /usr/include/c++/14/vector:72, from ReadDistribution.h:4: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -902,13 +944,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression In file included from CollapsedSampler.h:3, from estimateExpression.cpp:10: Sampler.h: In member function 'pairD Sampler::getSumNorms() const': Sampler.h:83:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 83 | pairD getSumNorms() const { return sumNorm; } | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from estimateExpression.cpp:1: @@ -929,7 +972,6 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from estimateHyperPar.cpp:6: @@ -974,7 +1016,7 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'int estimateHyperPar(int*, char**)' at estimateHyperPar.cpp:295:8: @@ -995,12 +1037,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bitseq-0.7.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile make[1]: Leaving directory '/build/reproducible-path/bitseq-0.7.5+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp @@ -1085,20 +1121,20 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateExpression contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateHyperPar contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getVariance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateDE contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/extractSamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getVariance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateHyperPar contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateExpression contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getFoldChange contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bitseq/usr/bin/parseAlignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/bitseq/usr/bin/getPPLR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/bitseq/usr/bin/estimateDE contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/bitseq/usr/bin/parseAlignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bitseq-dbgsym' in '../bitseq-dbgsym_0.7.5+dfsg-6_armhf.deb'. dpkg-deb: building package 'bitseq' in '../bitseq_0.7.5+dfsg-6_armhf.deb'. +dpkg-deb: building package 'bitseq-dbgsym' in '../bitseq-dbgsym_0.7.5+dfsg-6_armhf.deb'. dpkg-genbuildinfo --build=binary -O../bitseq_0.7.5+dfsg-6_armhf.buildinfo dpkg-genchanges --build=binary -O../bitseq_0.7.5+dfsg-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1106,12 +1142,14 @@ 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/663/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/663/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/17149 and its subdirectories -I: Current time: Sun Dec 8 01:25:14 -12 2024 -I: pbuilder-time-stamp: 1733664314 +I: removing directory /srv/workspace/pbuilder/663 and its subdirectories +I: Current time: Mon Dec 9 03:29:43 +14 2024 +I: pbuilder-time-stamp: 1733664583