Diff of the two buildlogs: -- --- b1/build.log 2024-03-24 13:46:37.734455760 +0000 +++ b2/build.log 2024-03-24 13:50:16.061140286 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 24 01:42:46 -12 2024 -I: pbuilder-time-stamp: 1711287766 +I: Current time: Mon Mar 25 03:46:46 +14 2024 +I: pbuilder-time-stamp: 1711288006 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/12189/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19592/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 Mar 24 13:46 /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/19592/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19592/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=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='f7f231fb5d954baba18d8eb93d863a9d' - 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='12189' - PS1='# ' - PS2='> ' + INVOCATION_ID=50dbb1eacc66438ebc6f2e5880db54bc + 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=19592 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.Zt7kuCDG/pbuilderrc_JN1f --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.Zt7kuCDG/b1 --logfile b1/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+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.Zt7kuCDG/pbuilderrc_sIzx --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.Zt7kuCDG/b2 --logfile b2/build.log bitseq_0.7.5+dfsg-6.dsc' + SUDO_GID=110 + SUDO_UID=103 + 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 virt32a 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 22 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/12189/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 23 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/19592/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -184,7 +216,7 @@ Get: 56 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.2-1 [653 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.24.2-2 [4016 kB] -Fetched 47.1 MB in 1s (49.8 MB/s) +Fetched 47.1 MB in 2s (26.6 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 ... 19577 files and directories currently installed.) @@ -383,8 +415,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Mar 24 13:43:35 UTC 2024. -Universal Time is now: Sun Mar 24 13:43:35 UTC 2024. +Local time is now: Sun Mar 24 13:47:26 UTC 2024. +Universal Time is now: Sun Mar 24 13:47:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -441,7 +473,11 @@ 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/19592/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/19592/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 @@ -451,7 +487,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 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' @@ -462,12 +498,45 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.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 . -ffunction-sections -fdata-sections -c FileHeader.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 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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.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++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from misc.cpp:1: @@ -505,7 +574,6 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | 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 -ffunction-sections -fdata-sections -c MyTimer.cpp In file included from /usr/include/c++/13/vector:72, from ArgumentParser.h:6, from ArgumentParser.cpp:5: @@ -513,18 +581,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector tokenizeD(const std::string&, const std::string&)' at ArgumentParser.cpp:23:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector tokenizeD(const std::string&, const std::string&)' at ArgumentParser.cpp:28:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/13/bits/stl_algo.h:4861:18, inlined from 'void ns_misc::computeCI(double, std::vector*, double*, double*)' at misc.cpp:89:8: @@ -545,6 +601,19 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector tokenizeD(const std::string&, const std::string&)' at ArgumentParser.cpp:23:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector tokenizeD(const std::string&, const std::string&)' at ArgumentParser.cpp:28:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 /usr/include/c++/13/vector:72, from ArgumentParser.h:6, from misc.h:6, @@ -579,39 +648,6 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | 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 -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++/13/vector:72, from TranscriptInfo.h:4, from TranscriptInfo.cpp:4: @@ -619,7 +655,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _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 . -c CollapsedSampler.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = transcriptT; _Alloc = std::allocator]', inlined from 'bool TranscriptInfo::setInfo(std::vector >, std::vector >, std::vector)' at TranscriptInfo.cpp:54:28: @@ -631,6 +666,7 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp In file included from CollapsedSampler.h:3, from CollapsedSampler.cpp:5: @@ -641,6 +677,7 @@ 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 -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp In file included from GibbsSampler.h:2, from GibbsSampler.cpp:5: Sampler.h: In member function 'pairD Sampler::getSumNorms() const': @@ -652,7 +689,7 @@ 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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp In file included from /usr/include/c++/13/vector:72, from TagAlignments.h:5, from TagAlignments.cpp:3: @@ -666,20 +703,20 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp In file included from /usr/include/c++/13/vector:72, from Sampler.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Sampler::appendFile()' at Sampler.cpp:123:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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 -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 In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from lowess.cpp:17: @@ -700,6 +737,7 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | 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 -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++/13/bits/stl_algo.h:4861:18, 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: @@ -720,7 +758,8 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | 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 -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 -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 +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 In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from TranscriptExpression.cpp:1: @@ -732,7 +771,6 @@ /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ -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 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, @@ -766,8 +804,7 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | 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 -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 In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/random/detail/polynomial.hpp:18, from /usr/include/boost/random/mersenne_twister.hpp:32, @@ -783,12 +820,10 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator::param_type*, std::vector::param_type> >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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))){ @@ -801,19 +836,8 @@ ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] 687 | (! frag->second->core.flag & BAM_FREVERSE))){ | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from TranscriptSequence.h:6, - from TranscriptSequence.cpp:6: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = trSeqInfoT; _Alloc = std::allocator]', - inlined from 'bool TranscriptSequence::readSequence(std::string, refFormatT)' at TranscriptSequence.cpp:74:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.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 -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 In file included from /usr/include/c++/13/map:62, from ReadDistribution.h:5, from ReadDistribution.cpp:7: @@ -821,7 +845,7 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _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 -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++/13/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: @@ -841,7 +865,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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++/13/vector:72, + from TranscriptSequence.h:6, + from TranscriptSequence.cpp:6: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = trSeqInfoT; _Alloc = std::allocator]', + inlined from 'bool TranscriptSequence::readSequence(std::string, refFormatT)' at TranscriptSequence.cpp:74:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 -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++/13/vector:72, from ReadDistribution.h:4: /usr/include/c++/13/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]': @@ -949,15 +987,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 . -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 -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 estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar 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++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from estimateExpression.cpp:1: @@ -978,6 +1015,26 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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++/13/bits/stl_algo.h:4861:18, + inlined from 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)' at estimateExpression.cpp:394:14: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)' at estimateExpression.cpp:394:14: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from estimateHyperPar.cpp:6: @@ -1014,27 +1071,7 @@ /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _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 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 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++/13/bits/stl_algo.h:4861:18, - inlined from 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)' at estimateExpression.cpp:394:14: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)' at estimateExpression.cpp:394:14: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | 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 -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 file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ns_params::paramT; _Alloc = std::allocator]', inlined from 'int estimateHyperPar(int*, char**)' at estimateHyperPar.cpp:271:32: @@ -1076,7 +1113,6 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 file included from /usr/include/c++/13/vector:72, from ArgumentParser.h:6, from parseAlignment.cpp:7: @@ -1171,11 +1207,11 @@ dh_makeshlibs -a dh_shlibdeps -a 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/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/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/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/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/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/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/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/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/getVariance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb @@ -1191,12 +1227,14 @@ 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/19592/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19592/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/12189 and its subdirectories -I: Current time: Sun Mar 24 01:46:15 -12 2024 -I: pbuilder-time-stamp: 1711287975 +I: removing directory /srv/workspace/pbuilder/19592 and its subdirectories +I: Current time: Mon Mar 25 03:49:31 +14 2024 +I: pbuilder-time-stamp: 1711288171