Diff of the two buildlogs: -- --- b1/build.log 2024-05-06 23:16:28.103902514 +0000 +++ b2/build.log 2024-05-06 23:18:09.043598724 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 11:14:45 -12 2024 -I: pbuilder-time-stamp: 1715037285 +I: Current time: Tue May 7 13:16:32 +14 2024 +I: pbuilder-time-stamp: 1715037392 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 fix_FTBFS_boost1.67.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2354642/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/259410/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 6 23:16 /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/259410/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/259410/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='0ae560cce4e24db9a363cf9329696a06' - 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='2354642' - PS1='# ' - PS2='> ' + INVOCATION_ID=161d9585a3be47bba1035c7244298d2a + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=259410 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.44hwbP0b/pbuilderrc_yf51 --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.44hwbP0b/b1 --logfile b1/build.log progressivemauve_1.2.0+4713+dfsg-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.44hwbP0b/pbuilderrc_hu0x --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.44hwbP0b/b2 --logfile b2/build.log progressivemauve_1.2.0+4713+dfsg-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 6 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2354642/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/259410/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -190,7 +222,7 @@ Get: 56 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] -Fetched 45.3 MB in 1s (73.3 MB/s) +Fetched 45.3 MB in 0s (154 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19743 files and directories currently installed.) @@ -437,7 +469,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/progressivemauve-1.2.0+4713+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 > ../progressivemauve_1.2.0+4713+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/259410/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/259410/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/progressivemauve-1.2.0+4713+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 > ../progressivemauve_1.2.0+4713+dfsg-5_source.changes dpkg-buildpackage: info: source package progressivemauve dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -577,15 +613,7 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from toMultiFastA.cpp:2: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -In file included from /usr/include/c++/13/ext/hash_map:60, - from /usr/include/libMems/HomologyHMM/dptables.h:43, - from /usr/include/libMems/HomologyHMM/homology.h:27, - from /usr/include/libMems/Islands.h:25, - from addUnalignedIntervals.cpp:2: + from getAlignmentWindows.cpp:14: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -608,7 +636,15 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from getAlignmentWindows.cpp:14: + from addUnalignedIntervals.cpp:2: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +In file included from /usr/include/c++/13/ext/hash_map:60, + from /usr/include/libMems/HomologyHMM/dptables.h:43, + from /usr/include/libMems/HomologyHMM/homology.h:27, + from /usr/include/libMems/Islands.h:25, + from toMultiFastA.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -647,7 +683,6 @@ 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o alignmentProjector.o alignmentProjector.cpp -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -657,7 +692,10 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o projectAndStrip.o projectAndStrip.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o randomGeneSample.o randomGeneSample.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -666,8 +704,7 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o randomGeneSample.o randomGeneSample.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o getOrthologList.o getOrthologList.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -676,8 +713,6 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o getOrthologList.o getOrthologList.cpp -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bbFilter.o bbFilter.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -686,6 +721,8 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bbFilter.o bbFilter.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bbAnalyze.o bbAnalyze.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -695,11 +732,6 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bbAnalyze.o bbAnalyze.cpp -projectAndStrip.cpp: In function 'int main(int, char**)': -projectAndStrip.cpp:65:81: warning: conversion from 'long unsigned int' to '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 65 | not_ids[seq_ids[i]] = (std::numeric_limits::max)(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -709,6 +741,10 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +projectAndStrip.cpp: In function 'int main(int, char**)': +projectAndStrip.cpp:65:81: warning: conversion from 'long unsigned int' to '__gnu_cxx::__alloc_traits, unsigned int>::value_type' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 65 | not_ids[seq_ids[i]] = (std::numeric_limits::max)(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o backbone_global_to_local.o backbone_global_to_local.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o xmfa2maf.o xmfa2maf.cpp In file included from /usr/include/c++/13/ext/hash_map:60, @@ -745,15 +781,15 @@ g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE @@ -819,12 +855,14 @@ 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/259410/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/259410/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/2354642 and its subdirectories -I: Current time: Mon May 6 11:16:27 -12 2024 -I: pbuilder-time-stamp: 1715037387 +I: removing directory /srv/workspace/pbuilder/259410 and its subdirectories +I: Current time: Tue May 7 13:18:07 +14 2024 +I: pbuilder-time-stamp: 1715037487