Diff of the two buildlogs: -- --- b1/build.log 2024-04-11 17:42:17.078501828 +0000 +++ b2/build.log 2024-04-11 17:54:55.862142645 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 11 05:34:37 -12 2024 -I: pbuilder-time-stamp: 1712856877 +I: Current time: Fri Apr 12 07:42:46 +14 2024 +I: pbuilder-time-stamp: 1712857366 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying fix_syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21681/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30046/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4pro0. +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 Apr 11 17:43 /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/30046/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30046/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='226c44d9db0c4656bf58b9e027a90b85' - 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='21681' - PS1='# ' - PS2='> ' + INVOCATION_ID=207c09ed6f424de39241d1b83d0248c7 + 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=30046 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.0kXMf4DF/pbuilderrc_gYxc --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.0kXMf4DF/b1 --logfile b1/build.log clustalo_1.2.4-8.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.0kXMf4DF/pbuilderrc_BKoY --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.0kXMf4DF/b2 --logfile b2/build.log clustalo_1.2.4-8.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 virt64a 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-armmp #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 11 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21681/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 9 11:26 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/30046/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -232,7 +264,7 @@ Get: 110 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf sphinx-common all 7.2.6-6 [702 kB] -Fetched 88.0 MB in 2s (40.8 MB/s) +Fetched 88.0 MB in 6s (14.8 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 ... 19635 files and directories currently installed.) @@ -699,7 +731,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/clustalo-1.2.4/ && 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 > ../clustalo_1.2.4-8_source.changes +I: user script /srv/workspace/pbuilder/30046/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/30046/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/clustalo-1.2.4/ && 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 > ../clustalo_1.2.4-8_source.changes dpkg-buildpackage: info: source package clustalo dpkg-buildpackage: info: source version 1.2.4-8 dpkg-buildpackage: info: source distribution unstable @@ -938,7 +974,7 @@ # nothing to do here make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4' dh_auto_build -Nlibclustalo-doc - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' Making all in src make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' @@ -946,7 +982,7 @@ make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' Making all in hhalign make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' -/bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp +/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:70: hhhmm-C.h: In member function 'void HMM::UseSecStrucDependentGapPenalties()': @@ -957,36 +993,42 @@ 1734 | unsigned char iis[par.maxResLen]; // inside-integer array | ^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1 -/bin/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libhhalign.la hhalign.lo -largtable2 -lm +/bin/sh ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libhhalign.la hhalign.lo -largtable2 -lm libtool: link: ar cr .libs/libhhalign.a .libs/hhalign.o libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign' Making all in squid make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid' -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o a2m.lo a2m.c -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alignio.lo alignio.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o a2m.lo a2m.c +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alignio.lo alignio.c +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal.lo clustal.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1 -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal.lo clustal.c -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cluster.lo cluster.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -fPIC -DPIC -o .libs/clustal.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1 +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cluster.lo cluster.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1 -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1 +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eps.lo 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-o util.lo util.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1 +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o util.lo util.c +/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -fPIC -DPIC -o .libs/tree.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1 -/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c weights.c -fPIC -DPIC -o .libs/weights.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1 -/bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1 +/bin/sh ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm libtool: link: ar cr .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o libtool: link: ranlib .libs/libclustal.a libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" ) @@ -1163,14 +1199,14 @@ make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mymain.o mymain.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o clustal-omega.c: In function 'PrintLongVersion': clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__); | ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/arm-linux-gnueabihf clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/arm-linux-gnueabihf clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/squid/.libs/libsquid.a") @@ -1179,7 +1215,7 @@ libtool: link: ranlib .libs/libclustalo.a libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/arm-linux-gnueabihf/libargtable2.so -lm -fopenmp /usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile': ./src/clustal-omega.c:393:(.text+0x4e0): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' @@ -1193,7 +1229,7 @@ debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4' dh_auto_test -a - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4' Making check in src make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' @@ -1274,14 +1310,14 @@ make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src' /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' - /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' + /bin/sh ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: chmod 644 /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: ranlib /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c clustalo '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c clustalo /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin/clustalo /usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' @@ -1415,8 +1451,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-8_armhf.deb'. -dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_armhf.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-8_armhf.deb'. +dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_armhf.deb'. dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-8_all.deb'. dpkg-genbuildinfo --build=binary -O../clustalo_1.2.4-8_armhf.buildinfo dpkg-genchanges --build=binary -O../clustalo_1.2.4-8_armhf.changes @@ -1425,12 +1461,14 @@ 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/30046/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30046/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/21681 and its subdirectories -I: Current time: Thu Apr 11 05:42:12 -12 2024 -I: pbuilder-time-stamp: 1712857332 +I: removing directory /srv/workspace/pbuilder/30046 and its subdirectories +I: Current time: Fri Apr 12 07:54:50 +14 2024 +I: pbuilder-time-stamp: 1712858090