Diff of the two buildlogs: -- --- b1/build.log 2023-04-15 00:10:35.816731351 +0000 +++ b2/build.log 2023-04-15 00:12:20.180097091 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 14 12:09:41 -12 2023 -I: pbuilder-time-stamp: 1681517381 +I: Current time: Fri May 17 20:33:39 +14 2024 +I: pbuilder-time-stamp: 1715927619 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz] I: copying [./hmmer2_2.3.2+dfsg-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Dec 11 04:03:58 2022 -12 +gpgv: Signature made Mon Dec 12 06:03:58 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,11 +33,20 @@ dpkg-source: info: applying add-runstatedir-option.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14145/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4876/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/4876/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4876/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -47,38 +56,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='14145' + PPID='4876' PS1='# ' PS2='> ' 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.36Tv3JcS/pbuilderrc_9cDF --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.36Tv3JcS/b1 --logfile b1/build.log hmmer2_2.3.2+dfsg-8.dsc' + 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.36Tv3JcS/pbuilderrc_enyA --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.36Tv3JcS/b2 --logfile b2/build.log --extrapackages usrmerge hmmer2_2.3.2+dfsg-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink10-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 14 00:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14145/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 16 07:13 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4876/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -163,7 +172,7 @@ Get: 37 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 rename all 2.01-1 [21.0 kB] -Fetched 18.7 MB in 1s (32.4 MB/s) +Fetched 18.7 MB in 1s (30.2 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 ... 19616 files and directories currently installed.) @@ -334,8 +343,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/hmmer2-2.3.2+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 > ../hmmer2_2.3.2+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/4876/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/4876/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/hmmer2-2.3.2+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 > ../hmmer2_2.3.2+dfsg-8_source.changes dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -445,14 +463,14 @@ gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c histogram.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmio.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c mathsupport.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c masks.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c misc.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c modelmakers.c histogram.c: In function 'ExtremeValueSetHistogram': histogram.c:725:23: warning: implicit declaration of function 'IncompleteGamma' [-Wimplicit-function-declaration] 725 | h->chip = (float) IncompleteGamma((double)(nbins-1-ndegrees)/2., | ^~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c mathsupport.c +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c masks.c +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c misc.c +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c modelmakers.c mathsupport.c: In function 'Logp_cvec': mathsupport.c:229:15: warning: implicit declaration of function 'Gammln' [-Wimplicit-function-declaration] 229 | lnp += Gammln(alpha[x] + cvec[x]); @@ -468,12 +486,12 @@ gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmconvert.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmemit.c -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmfetch.c hmmcalibrate.c: In function 'workpool_start': hmmcalibrate.c:646:3: warning: implicit declaration of function 'pthread_setconcurrency' [-Wimplicit-function-declaration] 646 | pthread_setconcurrency(num_threads+1); | ^~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmemit.c +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmpfam.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmsearch.c @@ -531,12 +549,12 @@ gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `pkg-config --libs libsquid` -lm -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `pkg-config --libs libsquid` -lm +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `pkg-config --libs libsquid` -lm -gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `pkg-config --libs libsquid` -lm +gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' @@ -678,8 +696,8 @@ System information: -Fri Apr 14 12:10:23 -12 2023 -Linux codethink10-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux +Fri May 17 20:35:01 +14 2024 +Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux make[3]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi @@ -742,14 +760,14 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-8_arm64.deb'. -dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-8_arm64.deb'. +dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-8_arm64.deb'. dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-8_all.deb'. +dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -757,12 +775,14 @@ 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/4876/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4876/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/14145 and its subdirectories -I: Current time: Fri Apr 14 12:10:34 -12 2023 -I: pbuilder-time-stamp: 1681517434 +I: removing directory /srv/workspace/pbuilder/4876 and its subdirectories +I: Current time: Fri May 17 20:35:18 +14 2024 +I: pbuilder-time-stamp: 1715927718