Diff of the two buildlogs: -- --- b1/build.log 2023-04-11 22:45:06.453075146 +0000 +++ b2/build.log 2023-04-11 22:50:31.918219042 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 11 10:39:57 -12 2023 -I: pbuilder-time-stamp: 1681252797 +I: Current time: Tue May 14 19:08:10 +14 2024 +I: pbuilder-time-stamp: 1715663290 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 [./minimap2_2.24+dfsg.orig.tar.xz] I: copying [./minimap2_2.24+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 30 07:57:09 2022 -12 +gpgv: Signature made Thu Dec 1 09:57:09 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,11 +34,20 @@ dpkg-source: info: applying reenable-simde.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1395/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1888/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/1888/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1888/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' @@ -48,38 +57,38 @@ 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='1395' + PPID='1888' 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.9NyaYsfM/pbuilderrc_UMQp --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.9NyaYsfM/b1 --logfile b1/build.log minimap2_2.24+dfsg-3.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.9NyaYsfM/pbuilderrc_lDTk --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.9NyaYsfM/b2 --logfile b2/build.log --extrapackages usrmerge minimap2_2.24+dfsg-3.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 10 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1395/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 13 06:50 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1888/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -424,7 +433,7 @@ Get: 283 http://deb.debian.org/debian bookworm/main arm64 texlive-pictures all 2022.20230122-2 [15.8 MB] Get: 284 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-extra all 2022.20230122-2 [19.2 MB] Get: 285 http://deb.debian.org/debian bookworm/main arm64 texlive-science all 2022.20230122-2 [3723 kB] -Fetched 318 MB in 6s (53.8 MB/s) +Fetched 318 MB in 6s (57.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libargon2-1:arm64. (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.) @@ -1613,8 +1622,17 @@ 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/minimap2-2.24+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 > ../minimap2_2.24+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1888/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/1888/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/minimap2-2.24+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 > ../minimap2_2.24+dfsg-3_source.changes dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.24+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1659,8 +1677,6 @@ cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 options.c -o options.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 index.c -o index.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 lchain.c -o lchain.o -cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 align.c -o align.o -cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 hit.c -o hit.o index.c: In function 'mm_idx_load': index.c:519:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 519 | fread(&l, 1, 1, fp); @@ -1686,6 +1702,8 @@ index.c:553:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 553 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 align.c -o align.o +cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 hit.c -o hit.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 seed.c -o seed.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 map.c -o map.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 format.c -o format.o @@ -1695,14 +1713,14 @@ cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o -ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined - 6 | #define SIMDE_ENABLE_NATIVE_ALIASES - | -: note: this is the location of the previous definition ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition +ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined + 6 | #define SIMDE_ENABLE_NATIVE_ALIASES + | +: note: this is the location of the previous definition cc -c -g -O2 -ffile-prefix-map=/build/minimap2-2.24+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=2 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES @@ -3020,32 +3038,32 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/minimap2-2.24+dfsg' debian/test_script -[M::mm_idx_gen::0.003*1.55] collected minimizers -[M::mm_idx_gen::0.005*2.09] sorted minimizers -[M::main::0.005*2.08] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.005*1.95] mid_occ = 10 +[M::mm_idx_gen::0.003*1.57] collected minimizers +[M::mm_idx_gen::0.005*2.13] sorted minimizers +[M::main::0.005*2.11] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.005*1.99] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.006*1.86] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 -[M::worker_pipeline::0.030*1.18] mapped 1 sequences +[M::mm_idx_stat::0.006*1.90] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::worker_pipeline::0.030*1.19] mapped 1 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa -[M::main] Real time: 0.032 sec; CPU: 0.037 sec; Peak RSS: 0.004 GB -[M::mm_idx_gen::0.003*1.54] collected minimizers -[M::mm_idx_gen::0.004*2.06] sorted minimizers -[M::main::0.008*1.60] loaded/built the index for 1 target sequence(s) +[M::main] Real time: 0.032 sec; CPU: 0.038 sec; Peak RSS: 0.004 GB +[M::mm_idx_gen::0.003*1.57] collected minimizers +[M::mm_idx_gen::0.005*2.08] sorted minimizers +[M::main::0.008*1.59] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.008*1.56] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::mm_idx_stat::0.009*1.56] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa -[M::main] Real time: 0.010 sec; CPU: 0.015 sec; Peak RSS: 0.003 GB -[M::main::0.008*1.11] loaded/built the index for 1 target sequence(s) +[M::main] Real time: 0.011 sec; CPU: 0.016 sec; Peak RSS: 0.003 GB +[M::main::0.008*1.12] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.008*1.11] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.009*1.10] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 -[M::worker_pipeline::0.033*1.04] mapped 1 sequences +[M::worker_pipeline::0.033*1.05] mapped 1 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa -[M::main] Real time: 0.035 sec; CPU: 0.037 sec; Peak RSS: 0.005 GB +[M::main] Real time: 0.036 sec; CPU: 0.037 sec; Peak RSS: 0.005 GB rm test.sam make[1]: Leaving directory '/build/minimap2-2.24+dfsg' create-stamp debian/debhelper-build-stamp @@ -3131,12 +3149,14 @@ 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/1888/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1888/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/1395 and its subdirectories -I: Current time: Tue Apr 11 10:45:05 -12 2023 -I: pbuilder-time-stamp: 1681253105 +I: removing directory /srv/workspace/pbuilder/1888 and its subdirectories +I: Current time: Tue May 14 19:13:30 +14 2024 +I: pbuilder-time-stamp: 1715663610