Diff of the two buildlogs: -- --- b1/build.log 2024-04-05 12:46:17.175627183 +0000 +++ b2/build.log 2024-04-05 12:56:31.217511904 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 5 00:39:10 -12 2024 -I: pbuilder-time-stamp: 1712320750 +I: Current time: Sat Apr 6 02:46:43 +14 2024 +I: pbuilder-time-stamp: 1712321203 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying ld_as_needed I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27576/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8061/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 5 12:46 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/8061/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8061/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='d737e0815b694b74ba0f21b7a490e121' - 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='27576' - PS1='# ' - PS2='> ' + INVOCATION_ID=1a2bd815c5af4085a3263f9724ad89bc + 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=8061 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.bwPamMOD/pbuilderrc_jrfV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bwPamMOD/b1 --logfile b1/build.log reapr_1.0.18+dfsg-6.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bwPamMOD/pbuilderrc_TcuN --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bwPamMOD/b2 --logfile b2/build.log reapr_1.0.18+dfsg-6.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32c 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 2 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27576/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 5 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/8061/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -294,7 +326,7 @@ Get: 155 http://deb.debian.org/debian unstable/main armhf smalt armhf 0.7.6-13 [98.2 kB] Get: 156 http://deb.debian.org/debian unstable/main armhf snpomatic armhf 1.0-7 [69.1 kB] Get: 157 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.19+ds-1.1+b1 [410 kB] -Fetched 97.2 MB in 3s (33.1 MB/s) +Fetched 97.2 MB in 4s (27.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package tzdata. (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 ... 19466 files and directories currently installed.) @@ -812,8 +844,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 5 12:40:18 UTC 2024. -Universal Time is now: Fri Apr 5 12:40:18 UTC 2024. +Local time is now: Fri Apr 5 12:48:32 UTC 2024. +Universal Time is now: Fri Apr 5 12:48:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-13) ... @@ -968,7 +1000,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/reapr-1.0.18+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 > ../reapr_1.0.18+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/8061/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/8061/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/reapr-1.0.18+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 > ../reapr_1.0.18+dfsg-6_source.changes dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -1219,7 +1255,7 @@ make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg' mkdir /build/reproducible-path/reapr-1.0.18+dfsg/debian/test ln -s /build/reproducible-path/reapr-1.0.18+dfsg/src/reapr.pl /build/reproducible-path/reapr-1.0.18+dfsg/debian/test/reapr -PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/reapr-1.0.18+dfsg/src:/build/reproducible-path/reapr-1.0.18+dfsg/debian/test /build/reproducible-path/reapr-1.0.18+dfsg/debian/tests/test-example +PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reproducible-path/reapr-1.0.18+dfsg/src:/build/reproducible-path/reapr-1.0.18+dfsg/debian/test /build/reproducible-path/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 @@ -2200,8 +2236,8 @@ foo 994610 C Y + foo 998107 - T + foo 999725 G R + -[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.520.smaltmap.smalt_index foo1.fasta -# Command line: smalt index -k 13 -s 2 out.bam.tmp.520.smaltmap.smalt_index foo1.fasta +[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.15610.smaltmap.smalt_index foo1.fasta +# Command line: smalt index -k 13 -s 2 out.bam.tmp.15610.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... @@ -2224,9 +2260,9 @@ # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... -# smalt: Total elapsed wall clock time: 1 seconds -[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.520.smaltmap.smalt_sample out.bam.tmp.520.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq -# Command line: smalt sample -u 1000 -o out.bam.tmp.520.smaltmap.smalt_sample out.bam.tmp.520.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# smalt: Total elapsed wall clock time: 2 seconds +[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.15610.smaltmap.smalt_sample out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# Command line: smalt sample -u 1000 -o out.bam.tmp.15610.smaltmap.smalt_sample out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... @@ -2245,10 +2281,10 @@ # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds -# smalt: Time spent mapping reads:7 seconds -# smalt: Total elapsed wall clock time: 7 seconds -[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.520.smaltmap.smalt_sample -f samsoft out.bam.tmp.520.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.520.smaltmap.raw.bam -# Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.520.smaltmap.smalt_sample -f samsoft out.bam.tmp.520.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq +# smalt: Time spent mapping reads:14 seconds +# smalt: Total elapsed wall clock time: 14 seconds +[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.15610.smaltmap.smalt_sample -f samsoft out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.15610.smaltmap.raw.bam +# Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.15610.smaltmap.smalt_sample -f samsoft out.bam.tmp.15610.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram @@ -2268,17 +2304,17 @@ # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds -# smalt: Time spent mapping reads:44 seconds -# smalt: Total elapsed wall clock time: 44 seconds -[REAPR smaltmap] Running: samtools sort out.bam.tmp.520.smaltmap.raw.bam -O bam -o out.bam.tmp.520.smaltmap.raw.bam.sort.bam -[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.520.smaltmap.raw.bam.sort.bam out.bam.tmp.520.smaltmap.rmdup.bam +# smalt: Time spent mapping reads:1 minutes and 7 seconds +# smalt: Total elapsed wall clock time: 1 minutes and 7 seconds +[REAPR smaltmap] Running: samtools sort out.bam.tmp.15610.smaltmap.raw.bam -O bam -o out.bam.tmp.15610.smaltmap.raw.bam.sort.bam +[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.15610.smaltmap.raw.bam.sort.bam out.bam.tmp.15610.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' -[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.520.smaltmap.header -[REAPR smaltmap] Running: samtools view -H out.bam.tmp.520.smaltmap.rmdup.bam >> out.bam.tmp.520.smaltmap.header -[REAPR smaltmap] Running: samtools reheader out.bam.tmp.520.smaltmap.header out.bam.tmp.520.smaltmap.rmdup.bam > out.bam +[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.15610.smaltmap.header +[REAPR smaltmap] Running: samtools view -H out.bam.tmp.15610.smaltmap.rmdup.bam >> out.bam.tmp.15610.smaltmap.header +[REAPR smaltmap] Running: samtools reheader out.bam.tmp.15610.smaltmap.header out.bam.tmp.15610.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam -[REAPR smaltmap] Running: rm out.bam.tmp.520.smaltmap.* +[REAPR smaltmap] Running: rm out.bam.tmp.15610.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck @@ -2331,12 +2367,12 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_gapresize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fcdEstimate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_break contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_stats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_score contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_break contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_fcdrate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_gapresize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/task_stats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/reapr/usr/lib/reapr/bam2fcdEstimate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined @@ -2352,12 +2388,14 @@ 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/8061/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8061/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/27576 and its subdirectories -I: Current time: Fri Apr 5 00:46:12 -12 2024 -I: pbuilder-time-stamp: 1712321172 +I: removing directory /srv/workspace/pbuilder/8061 and its subdirectories +I: Current time: Sat Apr 6 02:56:26 +14 2024 +I: pbuilder-time-stamp: 1712321786