Diff of the two buildlogs: -- --- b1/build.log 2024-01-17 13:50:43.937220603 +0000 +++ b2/build.log 2024-01-17 13:52:10.613953218 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 18 08:12:52 -12 2025 -I: pbuilder-time-stamp: 1739909572 +I: Current time: Thu Jan 18 03:50:47 +14 2024 +I: pbuilder-time-stamp: 1705499447 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: copying [./golang-github-biogo-biogo_1.0.3-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.yswBRN0S/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.oNQsrxaX/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 5 13:01:30 2020 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" @@ -29,51 +29,82 @@ dpkg-source: info: unpacking golang-github-biogo-biogo_1.0.3-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/52354/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Jan 17 13:50 /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/1370/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1370/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='6cf89c46288049518087e2cc32b3f799' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='52354' - PS1='# ' - PS2='> ' + INVOCATION_ID=28f732ac2b0941b6b42d93c31fc34bf1 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-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=1370 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.YLlfPi08/pbuilderrc_D7P0 --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YLlfPi08/b1 --logfile b1/build.log golang-github-biogo-biogo_1.0.3-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.YLlfPi08/pbuilderrc_lwyY --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YLlfPi08/b2 --logfile b2/build.log golang-github-biogo-biogo_1.0.3-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash @@ -133,7 +164,7 @@ -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 8 15:47 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 17 13:50 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su @@ -159,7 +190,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/52354/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +283,7 @@ Get: 43 http://deb.debian.org/debian bullseye/main i386 golang-github-biogo-store-dev all 0.0~git20200525.8c94ae1-2 [34.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 golang-github-ulikunitz-xz-dev all 0.5.6-2 [352 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 golang-github-biogo-hts-dev all 1.1.0+dfsg1-2 [292 kB] -Fetched 79.5 MB in 3s (25.8 MB/s) +Fetched 79.5 MB in 38s (2108 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17763 files and directories currently installed.) @@ -448,7 +479,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/golang-github-biogo-biogo-1.0.3/ && 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 > ../golang-github-biogo-biogo_1.0.3-1_source.changes +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/golang-github-biogo-biogo-1.0.3/ && 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 > ../golang-github-biogo-biogo_1.0.3-1_source.changes dpkg-buildpackage: info: source package golang-github-biogo-biogo dpkg-buildpackage: info: source version 1.0.3-1 dpkg-buildpackage: info: source distribution unstable @@ -466,24 +501,24 @@ dh_autoreconf -O--builddirectory=_build -O--buildsystem=golang dh_auto_configure -O--builddirectory=_build -O--buildsystem=golang dh_auto_build -O--builddirectory=_build -O--buildsystem=golang - cd _build && go install -trimpath -v -p 16 github.com/biogo/biogo github.com/biogo/biogo/align github.com/biogo/biogo/align/matrix github.com/biogo/biogo/align/pals github.com/biogo/biogo/align/pals/dp github.com/biogo/biogo/align/pals/filter github.com/biogo/biogo/alphabet github.com/biogo/biogo/complexity github.com/biogo/biogo/concurrent github.com/biogo/biogo/errors github.com/biogo/biogo/feat github.com/biogo/biogo/feat/gene github.com/biogo/biogo/feat/genome github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/mouse/mm10 github.com/biogo/biogo/index/kmerindex github.com/biogo/biogo/io/featio github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/io/featio/gff github.com/biogo/biogo/io/seqio github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/io/seqio/fai github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/io/seqio/fastq github.com/biogo/biogo/morass github.com/biogo/biogo/pwm github.com/biogo/biogo/seq github.com/biogo/biogo/seq/alignment github.com/biogo/biogo/seq/linear github.com/biogo/biogo/seq/multi github.com/biogo/biogo/seq/quality github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/util -internal/unsafeheader + cd _build && go install -trimpath -v -p 7 github.com/biogo/biogo github.com/biogo/biogo/align github.com/biogo/biogo/align/matrix github.com/biogo/biogo/align/pals github.com/biogo/biogo/align/pals/dp github.com/biogo/biogo/align/pals/filter github.com/biogo/biogo/alphabet github.com/biogo/biogo/complexity github.com/biogo/biogo/concurrent github.com/biogo/biogo/errors github.com/biogo/biogo/feat github.com/biogo/biogo/feat/gene github.com/biogo/biogo/feat/genome github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/mouse/mm10 github.com/biogo/biogo/index/kmerindex github.com/biogo/biogo/io/featio github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/io/featio/gff github.com/biogo/biogo/io/seqio github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/io/seqio/fai github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/io/seqio/fastq github.com/biogo/biogo/morass github.com/biogo/biogo/pwm github.com/biogo/biogo/seq github.com/biogo/biogo/seq/alignment github.com/biogo/biogo/seq/linear github.com/biogo/biogo/seq/multi github.com/biogo/biogo/seq/quality github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/util github.com/biogo/biogo +internal/unsafeheader unicode/utf8 -github.com/biogo/store/llrb -internal/race -image/color -encoding -internal/cpu math/bits +internal/cpu +runtime/internal/atomic +internal/race runtime/internal/sys sync/atomic unicode -runtime/internal/atomic -math +encoding +github.com/biogo/store/llrb +image/color internal/bytealg -runtime/internal/math internal/testlog +runtime/internal/math +math runtime internal/reflectlite sync @@ -496,9 +531,9 @@ strconv syscall container/heap +strings hash bytes -strings text/tabwriter hash/adler32 reflect @@ -509,53 +544,53 @@ internal/syscall/unix internal/syscall/execenv time -internal/fmtsort -encoding/binary internal/poll os +internal/fmtsort +encoding/binary path/filepath fmt io/ioutil github.com/biogo/biogo/alphabet encoding/csv -github.com/biogo/biogo/util -github.com/biogo/graph log -github.com/biogo/biogo/errors +github.com/biogo/biogo/util encoding/gob +github.com/biogo/graph compress/flate +github.com/biogo/biogo/errors github.com/biogo/biogo/concurrent github.com/biogo/hts/fai github.com/biogo/biogo/seq github.com/biogo/biogo/align/matrix github.com/biogo/biogo/io/seqio/fai +github.com/biogo/biogo/align github.com/biogo/biogo/io/seqio -github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/feat/genome -github.com/biogo/biogo/seq/quality -github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/seq/linear -github.com/biogo/biogo/align compress/zlib +github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/io/seqio/fasta -github.com/biogo/biogo/io/seqio/fastq -github.com/biogo/biogo/pwm github.com/biogo/biogo/complexity -github.com/biogo/biogo/feat/genome/cow/bt7 -github.com/biogo/biogo/feat/genome/mouse/mm10 -github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/index/kmerindex -github.com/biogo/biogo/seq/multi +github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/io/featio/gff -github.com/biogo/biogo/seq/alignment +github.com/biogo/biogo/feat/genome/mouse/mm10 +github.com/biogo/biogo/io/featio/bed +github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/morass +github.com/biogo/biogo/io/seqio/fastq +github.com/biogo/biogo/seq/alignment +github.com/biogo/biogo/seq/multi github.com/biogo/biogo/align/pals/filter -github.com/biogo/biogo/io/seqio/alignio +github.com/biogo/biogo/pwm +github.com/biogo/biogo/seq/quality github.com/biogo/biogo/align/pals/dp +github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/align/pals dh_auto_test -O--builddirectory=_build -O--buildsystem=golang - cd _build && go test -vet=off -v -p 16 github.com/biogo/biogo github.com/biogo/biogo/align github.com/biogo/biogo/align/matrix github.com/biogo/biogo/align/pals github.com/biogo/biogo/align/pals/dp github.com/biogo/biogo/align/pals/filter github.com/biogo/biogo/alphabet github.com/biogo/biogo/complexity github.com/biogo/biogo/concurrent github.com/biogo/biogo/errors github.com/biogo/biogo/feat github.com/biogo/biogo/feat/gene github.com/biogo/biogo/feat/genome github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/mouse/mm10 github.com/biogo/biogo/index/kmerindex github.com/biogo/biogo/io/featio github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/io/featio/gff github.com/biogo/biogo/io/seqio github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/io/seqio/fai github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/io/seqio/fastq github.com/biogo/biogo/morass github.com/biogo/biogo/pwm github.com/biogo/biogo/seq github.com/biogo/biogo/seq/alignment github.com/biogo/biogo/seq/linear github.com/biogo/biogo/seq/multi github.com/biogo/biogo/seq/quality github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/util + cd _build && go test -vet=off -v -p 7 github.com/biogo/biogo github.com/biogo/biogo/align github.com/biogo/biogo/align/matrix github.com/biogo/biogo/align/pals github.com/biogo/biogo/align/pals/dp github.com/biogo/biogo/align/pals/filter github.com/biogo/biogo/alphabet github.com/biogo/biogo/complexity github.com/biogo/biogo/concurrent github.com/biogo/biogo/errors github.com/biogo/biogo/feat github.com/biogo/biogo/feat/gene github.com/biogo/biogo/feat/genome github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/mouse/mm10 github.com/biogo/biogo/index/kmerindex github.com/biogo/biogo/io/featio github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/io/featio/gff github.com/biogo/biogo/io/seqio github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/io/seqio/fai github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/io/seqio/fastq github.com/biogo/biogo/morass github.com/biogo/biogo/pwm github.com/biogo/biogo/seq github.com/biogo/biogo/seq/alignment github.com/biogo/biogo/seq/linear github.com/biogo/biogo/seq/multi github.com/biogo/biogo/seq/quality github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/util ? github.com/biogo/biogo [no test files] === RUN Test OK: 2 passed @@ -575,37 +610,37 @@ === RUN ExampleSWAffine_Align --- PASS: ExampleSWAffine_Align (0.00s) PASS -ok github.com/biogo/biogo/align 0.015s +ok github.com/biogo/biogo/align 0.012s ? github.com/biogo/biogo/align/matrix [no test files] === RUN Test OK: 5 passed ---- PASS: Test (0.00s) +--- PASS: Test (0.01s) PASS -ok github.com/biogo/biogo/align/pals 0.018s +ok github.com/biogo/biogo/align/pals 0.017s === RUN Test OK: 1 passed ---- PASS: Test (0.02s) +--- PASS: Test (0.01s) PASS -ok github.com/biogo/biogo/align/pals/dp 0.033s +ok github.com/biogo/biogo/align/pals/dp 0.013s === RUN Test OK: 1 passed ---- PASS: Test (0.03s) +--- PASS: Test (0.02s) PASS -ok github.com/biogo/biogo/align/pals/filter 0.049s +ok github.com/biogo/biogo/align/pals/filter 0.028s === RUN Test OK: 10 passed ---- PASS: Test (0.00s) +--- PASS: Test (0.03s) === RUN Example_allValid --- PASS: Example_allValid (0.00s) === RUN Example_complement --- PASS: Example_complement (0.00s) PASS -ok github.com/biogo/biogo/alphabet 0.031s +ok github.com/biogo/biogo/alphabet 0.051s === RUN Test OK: 4 passed ---- PASS: Test (0.88s) +--- PASS: Test (0.92s) PASS -ok github.com/biogo/biogo/complexity 0.899s +ok github.com/biogo/biogo/complexity 0.938s === RUN Test OK: 1 passed --- PASS: Test (0.00s) @@ -616,86 +651,161 @@ === RUN ExampleLazily --- PASS: ExampleLazily (0.00s) PASS -ok github.com/biogo/biogo/concurrent 1.030s +ok github.com/biogo/biogo/concurrent 1.021s === RUN Test OK: 4 passed ---- PASS: Test (0.02s) +--- PASS: Test (0.01s) PASS -ok github.com/biogo/biogo/errors 0.024s +ok github.com/biogo/biogo/errors 0.015s === RUN Test OK: 6 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/feat 0.018s +ok github.com/biogo/biogo/feat 0.008s === RUN Test OK: 4 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/feat/gene 0.036s +ok github.com/biogo/biogo/feat/gene 0.011s ? github.com/biogo/biogo/feat/genome [no test files] ? github.com/biogo/biogo/feat/genome/cow/bt7 [no test files] ? github.com/biogo/biogo/feat/genome/drosophila/dm3 [no test files] ? github.com/biogo/biogo/feat/genome/human/hg19 [no test files] ? github.com/biogo/biogo/feat/genome/mouse/mm10 [no test files] === RUN Test -OK: 5 passed ---- PASS: Test (9.62s) -PASS -ok github.com/biogo/biogo/index/kmerindex 9.723s +runtime: out of memory: cannot allocate 1077936128-byte block (1731854336 in use) +fatal error: out of memory + +runtime stack: +runtime.throw(0x81f6f0e, 0xd) + /usr/lib/go-1.15/src/runtime/panic.go:1116 +0x6a +runtime.largeAlloc(0x40000004, 0x8cf0101, 0x8cf3000) + /usr/lib/go-1.15/src/runtime/malloc.go:1179 +0x15d +runtime.mallocgc.func1() + /usr/lib/go-1.15/src/runtime/malloc.go:1071 +0x39 +runtime.systemstack(0x8c00700) + /usr/lib/go-1.15/src/runtime/asm_386.s:391 +0x53 +runtime.mstart() + /usr/lib/go-1.15/src/runtime/proc.go:1116 + +goroutine 7 [running]: +runtime.systemstack_switch() + /usr/lib/go-1.15/src/runtime/asm_386.s:352 fp=0x8cf3ccc sp=0x8cf3cc8 pc=0x80a6ea0 +runtime.mallocgc(0x40000004, 0x81cacc0, 0x8200e01, 0x81aa3e7) + /usr/lib/go-1.15/src/runtime/malloc.go:1070 +0x6bc fp=0x8cf3d1c sp=0x8cf3ccc pc=0x805333c +runtime.makeslice(0x81cacc0, 0x10000001, 0x10000001, 0x8cf3d48) + /usr/lib/go-1.15/src/runtime/slice.go:98 +0x4f fp=0x8cf3d30 sp=0x8cf3d1c pc=0x808dccf +github.com/biogo/biogo/index/kmerindex.New(0xe, 0x8c99540, 0x5, 0x81c9940, 0x8310948) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/github.com/biogo/biogo/index/kmerindex/kmerindex.go:71 +0x93 fp=0x8cf3d58 sp=0x8cf3d30 pc=0x81a9203 +github.com/biogo/biogo/index/kmerindex.(*S).TestKmerIndexCheck(0x8c9c268, 0x8cec0a0) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/github.com/biogo/biogo/index/kmerindex/kmerindex_test.go:43 +0x4a fp=0x8cf3dbc sp=0x8cf3d58 pc=0x81aa75a +runtime.call16(0x8c10020, 0x8d52048, 0x8c0e040, 0x8, 0x8) + /usr/lib/go-1.15/src/runtime/asm_386.s:561 +0x30 fp=0x8cf3dd0 sp=0x8cf3dbc pc=0x80a71b0 +reflect.Value.call(0x81ef7c0, 0x8c9c268, 0x8213, 0x81f4d2a, 0x4, 0x9488788, 0x1, 0x1, 0x831a3c0, 0x6ce00351, ...) + /usr/lib/go-1.15/src/reflect/value.go:476 +0x6ed fp=0x8cf3eec sp=0x8cf3dd0 pc=0x80f22ed +reflect.Value.Call(0x81ef7c0, 0x8c9c268, 0x8213, 0x9488788, 0x1, 0x1, 0x0, 0x0, 0x0) + /usr/lib/go-1.15/src/reflect/value.go:337 +0x7a fp=0x8cf3f28 sp=0x8cf3eec pc=0x80f1a5a +gopkg.in/check%2ev1.(*suiteRunner).forkTest.func1(0x8cec0a0) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:781 +0x57b fp=0x8cf3fbc sp=0x8cf3f28 pc=0x81a4cfb +gopkg.in/check%2ev1.(*suiteRunner).forkCall.func1(0x8ce60a0, 0x8cec0a0, 0x8d4b750) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:675 +0x83 fp=0x8cf3fe0 sp=0x8cf3fbc pc=0x81a45e3 +runtime.goexit() + /usr/lib/go-1.15/src/runtime/asm_386.s:1333 +0x1 fp=0x8cf3fe4 sp=0x8cf3fe0 pc=0x80a83e1 +created by gopkg.in/check%2ev1.(*suiteRunner).forkCall + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:672 +0x17e + +goroutine 1 [chan receive]: +testing.(*T).Run(0x8c82a80, 0x81f4d7e, 0x4, 0x8200ee4, 0x402) + /usr/lib/go-1.15/src/testing/testing.go:1169 +0x230 +testing.runTests.func1(0x8c829a0) + /usr/lib/go-1.15/src/testing/testing.go:1439 +0x5a +testing.tRunner(0x8c829a0, 0x8c93eec) + /usr/lib/go-1.15/src/testing/testing.go:1123 +0xc4 +testing.runTests(0x8c96060, 0x8315d60, 0x1, 0x1, 0x18dbd86e, 0xc1621557, 0xb2dccb52, 0x8b, 0x831a3c0, 0x0) + /usr/lib/go-1.15/src/testing/testing.go:1437 +0x25a +testing.(*M).Run(0x8ce6000, 0x0) + /usr/lib/go-1.15/src/testing/testing.go:1345 +0x178 +main.main() + _testmain.go:43 +0x104 + +goroutine 20 [chan receive]: +gopkg.in/check%2ev1.(*suiteRunner).runTest(...) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:819 +gopkg.in/check%2ev1.(*suiteRunner).run(0x8ce60a0, 0x8c9c268) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:624 +0xf7 +gopkg.in/check%2ev1.Run(0x81ef7c0, 0x8c9c268, 0x8c3c778, 0x82b74e0) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/run.go:92 +0x3d +gopkg.in/check%2ev1.RunAll(0x8cf2f78, 0x0) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/run.go:84 +0x80 +gopkg.in/check%2ev1.TestingT(0x8c82a80) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/run.go:72 +0x2d9 +github.com/biogo/biogo/index/kmerindex.Test(0x8c82a80) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/github.com/biogo/biogo/index/kmerindex/kmerindex_test.go:20 +0x21 +testing.tRunner(0x8c82a80, 0x8200ee4) + /usr/lib/go-1.15/src/testing/testing.go:1123 +0xc4 +created by testing.(*T).Run + /usr/lib/go-1.15/src/testing/testing.go:1168 +0x211 + +goroutine 21 [select]: +gopkg.in/check%2ev1.(*resultTracker)._loopRoutine(0x8ce6050) + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:470 +0x95 +created by gopkg.in/check%2ev1.(*resultTracker).start + /build/reproducible-path/golang-github-biogo-biogo-1.0.3/_build/src/gopkg.in/check.v1/check.go:450 +0x33 +FAIL github.com/biogo/biogo/index/kmerindex 1.810s === RUN Test OK: 2 passed ---- PASS: Test (0.01s) +--- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/io/featio 0.039s +ok github.com/biogo/biogo/io/featio 0.011s === RUN Test OK: 4 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/io/featio/bed 0.026s +ok github.com/biogo/biogo/io/featio/bed 0.017s === RUN Test OK: 5 passed ---- PASS: Test (0.00s) +--- PASS: Test (0.03s) PASS -ok github.com/biogo/biogo/io/featio/gff 0.023s +ok github.com/biogo/biogo/io/featio/gff 0.042s === RUN TestSeqio --- PASS: TestSeqio (0.00s) === RUN Test OK: 3 passed ---- PASS: Test (0.00s) +--- PASS: Test (0.01s) PASS ok github.com/biogo/biogo/io/seqio 0.018s === RUN Test OK: 2 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/io/seqio/alignio 0.040s +ok github.com/biogo/biogo/io/seqio/alignio 0.011s === RUN Test OK: 1 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/io/seqio/fai 0.017s +ok github.com/biogo/biogo/io/seqio/fai 0.021s === RUN Test OK: 2 passed --- PASS: Test (0.01s) === RUN ExampleReader --- PASS: ExampleReader (0.00s) PASS -ok github.com/biogo/biogo/io/seqio/fasta 0.018s +ok github.com/biogo/biogo/io/seqio/fasta 0.020s === RUN Test OK: 2 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/io/seqio/fastq 0.026s +ok github.com/biogo/biogo/io/seqio/fastq 0.010s === RUN Test OK: 7 passed ---- PASS: Test (3.38s) +--- PASS: Test (2.55s) PASS -ok github.com/biogo/biogo/morass 3.415s +ok github.com/biogo/biogo/morass 2.559s ? github.com/biogo/biogo/pwm [no test files] === RUN TestSeq --- PASS: TestSeq (0.00s) PASS -ok github.com/biogo/biogo/seq 0.040s +ok github.com/biogo/biogo/seq 0.008s === RUN Test OK: 1 passed --- PASS: Test (0.00s) @@ -736,7 +846,7 @@ === RUN ExampleQSeq_truncate --- PASS: ExampleQSeq_truncate (0.00s) PASS -ok github.com/biogo/biogo/seq/alignment 0.018s +ok github.com/biogo/biogo/seq/alignment 0.011s === RUN Test OK: 1 passed --- PASS: Test (0.00s) @@ -763,7 +873,7 @@ === RUN ExampleSeq_compose --- PASS: ExampleSeq_compose (0.00s) PASS -ok github.com/biogo/biogo/seq/linear 0.008s +ok github.com/biogo/biogo/seq/linear 0.011s === RUN Test OK: 1 passed --- PASS: Test (0.00s) @@ -796,12 +906,12 @@ === RUN ExampleSet_Len --- PASS: ExampleSet_Len (0.00s) PASS -ok github.com/biogo/biogo/seq/multi 0.018s +ok github.com/biogo/biogo/seq/multi 0.011s === RUN Test OK: 1 passed --- PASS: Test (0.00s) PASS -ok github.com/biogo/biogo/seq/quality 0.007s +ok github.com/biogo/biogo/seq/quality 0.014s === RUN Test OK: 4 passed --- PASS: Test (0.00s) @@ -814,44 +924,28 @@ === RUN ExampleStitch --- PASS: ExampleStitch (0.00s) PASS -ok github.com/biogo/biogo/seq/sequtils 0.011s +ok github.com/biogo/biogo/seq/sequtils 0.008s === RUN Test OK: 11 passed --- PASS: Test (0.01s) PASS -ok github.com/biogo/biogo/util 0.013s - create-stamp debian/debhelper-build-stamp - dh_testroot -O--builddirectory=_build -O--buildsystem=golang - dh_prep -O--builddirectory=_build -O--buildsystem=golang - dh_auto_install -O--builddirectory=_build -O--buildsystem=golang - dh_installdocs -O--builddirectory=_build -O--buildsystem=golang - dh_installchangelogs -O--builddirectory=_build -O--buildsystem=golang - dh_installsystemduser -O--builddirectory=_build -O--buildsystem=golang - dh_perl -O--builddirectory=_build -O--buildsystem=golang - dh_link -O--builddirectory=_build -O--buildsystem=golang - dh_strip_nondeterminism -O--builddirectory=_build -O--buildsystem=golang - dh_compress -O--builddirectory=_build -O--buildsystem=golang - dh_fixperms -O--builddirectory=_build -O--buildsystem=golang - dh_missing -O--builddirectory=_build -O--buildsystem=golang - dh_installdeb -O--builddirectory=_build -O--buildsystem=golang - dh_golang -O--builddirectory=_build -O--buildsystem=golang - dh_gencontrol -O--builddirectory=_build -O--buildsystem=golang - dh_md5sums -O--builddirectory=_build -O--buildsystem=golang - dh_builddeb -O--builddirectory=_build -O--buildsystem=golang -dpkg-deb: building package 'golang-github-biogo-biogo-dev' in '../golang-github-biogo-biogo-dev_1.0.3-1_all.deb'. - dpkg-genbuildinfo --build=binary - dpkg-genchanges --build=binary >../golang-github-biogo-biogo_1.0.3-1_i386.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: including full source code in upload +ok github.com/biogo/biogo/util 0.019s +FAIL +dh_auto_test: error: cd _build && go test -vet=off -v -p 7 github.com/biogo/biogo github.com/biogo/biogo/align github.com/biogo/biogo/align/matrix github.com/biogo/biogo/align/pals github.com/biogo/biogo/align/pals/dp github.com/biogo/biogo/align/pals/filter github.com/biogo/biogo/alphabet github.com/biogo/biogo/complexity github.com/biogo/biogo/concurrent github.com/biogo/biogo/errors github.com/biogo/biogo/feat github.com/biogo/biogo/feat/gene github.com/biogo/biogo/feat/genome github.com/biogo/biogo/feat/genome/cow/bt7 github.com/biogo/biogo/feat/genome/drosophila/dm3 github.com/biogo/biogo/feat/genome/human/hg19 github.com/biogo/biogo/feat/genome/mouse/mm10 github.com/biogo/biogo/index/kmerindex github.com/biogo/biogo/io/featio github.com/biogo/biogo/io/featio/bed github.com/biogo/biogo/io/featio/gff github.com/biogo/biogo/io/seqio github.com/biogo/biogo/io/seqio/alignio github.com/biogo/biogo/io/seqio/fai github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/io/seqio/fastq github.com/biogo/biogo/morass github.com/biogo/biogo/pwm github.com/biogo/biogo/seq github.com/biogo/biogo/seq/alignment github.com/biogo/biogo/seq/linear github.com/biogo/biogo/seq/multi github.com/biogo/biogo/seq/quality github.com/biogo/biogo/seq/sequtils github.com/biogo/biogo/util returned exit code 1 +make: *** [debian/rules:4: binary] Error 25 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Wed Jan 17 13:52:08 UTC 2024 +Filesystem Size Used Avail Use% Mounted on +tmpfs 4.0G 0 4.0G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/1370/tmp/hooks/C01_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/52354 and its subdirectories -I: Current time: Tue Feb 18 08:13:43 -12 2025 -I: pbuilder-time-stamp: 1739909623 +I: removing directory /srv/workspace/pbuilder/1370 and its subdirectories