Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 11:35:13.433273817 +0000 +++ b2/build.log 2024-12-20 11:37:44.054434904 +0000 @@ -1,7 +1,7 @@ W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 19 23:33:32 -12 2024 -I: pbuilder-time-stamp: 1734694412 +I: Current time: Fri Jan 23 07:58:25 +14 2026 +I: pbuilder-time-stamp: 1769104705 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,51 +31,83 @@ dpkg-source: info: applying use-new-mpb.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3475427/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1187270/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 22 17:58 /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/1187270/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1187270/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='3475427' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=1187270 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.e88Y8SBG/pbuilderrc_sArO --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.e88Y8SBG/b1 --logfile b1/build.log seqkit_2.8.2+ds-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://192.168.101.4:3128' + 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.e88Y8SBG/pbuilderrc_DQWs --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.e88Y8SBG/b2 --logfile b2/build.log seqkit_2.8.2+ds-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3475427/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1187270/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -324,7 +356,7 @@ Get: 147 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.20-3+b1 [629 kB] -Fetched 123 MB in 1s (144 MB/s) +Fetched 123 MB in 1s (173 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 ... 20084 files and directories currently installed.) @@ -818,8 +850,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Dec 20 11:33:55 UTC 2024. -Universal Time is now: Fri Dec 20 11:33:55 UTC 2024. +Local time is now: Thu Jan 22 17:59:00 UTC 2026. +Universal Time is now: Thu Jan 22 17:59:00 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up golang-github-cespare-xxhash-dev (2.3.0-1) ... @@ -941,7 +973,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/seqkit-2.8.2+ds/ && 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 > ../seqkit_2.8.2+ds-2_source.changes +I: user script /srv/workspace/pbuilder/1187270/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1187270/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/seqkit-2.8.2+ds/ && 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 > ../seqkit_2.8.2+ds-2_source.changes dpkg-buildpackage: info: source package seqkit dpkg-buildpackage: info: source version 2.8.2+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -960,40 +996,38 @@ dh_auto_configure -O--buildsystem=golang -O--builddirectory=build dh_auto_build -O--buildsystem=golang -O--builddirectory=build cd build && go install -trimpath -v -p 12 github.com/shenwei356/seqkit/benchmark github.com/shenwei356/seqkit/seqkit github.com/shenwei356/seqkit/seqkit/cmd -internal/byteorder internal/unsafeheader -internal/godebugs -internal/goos -internal/profilerecord -cmp +internal/byteorder internal/itoa -internal/coverage/rtcov -internal/race +internal/goos internal/goarch internal/goexperiment -internal/runtime/syscall +cmp +internal/coverage/rtcov +internal/godebugs +internal/profilerecord +runtime/internal/math +runtime/internal/sys internal/cpu math/bits +internal/race +internal/runtime/syscall +internal/asan +internal/abi +internal/msan unicode/utf8 sync/atomic +internal/chacha8rand unicode -internal/asan -internal/msan log/internal internal/nettrace -internal/abi image/color -internal/chacha8rand -runtime/internal/math -runtime/internal/sys internal/goversion internal/platform golang.org/x/image/math/f64 -internal/bytealg -internal/runtime/atomic crypto/internal/alias -crypto/subtle math +crypto/subtle crypto/internal/boring/sig encoding unicode/utf16 @@ -1005,117 +1039,119 @@ container/list vendor/golang.org/x/crypto/cryptobyte/asn1 vendor/golang.org/x/crypto/internal/alias +internal/bytealg +internal/runtime/atomic github.com/rivo/uniseg github.com/VividCortex/ewma -internal/runtime/exithook internal/stringslite +internal/runtime/exithook +runtime github.com/klauspost/compress github.com/shenwei356/util/math github.com/vbauerster/mpb/internal -runtime internal/reflectlite iter -internal/weak sync -maps +internal/weak slices +maps internal/bisect -errors -internal/singleflight -sort internal/testlog +internal/singleflight runtime/cgo -internal/oserror +errors +sort +internal/godebug strconv io +internal/oserror path vendor/golang.org/x/net/dns/dnsmessage math/rand/v2 gonum.org/v1/plot/palette crypto/internal/edwards25519/field crypto/internal/nistec/fiat -internal/godebug syscall -reflect strings bytes -math/rand +crypto/cipher hash -crypto/rc4 +github.com/biogo/biogo/feat internal/saferio container/heap internal/concurrent -crypto/internal/randutil -crypto/cipher +reflect +unique +regexp/syntax crypto hash/crc32 -unique -hash/adler32 -hash/crc64 -crypto/internal/edwards25519 -github.com/biogo/biogo/feat bufio -regexp/syntax -crypto/md5 go/build/constraint -html +hash/adler32 +crypto/rc4 +crypto/md5 crypto/internal/boring +math/rand +html +crypto/sha1 github.com/dsnet/compress/internal/errors -crypto/des -image net/netip -crypto/sha1 -github.com/dsnet/compress +crypto/internal/randutil crypto/sha256 +image +github.com/dsnet/compress +hash/crc64 crypto/aes +crypto/des crypto/sha512 +crypto/internal/edwards25519 crypto/hmac vendor/golang.org/x/text/transform +vendor/golang.org/x/crypto/hkdf net/http/internal/ascii github.com/twotwotwo/sorts -vendor/golang.org/x/crypto/hkdf -regexp github.com/shenwei356/util/randutil +regexp time internal/syscall/unix internal/syscall/execenv +github.com/twotwotwo/sorts/sortutil +github.com/shenwei356/bio/util image/internal/imageutil image/draw image/jpeg -github.com/twotwotwo/sorts/sortutil -github.com/shenwei356/bio/util +golang.org/x/image/draw github.com/shenwei356/natsort github.com/acarl005/stripansi -golang.org/x/image/draw -internal/poll io/fs +internal/poll context -internal/fmtsort -encoding/binary internal/filepathlite embed crypto/internal/nistec os +internal/fmtsort +encoding/binary +golang.org/x/sys/unix encoding/base64 -golang.org/x/image/ccitt -github.com/klauspost/compress/internal/snapref github.com/cespare/xxhash -vendor/golang.org/x/crypto/internal/poly1305 -golang.org/x/sys/unix +github.com/klauspost/compress/internal/snapref vendor/golang.org/x/crypto/chacha20 +vendor/golang.org/x/crypto/internal/poly1305 index/suffixarray +golang.org/x/image/ccitt encoding/pem vendor/golang.org/x/crypto/chacha20poly1305 -github.com/shenwei356/bwt crypto/ecdh +github.com/shenwei356/bwt fmt +net +path/filepath +internal/lazyregexp io/ioutil vendor/golang.org/x/sys/cpu -github.com/mattn/go-runewidth os/signal -path/filepath -internal/lazyregexp -net +github.com/mattn/go-runewidth os/exec vendor/golang.org/x/crypto/sha3 internal/goroot @@ -1135,81 +1171,77 @@ encoding/json github.com/golang/freetype/raster golang.org/x/image/font -encoding/xml -go/scanner golang.org/x/image/font/basicfont github.com/biogo/biogo/seq +encoding/xml compress/lzw +go/scanner runtime/debug -go/ast -image/gif -compress/gzip github.com/biogo/biogo/io/seqio github.com/biogo/biogo/seq/linear -github.com/biogo/biogo/io/seqio/fasta -github.com/mattn/go-isatty github.com/biogo/biogo/align -github.com/biogo/hts/bgzf -golang.org/x/term +compress/gzip github.com/golang/freetype/truetype -github.com/mattn/go-colorable -gonum.org/v1/plot/vg/fonts +github.com/biogo/biogo/io/seqio/fasta +go/ast +github.com/biogo/hts/bgzf compress/zlib github.com/shenwei356/seqkit/benchmark -github.com/biogo/hts/bgzf/index +gonum.org/v1/plot/vg/fonts image/png -golang.org/x/crypto/ssh/terminal +github.com/biogo/hts/bgzf/index github.com/biogo/hts/internal +github.com/biogo/hts/sam golang.org/x/image/tiff +image/gif github.com/ajstarks/svgo -github.com/biogo/hts/sam math/big +github.com/biogo/hts/bam github.com/dsnet/compress/internal/prefix -github.com/fsnotify/fsnotify/internal -github.com/fogleman/gg github.com/iafan/cwalk github.com/klauspost/compress/fse -github.com/fsnotify/fsnotify +github.com/mattn/go-isatty +golang.org/x/term +github.com/fsnotify/fsnotify/internal +golang.org/x/crypto/ssh/terminal github.com/klauspost/compress/flate github.com/logrusorgru/aurora -github.com/pkg/errors +github.com/mattn/go-colorable +github.com/fsnotify/fsnotify github.com/dsnet/compress/bzip2 +go/doc +go/internal/typeparams +go/parser +github.com/pkg/errors github.com/ulikunitz/xz/internal/xlog -vendor/golang.org/x/text/unicode/bidi github.com/klauspost/compress/huff0 +vendor/golang.org/x/text/unicode/bidi +github.com/ulikunitz/xz/lzma +github.com/fogleman/gg vendor/golang.org/x/text/unicode/norm vendor/golang.org/x/net/http2/hpack -github.com/ulikunitz/xz/lzma -go/doc -go/internal/typeparams -go/parser +mime github.com/jung-kurt/gofpdf vendor/golang.org/x/text/secure/bidirule -mime mime/quotedprintable -github.com/biogo/hts/bam net/http/internal os/user github.com/shenwei356/util/byteutil -vendor/golang.org/x/net/idna -github.com/shenwei356/bio/seq -github.com/ulikunitz/xz +go/build github.com/edsrzf/mmap-go +github.com/shenwei356/bio/seq github.com/shenwei356/bwt/fmi +github.com/shenwei356/bio/seqio/fai github.com/shenwei356/util/pathutil -github.com/klauspost/pgzip +vendor/golang.org/x/net/idna github.com/shenwei356/util/stringutil gopkg.in/yaml.v2 encoding/csv -flag -text/template/parse -github.com/vbauerster/mpb/cwriter -github.com/vbauerster/mpb/decor -github.com/shenwei356/bio/seqio/fai -go/build +github.com/klauspost/pgzip github.com/cznic/sortutil github.com/dustin/go-humanize crypto/rand +github.com/ulikunitz/xz crypto/elliptic crypto/internal/bigmod crypto/internal/boring/bbig @@ -1219,35 +1251,39 @@ crypto/internal/hpke crypto/internal/mlkem768 crypto/dsa +gonum.org/v1/plot/vg crypto/rsa github.com/shenwei356/stable -github.com/vbauerster/mpb -text/template -gonum.org/v1/plot/vg -vendor/golang.org/x/crypto/cryptobyte -crypto/x509/pkix +flag +text/template/parse gonum.org/v1/plot/vg/vgeps gonum.org/v1/plot/vg/vgimg gonum.org/v1/plot/vg/vgsvg gonum.org/v1/plot/tools/bezier +github.com/vbauerster/mpb/cwriter +github.com/vbauerster/mpb/decor +vendor/golang.org/x/crypto/cryptobyte +crypto/x509/pkix +github.com/vbauerster/mpb crypto/ecdsa -github.com/smallfish/simpleyaml +text/template gonum.org/v1/plot/vg/vgpdf gonum.org/v1/plot/vg/draw +github.com/smallfish/simpleyaml gonum.org/v1/plot +gonum.org/v1/plot/plotter log/syslog +crypto/x509 net/textproto vendor/golang.org/x/net/http/httpproxy -crypto/x509 github.com/spf13/pflag -gonum.org/v1/plot/plotter github.com/op/go-logging vendor/golang.org/x/net/http/httpguts mime/multipart gonum.org/v1/plot/plotutil -github.com/spf13/cobra -crypto/tls github.com/bsipos/thist +crypto/tls +github.com/spf13/cobra net/http/httptrace net/http github.com/shenwei356/xopen @@ -1298,14 +1334,14 @@ dh_installdeb -O--buildsystem=golang -O--builddirectory=build dh_golang -O--buildsystem=golang -O--builddirectory=build dh_gencontrol -O--buildsystem=golang -O--builddirectory=build -dpkg-gencontrol: warning: Depends field of package seqkit-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package seqkit: substitution variable ${misc:Static-Built-Using} unused, but is defined +dpkg-gencontrol: warning: Depends field of package seqkit-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package seqkit: substitution variable ${misc:Static-Built-Using} unused, but is defined dh_md5sums -O--buildsystem=golang -O--builddirectory=build dh_builddeb -O--buildsystem=golang -O--builddirectory=build -dpkg-deb: building package 'seqkit' in '../seqkit_2.8.2+ds-2_arm64.deb'. -dpkg-deb: building package 'seqkit-examples' in '../seqkit-examples_2.8.2+ds-2_all.deb'. dpkg-deb: building package 'seqkit-dbgsym' in '../seqkit-dbgsym_2.8.2+ds-2_arm64.deb'. +dpkg-deb: building package 'seqkit-examples' in '../seqkit-examples_2.8.2+ds-2_all.deb'. +dpkg-deb: building package 'seqkit' in '../seqkit_2.8.2+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../seqkit_2.8.2+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../seqkit_2.8.2+ds-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1313,12 +1349,14 @@ 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/1187270/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1187270/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/3475427 and its subdirectories -I: Current time: Thu Dec 19 23:35:12 -12 2024 -I: pbuilder-time-stamp: 1734694512 +I: removing directory /srv/workspace/pbuilder/1187270 and its subdirectories +I: Current time: Fri Jan 23 08:00:42 +14 2026 +I: pbuilder-time-stamp: 1769104842