Diff of the two buildlogs: -- --- b1/build.log 2025-01-11 17:55:02.691620238 +0000 +++ b2/build.log 2025-01-11 18:01:40.933370083 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 11 05:53:19 -12 2025 -I: pbuilder-time-stamp: 1736617999 +I: Current time: Sat Feb 14 14:18:07 +14 2026 +I: pbuilder-time-stamp: 1771028287 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/1507591/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3125919/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Feb 14 00:18 /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/3125919/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3125919/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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3300cf09d7264f03a27c338be898b982' - 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='1507591' - PS1='# ' - PS2='> ' + INVOCATION_ID=adadd034c6cd42c5a2d02ae2e54b568e + 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=3125919 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.ouySAX3V/pbuilderrc_oMRB --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ouySAX3V/b1 --logfile b1/build.log seqkit_2.9.0+ds-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - 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.ouySAX3V/pbuilderrc_g2GM --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ouySAX3V/b2 --logfile b2/build.log seqkit_2.9.0+ds-1.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/1507591/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3125919/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -326,7 +358,7 @@ Get: 153 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] -Fetched 125 MB in 1s (204 MB/s) +Fetched 125 MB in 3s (40.7 MB/s) Preconfiguring packages ... 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 ... 19968 files and directories currently installed.) @@ -837,8 +869,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jan 11 17:53:48 UTC 2025. -Universal Time is now: Sat Jan 11 17:53:48 UTC 2025. +Local time is now: Sat Feb 14 00:20:07 UTC 2026. +Universal Time is now: Sat Feb 14 00:20:07 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up golang-github-cespare-xxhash-dev (2.3.0-1) ... @@ -967,7 +999,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/seqkit-2.9.0+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_2.9.0+ds-1_source.changes +I: user script /srv/workspace/pbuilder/3125919/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3125919/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/seqkit-2.9.0+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_2.9.0+ds-1_source.changes dpkg-buildpackage: info: source package seqkit dpkg-buildpackage: info: source version 2.9.0+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -987,58 +1023,58 @@ 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/goarch -internal/godebugs -internal/itoa -cmp -internal/profilerecord internal/coverage/rtcov +internal/itoa internal/byteorder +internal/godebugs internal/unsafeheader -internal/goexperiment internal/goos -internal/cpu +internal/profilerecord runtime/internal/math -internal/runtime/syscall +cmp +internal/cpu internal/race -internal/abi +internal/goexperiment math/bits -unicode/utf8 +internal/chacha8rand +internal/abi sync/atomic unicode -runtime/internal/sys +internal/runtime/syscall internal/asan +runtime/internal/sys internal/msan +unicode/utf8 log/internal -internal/chacha8rand internal/nettrace image/color -math -internal/bytealg internal/goversion -internal/runtime/atomic internal/platform +math golang.org/x/image/math/f64 crypto/internal/alias crypto/subtle crypto/internal/boring/sig encoding unicode/utf16 -github.com/dsnet/compress/internal github.com/dsnet/compress/bzip2/internal/sais image/color/palette +github.com/dsnet/compress/internal github.com/elliotwutingfeng/asciiset github.com/ulikunitz/xz/internal/hash +internal/bytealg container/list -internal/runtime/exithook vendor/golang.org/x/crypto/cryptobyte/asn1 vendor/golang.org/x/crypto/internal/alias -github.com/VividCortex/ewma +internal/runtime/atomic github.com/rivo/uniseg +github.com/VividCortex/ewma +internal/runtime/exithook internal/stringslite -runtime github.com/klauspost/compress github.com/shenwei356/util/math github.com/vbauerster/mpb/internal +runtime internal/reflectlite iter sync @@ -1046,107 +1082,108 @@ slices maps internal/bisect -internal/singleflight internal/testlog +internal/singleflight runtime/cgo errors sort strconv io internal/oserror -internal/godebug path vendor/golang.org/x/net/dns/dnsmessage math/rand/v2 gonum.org/v1/plot/palette -strings -syscall -internal/concurrent crypto/internal/nistec/fiat -bytes -hash crypto/internal/edwards25519/field -hash/crc32 -container/heap -internal/saferio -unique +internal/godebug +syscall reflect +strings +math/rand +hash +crypto/rc4 +internal/saferio +bytes +internal/concurrent +container/heap crypto +hash/crc32 hash/adler32 -crypto/rc4 -crypto/md5 -math/rand +unique crypto/internal/randutil hash/crc64 crypto/internal/edwards25519 -vendor/golang.org/x/text/transform -crypto/cipher +crypto/md5 +github.com/shenwei356/util/randutil net/netip github.com/biogo/biogo/feat -bufio regexp/syntax go/build/constraint html -crypto/internal/boring github.com/dsnet/compress/internal/errors -crypto/sha1 -crypto/sha256 -crypto/aes -crypto/des -crypto/sha512 -image -github.com/dsnet/compress -crypto/hmac net/http/internal/ascii +bufio +crypto/cipher +vendor/golang.org/x/text/transform github.com/twotwotwo/sorts -github.com/shenwei356/util/randutil -vendor/golang.org/x/crypto/hkdf +image github.com/twotwotwo/sorts/sortutil github.com/shenwei356/bio/util -regexp +github.com/dsnet/compress time -internal/syscall/execenv internal/syscall/unix +internal/syscall/execenv +crypto/internal/boring +crypto/des +crypto/sha1 +crypto/sha256 +crypto/aes +crypto/sha512 +crypto/hmac +regexp +vendor/golang.org/x/crypto/hkdf image/internal/imageutil image/draw image/jpeg -golang.org/x/image/draw github.com/shenwei356/natsort github.com/acarl005/stripansi -context -internal/poll +golang.org/x/image/draw io/fs -internal/fmtsort -encoding/binary +internal/poll +context internal/filepathlite embed crypto/internal/nistec os +internal/fmtsort +encoding/binary +crypto/ecdh golang.org/x/image/ccitt +golang.org/x/sys/unix encoding/base64 github.com/cespare/xxhash github.com/klauspost/compress/internal/snapref -golang.org/x/sys/unix -vendor/golang.org/x/crypto/internal/poly1305 vendor/golang.org/x/crypto/chacha20 +vendor/golang.org/x/crypto/internal/poly1305 index/suffixarray encoding/pem vendor/golang.org/x/crypto/chacha20poly1305 github.com/shenwei356/bwt -crypto/ecdh fmt -internal/lazyregexp path/filepath -os/signal -github.com/mattn/go-runewidth -vendor/golang.org/x/sys/cpu +internal/lazyregexp io/ioutil +vendor/golang.org/x/sys/cpu +github.com/mattn/go-runewidth +os/signal net -vendor/golang.org/x/crypto/sha3 os/exec +vendor/golang.org/x/crypto/sha3 internal/goroot github.com/mitchellh/go-homedir github.com/biogo/biogo/alphabet +internal/buildcfg log encoding/hex text/tabwriter @@ -1155,123 +1192,122 @@ golang.org/x/image/math/fixed go/token go/doc/comment -internal/buildcfg golang.org/x/image/tiff/lzw encoding/gob github.com/golang/freetype/raster golang.org/x/image/font -go/scanner -golang.org/x/image/font/basicfont encoding/json +golang.org/x/image/font/basicfont encoding/xml -github.com/golang/freetype/truetype +go/scanner github.com/biogo/biogo/seq -compress/lzw -go/ast -runtime/debug -math/big -image/gif github.com/biogo/biogo/io/seqio github.com/biogo/biogo/seq/linear -github.com/biogo/biogo/io/seqio/fasta github.com/biogo/biogo/align +github.com/biogo/biogo/io/seqio/fasta +github.com/golang/freetype/truetype +compress/lzw +go/ast +runtime/debug compress/gzip -github.com/mattn/go-isatty -golang.org/x/term github.com/shenwei356/seqkit/benchmark +compress/zlib +image/png github.com/biogo/hts/bgzf -github.com/mattn/go-colorable gonum.org/v1/plot/vg/fonts -compress/zlib +github.com/biogo/hts/bgzf/index +github.com/biogo/hts/internal +golang.org/x/image/tiff +github.com/mattn/go-isatty +golang.org/x/term +github.com/biogo/hts/sam +image/gif +github.com/mattn/go-colorable +math/big +github.com/fogleman/gg golang.org/x/crypto/ssh/terminal github.com/ajstarks/svgo github.com/dsnet/compress/internal/prefix -github.com/biogo/hts/bgzf/index -image/png -golang.org/x/image/tiff -go/doc -go/internal/typeparams -github.com/biogo/hts/internal github.com/fsnotify/fsnotify/internal -go/parser github.com/iafan/cwalk -github.com/biogo/hts/sam github.com/klauspost/compress/fse +github.com/jung-kurt/gofpdf github.com/klauspost/compress/flate -github.com/logrusorgru/aurora -github.com/dsnet/compress/bzip2 github.com/fsnotify/fsnotify -github.com/fogleman/gg -github.com/jung-kurt/gofpdf -github.com/pkg/errors -github.com/cznic/sortutil -github.com/dustin/go-humanize -crypto/rand +github.com/logrusorgru/aurora +go/doc +go/internal/typeparams github.com/klauspost/compress/huff0 +go/parser +github.com/pkg/errors +github.com/dsnet/compress/bzip2 github.com/ulikunitz/xz/internal/xlog -crypto/elliptic -crypto/internal/bigmod +vendor/golang.org/x/text/unicode/bidi github.com/biogo/hts/bam -crypto/internal/boring/bbig -encoding/asn1 github.com/ulikunitz/xz/lzma -crypto/ed25519 -crypto/internal/hpke -crypto/internal/mlkem768 -go/build -crypto/dsa -github.com/klauspost/compress/zstd -crypto/rsa -vendor/golang.org/x/text/unicode/bidi vendor/golang.org/x/text/unicode/norm vendor/golang.org/x/net/http2/hpack mime mime/quotedprintable -vendor/golang.org/x/crypto/cryptobyte -crypto/x509/pkix -vendor/golang.org/x/text/secure/bidirule net/http/internal -github.com/klauspost/pgzip os/user -github.com/ulikunitz/xz github.com/shenwei356/util/byteutil github.com/edsrzf/mmap-go -github.com/shenwei356/bwt/fmi github.com/shenwei356/bio/seq -crypto/ecdsa +vendor/golang.org/x/text/secure/bidirule github.com/shenwei356/bio/seqio/fai -github.com/shenwei356/stable +github.com/shenwei356/bwt/fmi github.com/shenwei356/util/pathutil -gonum.org/v1/plot/vg +go/build github.com/shenwei356/util/stringutil gopkg.in/yaml.v2 encoding/csv +github.com/ulikunitz/xz flag text/template/parse +github.com/vbauerster/mpb/cwriter +github.com/cznic/sortutil +github.com/dustin/go-humanize +crypto/rand +github.com/klauspost/pgzip +crypto/elliptic +github.com/klauspost/compress/zstd +crypto/internal/bigmod +crypto/internal/boring/bbig +encoding/asn1 +crypto/ed25519 +crypto/internal/hpke +gonum.org/v1/plot/vg +crypto/internal/mlkem768 +crypto/dsa vendor/golang.org/x/net/idna +github.com/shenwei356/stable +text/template 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 +crypto/rsa github.com/vbauerster/mpb/decor +vendor/golang.org/x/crypto/cryptobyte +crypto/x509/pkix github.com/vbauerster/mpb -text/template -github.com/smallfish/simpleyaml gonum.org/v1/plot/vg/vgpdf +crypto/ecdsa gonum.org/v1/plot/vg/draw +github.com/smallfish/simpleyaml gonum.org/v1/plot gonum.org/v1/plot/plotter +gonum.org/v1/plot/plotutil log/syslog -github.com/spf13/pflag +crypto/x509 net/textproto vendor/golang.org/x/net/http/httpproxy -crypto/x509 +github.com/spf13/pflag github.com/op/go-logging +github.com/bsipos/thist vendor/golang.org/x/net/http/httpguts mime/multipart -gonum.org/v1/plot/plotutil -github.com/bsipos/thist crypto/tls github.com/spf13/cobra net/http/httptrace @@ -1324,8 +1360,8 @@ 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 @@ -1339,12 +1375,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3125919/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3125919/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/1507591 and its subdirectories -I: Current time: Sat Jan 11 05:55:01 -12 2025 -I: pbuilder-time-stamp: 1736618101 +I: removing directory /srv/workspace/pbuilder/3125919 and its subdirectories +I: Current time: Sat Feb 14 14:24:39 +14 2026 +I: pbuilder-time-stamp: 1771028679