Diff of the two buildlogs: -- --- b1/build.log 2023-04-22 09:03:30.422459761 +0000 +++ b2/build.log 2023-04-22 09:06:56.025343722 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 24 03:21:47 -12 2024 -I: pbuilder-time-stamp: 1716564107 +I: Current time: Sat Apr 22 23:03:42 +14 2023 +I: pbuilder-time-stamp: 1682154222 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 [./seqkit_2.3.1+ds.orig.tar.xz] I: copying [./seqkit_2.3.1+ds-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Sep 28 23:36:28 2022 -12 +gpgv: Signature made Fri Sep 30 01:36:28 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,52 +28,84 @@ dpkg-source: info: applying use-upstream-go-logger.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24518/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12863/tmp/hooks/D01_modify_environment starting +debug: Running on codethink12-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 Apr 22 23:03 /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/12863/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12863/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' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + 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='24518' - 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=12863 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.K37zSnqN/pbuilderrc_Av9B --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.K37zSnqN/b1 --logfile b1/build.log seqkit_2.3.1+ds-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.K37zSnqN/pbuilderrc_rdyb --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.K37zSnqN/b2 --logfile b2/build.log --extrapackages usrmerge seqkit_2.3.1+ds-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 21 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/24518/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 22 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/12863/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -277,7 +309,7 @@ Get: 122 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] -Fetched 145 MB in 8s (18.2 MB/s) +Fetched 145 MB in 3s (49.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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.) @@ -787,8 +819,17 @@ 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/seqkit-2.3.1+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_2.3.1+ds-1_source.changes +I: user script /srv/workspace/pbuilder/12863/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/12863/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/seqkit-2.3.1+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_2.3.1+ds-1_source.changes dpkg-buildpackage: info: source package seqkit dpkg-buildpackage: info: source version 2.3.1+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -807,36 +848,36 @@ 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 8 github.com/shenwei356/seqkit/benchmark github.com/shenwei356/seqkit/seqkit github.com/shenwei356/seqkit/seqkit/cmd -internal/goarch -internal/unsafeheader internal/goexperiment internal/goos -internal/itoa -internal/cpu +internal/unsafeheader runtime/internal/syscall +internal/itoa math/bits +internal/goarch +internal/cpu unicode/utf8 +internal/race +sync/atomic internal/abi runtime/internal/math runtime/internal/sys -internal/race -sync/atomic unicode internal/nettrace image/color internal/goversion golang.org/x/image/math/f64 math +runtime/internal/atomic +internal/bytealg crypto/internal/subtle crypto/subtle -internal/bytealg -runtime/internal/atomic crypto/internal/boring/sig encoding unicode/utf16 +image/color/palette container/list vendor/golang.org/x/crypto/cryptobyte/asn1 -image/color/palette vendor/golang.org/x/crypto/internal/subtle github.com/ulikunitz/xz/internal/hash github.com/rivo/uniseg @@ -845,18 +886,18 @@ github.com/shenwei356/util/math internal/reflectlite sync +internal/testlog internal/singleflight math/rand -internal/testlog runtime/cgo github.com/shenwei356/util/randutil errors sort +internal/safefilepath io internal/oserror -internal/safefilepath -path strconv +path vendor/golang.org/x/net/dns/dnsmessage gonum.org/v1/plot/palette syscall @@ -864,42 +905,42 @@ container/heap github.com/shenwei356/bio/util bytes -hash strings +hash text/tabwriter hash/crc32 hash/adler32 -crypto/internal/randutil -hash/crc64 -vendor/golang.org/x/text/transform +crypto reflect +crypto/rc4 github.com/biogo/biogo/feat bufio regexp/syntax -crypto go/build/constraint -crypto/rc4 html +crypto/internal/randutil image +vendor/golang.org/x/text/transform net/http/internal/ascii github.com/twotwotwo/sorts +hash/crc64 internal/syscall/unix time internal/syscall/execenv github.com/twotwotwo/sorts/sortutil +regexp image/internal/imageutil image/draw image/jpeg -regexp golang.org/x/image/draw -internal/poll -io/fs -context github.com/shenwei356/natsort +context +io/fs +internal/poll embed +os internal/fmtsort encoding/binary -os crypto/md5 golang.org/x/image/ccitt crypto/cipher @@ -907,34 +948,26 @@ github.com/cespare/xxhash golang.org/x/sys/unix github.com/klauspost/compress/internal/snapref +fmt +internal/godebug +path/filepath +internal/lazyregexp +io/ioutil +internal/intern crypto/internal/nistec crypto/internal/edwards25519/field +net/netip encoding/pem crypto/internal/boring -crypto/des crypto/sha1 +os/exec crypto/aes +crypto/des crypto/sha512 crypto/internal/edwards25519 +net crypto/hmac -fmt -internal/godebug -path/filepath -internal/intern -internal/lazyregexp -io/ioutil -net/netip crypto/sha256 -vendor/golang.org/x/crypto/chacha20 -os/exec -vendor/golang.org/x/crypto/internal/poly1305 -vendor/golang.org/x/crypto/curve25519/internal/field -vendor/golang.org/x/crypto/hkdf -index/suffixarray -github.com/mattn/go-runewidth -vendor/golang.org/x/crypto/chacha20poly1305 -os/signal -net internal/goroot github.com/mitchellh/go-homedir github.com/biogo/biogo/alphabet @@ -944,118 +977,126 @@ net/url golang.org/x/image/math/fixed go/token -github.com/golang/freetype/raster -golang.org/x/image/font go/doc/comment +github.com/golang/freetype/raster github.com/biogo/biogo/seq +golang.org/x/image/font go/scanner -internal/buildcfg -compress/gzip github.com/biogo/biogo/io/seqio github.com/biogo/biogo/seq/linear -github.com/biogo/biogo/align github.com/biogo/biogo/io/seqio/fasta -github.com/biogo/hts/bgzf -github.com/golang/freetype/truetype +github.com/biogo/biogo/align +compress/gzip go/ast +github.com/golang/freetype/truetype github.com/shenwei356/seqkit/benchmark +internal/buildcfg +github.com/biogo/hts/bgzf github.com/mattn/go-isatty github.com/mattn/go-colorable github.com/biogo/hts/bgzf/index gonum.org/v1/plot/vg/fonts golang.org/x/term -github.com/biogo/hts/internal golang.org/x/image/font/basicfont +github.com/biogo/hts/internal compress/zlib -golang.org/x/crypto/ssh/terminal -github.com/biogo/hts/sam golang.org/x/image/tiff/lzw -image/png -golang.org/x/image/tiff encoding/gob +github.com/biogo/hts/sam +encoding/json +image/png go/doc +golang.org/x/crypto/ssh/terminal go/internal/typeparams go/parser -encoding/json -encoding/xml +golang.org/x/image/tiff github.com/fogleman/gg -github.com/biogo/hts/bam +encoding/xml compress/lzw image/gif +github.com/biogo/hts/bam runtime/debug math/big -go/build github.com/fsnotify/fsnotify github.com/iafan/cwalk github.com/klauspost/compress/fse -github.com/ajstarks/svgo +go/build github.com/klauspost/compress/flate -github.com/jung-kurt/gofpdf github.com/logrusorgru/aurora github.com/pkg/errors +vendor/golang.org/x/crypto/chacha20 github.com/klauspost/compress/huff0 -vendor/golang.org/x/crypto/curve25519 -vendor/golang.org/x/text/unicode/bidi +github.com/jung-kurt/gofpdf +github.com/ajstarks/svgo gonum.org/v1/plot/vg +vendor/golang.org/x/crypto/internal/poly1305 +vendor/golang.org/x/crypto/curve25519/internal/field gonum.org/v1/plot/vg/vgeps gonum.org/v1/plot/vg/vgimg gonum.org/v1/plot/vg/vgsvg gonum.org/v1/plot/tools/bezier -vendor/golang.org/x/text/secure/bidirule -github.com/klauspost/pgzip -vendor/golang.org/x/text/unicode/norm -vendor/golang.org/x/net/http2/hpack -mime +vendor/golang.org/x/crypto/chacha20poly1305 +vendor/golang.org/x/crypto/curve25519 github.com/cznic/sortutil github.com/dustin/go-humanize crypto/rand +github.com/klauspost/pgzip crypto/elliptic crypto/internal/boring/bbig encoding/asn1 -crypto/ed25519 +crypto/dsa github.com/klauspost/compress/zstd +crypto/ed25519 crypto/rsa -crypto/dsa +vendor/golang.org/x/crypto/hkdf +vendor/golang.org/x/text/unicode/bidi +vendor/golang.org/x/text/unicode/norm +vendor/golang.org/x/net/http2/hpack +mime +vendor/golang.org/x/crypto/cryptobyte +crypto/x509/pkix mime/quotedprintable +log/syslog +net/textproto net/http/internal +github.com/op/go-logging +vendor/golang.org/x/text/secure/bidirule os/user +crypto/ecdsa github.com/shenwei356/util/byteutil +mime/multipart +github.com/shenwei356/bio/seq github.com/edsrzf/mmap-go +crypto/x509 github.com/shenwei356/bio/seqio/fai -vendor/golang.org/x/crypto/cryptobyte -github.com/shenwei356/bio/seq -crypto/x509/pkix +index/suffixarray vendor/golang.org/x/net/idna -github.com/shenwei356/bwt -log/syslog -net/textproto -crypto/ecdsa -github.com/op/go-logging -github.com/shenwei356/bwt/fmi -crypto/x509 -mime/multipart -gonum.org/v1/plot/vg/vgpdf github.com/shenwei356/util/pathutil github.com/shenwei356/util/stringutil +gonum.org/v1/plot/vg/vgpdf gopkg.in/yaml.v2 +github.com/shenwei356/bwt encoding/csv -flag gonum.org/v1/plot/vg/draw -vendor/golang.org/x/net/http/httpguts -vendor/golang.org/x/net/http/httpproxy +flag +github.com/shenwei356/bwt/fmi text/template/parse +github.com/mattn/go-runewidth gonum.org/v1/plot +vendor/golang.org/x/net/http/httpguts +vendor/golang.org/x/net/http/httpproxy github.com/tatsushid/go-prettytable github.com/spf13/pflag -github.com/ulikunitz/xz/internal/xlog crypto/tls -github.com/ulikunitz/xz/lzma +github.com/ulikunitz/xz/internal/xlog +os/signal gonum.org/v1/plot/plotter +github.com/ulikunitz/xz/lzma text/template github.com/smallfish/simpleyaml github.com/ulikunitz/xz -gonum.org/v1/plot/plotutil github.com/spf13/cobra +gonum.org/v1/plot/plotutil github.com/bsipos/thist net/http/httptrace net/http @@ -1074,14 +1115,14 @@ dh_testroot -O--buildsystem=golang -O--builddirectory=build dh_prep -O--buildsystem=golang -O--builddirectory=build debian/rules override_dh_auto_install -make[1]: Entering directory '/build/seqkit-2.3.1+ds' +make[1]: Map '/build/seqkit-2.3.1+ds' wordt binnengegaan dh_auto_install -- --no-source cd build && mkdir -p /build/seqkit-2.3.1\+ds/debian/tmp/usr cd build && cp -r bin /build/seqkit-2.3.1\+ds/debian/tmp/usr -make[1]: Leaving directory '/build/seqkit-2.3.1+ds' +make[1]: Map '/build/seqkit-2.3.1+ds' wordt verlaten dh_install -O--buildsystem=golang -O--builddirectory=build debian/rules override_dh_installdocs -make[1]: Entering directory '/build/seqkit-2.3.1+ds' +make[1]: Map '/build/seqkit-2.3.1+ds' wordt binnengegaan # Regenerate bam and bam index files cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam @@ -1090,7 +1131,7 @@ samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai dh_installdocs -make[1]: Leaving directory '/build/seqkit-2.3.1+ds' +make[1]: Map '/build/seqkit-2.3.1+ds' wordt verlaten dh_installchangelogs -O--buildsystem=golang -O--builddirectory=build dh_installman -O--buildsystem=golang -O--builddirectory=build dh_installsystemduser -O--buildsystem=golang -O--builddirectory=build @@ -1112,9 +1153,9 @@ 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-dbgsym' in '../seqkit-dbgsym_2.3.1+ds-1_arm64.deb'. -dpkg-deb: building package 'seqkit-examples' in '../seqkit-examples_2.3.1+ds-1_all.deb'. -dpkg-deb: building package 'seqkit' in '../seqkit_2.3.1+ds-1_arm64.deb'. +dpkg-deb: pakket 'seqkit' wordt gebouwd in '../seqkit_2.3.1+ds-1_arm64.deb'. +dpkg-deb: pakket 'seqkit-dbgsym' wordt gebouwd in '../seqkit-dbgsym_2.3.1+ds-1_arm64.deb'. +dpkg-deb: pakket 'seqkit-examples' wordt gebouwd in '../seqkit-examples_2.3.1+ds-1_all.deb'. dpkg-genbuildinfo --build=binary -O../seqkit_2.3.1+ds-1_arm64.buildinfo dpkg-genchanges --build=binary -O../seqkit_2.3.1+ds-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1122,12 +1163,14 @@ 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/12863/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12863/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/24518 and its subdirectories -I: Current time: Fri May 24 03:26:28 -12 2024 -I: pbuilder-time-stamp: 1716564388 +I: removing directory /srv/workspace/pbuilder/12863 and its subdirectories +I: Current time: Sat Apr 22 23:06:55 +14 2023 +I: pbuilder-time-stamp: 1682154415