Diff of the two buildlogs: -- --- b1/build.log 2025-03-10 02:44:16.151284719 +0000 +++ b2/build.log 2025-03-10 02:45:00.517290576 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 9 14:43:42 -12 2025 -I: pbuilder-time-stamp: 1741574622 +I: Current time: Sun Apr 12 23:07:16 +14 2026 +I: pbuilder-time-stamp: 1775984836 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,51 +30,84 @@ dpkg-source: info: applying clang.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2318985/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/383600/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 Apr 12 09:07 /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/383600/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/383600/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=' ' - 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='2318985' - PS1='# ' - PS2='> ' + INVOCATION_ID=13791c4142b0403e9ccba83040886370 + 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=383600 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.nn1KmCre/pbuilderrc_OhBh --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.nn1KmCre/b1 --logfile b1/build.log ncbi-seg_0.0.20000620-7.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.nn1KmCre/pbuilderrc_cI6v --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.nn1KmCre/b2 --logfile b2/build.log ncbi-seg_0.0.20000620-7.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 codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) 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/2318985/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/383600/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] -Fetched 20.1 MB in 0s (157 MB/s) +Fetched 20.1 MB in 0s (89.7 MB/s) Preconfiguring packages ... 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 ... 19914 files and directories currently installed.) @@ -276,7 +308,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ncbi-seg-0.0.20000620/ && 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 > ../ncbi-seg_0.0.20000620-7_source.changes +I: user script /srv/workspace/pbuilder/383600/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/383600/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ncbi-seg-0.0.20000620/ && 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 > ../ncbi-seg_0.0.20000620-7_source.changes dpkg-buildpackage: info: source package ncbi-seg dpkg-buildpackage: info: source version 0.0.20000620-7 dpkg-buildpackage: info: source distribution unstable @@ -367,22 +403,113 @@ genwin.h:160:26: warning: type defaults to 'int' in declaration of 'findchar' [-Wimplicit-int] 160 | extern upper(), lower(), findchar(); | ^~~~~~~~ +In file included from genwin.c:9: +genwin.h:146:8: warning: type defaults to 'int' in declaration of 'closedbase' [-Wimplicit-int] + 146 | extern closedbase(); + | ^~~~~~~~~~ +genwin.h:149:8: warning: type defaults to 'int' in declaration of 'closeseq' [-Wimplicit-int] + 149 | extern closeseq(); + | ^~~~~~~~ +genwin.h:152:8: warning: type defaults to 'int' in declaration of 'shiftwin' [-Wimplicit-int] + 152 | extern shiftwin(), closewin(); + | ^~~~~~~~ +genwin.h:152:20: warning: type defaults to 'int' in declaration of 'closewin' [-Wimplicit-int] + 152 | extern shiftwin(), closewin(); + | ^~~~~~~~ +genwin.h:154:8: warning: type defaults to 'int' in declaration of 'compon' [-Wimplicit-int] + 154 | extern compon(), stateon(), enton(); + | ^~~~~~ +genwin.h:154:18: warning: type defaults to 'int' in declaration of 'stateon' [-Wimplicit-int] + 154 | extern compon(), stateon(), enton(); + | ^~~~~~~ +genwin.h:154:29: warning: type defaults to 'int' in declaration of 'enton' [-Wimplicit-int] + 154 | extern compon(), stateon(), enton(); + | ^~~~~ +genwin.h:158:8: warning: type defaults to 'int' in declaration of 'closemat' [-Wimplicit-int] + 158 | extern closemat(); + | ^~~~~~~~ +genwin.h:160:8: warning: type defaults to 'int' in declaration of 'upper' [-Wimplicit-int] + 160 | extern upper(), lower(), findchar(); + | ^~~~~ +genwin.h:160:17: warning: type defaults to 'int' in declaration of 'lower' [-Wimplicit-int] + 160 | extern upper(), lower(), findchar(); + | ^~~~~ +genwin.h:160:26: warning: type defaults to 'int' in declaration of 'findchar' [-Wimplicit-int] + 160 | extern upper(), lower(), findchar(); + | ^~~~~~~~ +genwin.c:62:1: warning: return type defaults to 'int' [-Wimplicit-int] + 62 | genwininit() + | ^~~~~~~~~~ +genwin.c: In function 'opendbase': +genwin.c:93:8: warning: implicit declaration of function 'blastdb' [-Wimplicit-function-declaration] + 93 | if (blastdb(name)) + | ^~~~~~~ +genwin.c: At top level: +genwin.c:144:8: warning: return type defaults to 'int' [-Wimplicit-int] + 144 | extern closedbase(dbase) + | ^~~~~~~~~~ +genwin.c:185:8: warning: return type defaults to 'int' [-Wimplicit-int] + 185 | extern closeseq(seq) + | ^~~~~~~~ +genwin.c:319:8: warning: return type defaults to 'int' [-Wimplicit-int] + 319 | extern closewin(win) + | ^~~~~~~~ +genwin.c:336:8: warning: return type defaults to 'int' [-Wimplicit-int] + 336 | extern compon(win) + | ^~~~~~ +genwin.c:364:8: warning: return type defaults to 'int' [-Wimplicit-int] + 364 | extern stateon(win) + | ^~~~~~~ +genwin.c:389:8: warning: return type defaults to 'int' [-Wimplicit-int] + 389 | extern enton(win) + | ^~~~~ +genwin.c: In function 'readentry': +genwin.c:510:9: warning: implicit declaration of function 'readhdr' [-Wimplicit-function-declaration] + 510 | if (!readhdr(seq)) + | ^~~~~~~ +genwin.c:528:4: warning: implicit declaration of function 'readseq' [-Wimplicit-function-declaration] + 528 | readseq(seq); + | ^~~~~~~ +genwin.c: At top level: +genwin.c:545:1: warning: return type defaults to 'int' [-Wimplicit-int] + 545 | readhdr(seq) + | ^~~~~~~ seg.c:49:1: warning: return type defaults to 'int' [-Wimplicit-int] 49 | main(argc, argv) | ^~~~ +genwin.c: In function 'readhdr': seg.c: In function 'main': seg.c:58:4: warning: implicit declaration of function 'genwininit' [-Wimplicit-function-declaration] 58 | genwininit(); | ^~~~~~~~~~ +genwin.c:670:10: warning: implicit declaration of function 'skipline' [-Wimplicit-function-declaration] + 670 | skipline(fp); + | ^~~~~~~~ +genwin.c: At top level: seg.c:60:4: warning: implicit declaration of function 'getparams' [-Wimplicit-function-declaration] 60 | getparams(argc, argv); | ^~~~~~~~~ +genwin.c:684:1: warning: return type defaults to 'int' [-Wimplicit-int] + 684 | skipline(fp) + | ^~~~~~~~ +genwin.c:718:1: warning: return type defaults to 'int' [-Wimplicit-int] + 718 | readseq(seq) + | ^~~~~~~ seg.c:61:4: warning: implicit declaration of function 'entropy_init' [-Wimplicit-function-declaration] 61 | entropy_init(window); | ^~~~~~~~~~~~ +genwin.c:794:8: warning: return type defaults to 'int' [-Wimplicit-int] + 794 | extern upper(string, len) + | ^~~~~ +genwin.c:807:8: warning: return type defaults to 'int' [-Wimplicit-int] + 807 | extern lower(string, len) + | ^~~~~ seg.c:72:7: warning: implicit declaration of function 'segseq' [-Wimplicit-function-declaration] 72 | segseq(seq, &segs, 0); | ^~~~~~ +genwin.c:862:1: warning: return type defaults to 'int' [-Wimplicit-int] + 862 | tfree(ptr) + | ^~~~~ seg.c:73:7: warning: implicit declaration of function 'mergesegs' [-Wimplicit-function-declaration] 73 | mergesegs(seq, segs); | ^~~~~~~~~ @@ -421,34 +548,6 @@ seg.c:233:16: warning: implicit declaration of function 'findlo' [-Wimplicit-function-declaration] 233 | loi = findlo(i, lowlim, H); | ^~~~~~ -In file included from genwin.c:9: -genwin.h:146:8: warning: type defaults to 'int' in declaration of 'closedbase' [-Wimplicit-int] - 146 | extern closedbase(); - | ^~~~~~~~~~ -genwin.h:149:8: warning: type defaults to 'int' in declaration of 'closeseq' [-Wimplicit-int] - 149 | extern closeseq(); - | ^~~~~~~~ -genwin.h:152:8: warning: type defaults to 'int' in declaration of 'shiftwin' [-Wimplicit-int] - 152 | extern shiftwin(), closewin(); - | ^~~~~~~~ -genwin.h:152:20: warning: type defaults to 'int' in declaration of 'closewin' [-Wimplicit-int] - 152 | extern shiftwin(), closewin(); - | ^~~~~~~~ -genwin.h:154:8: warning: type defaults to 'int' in declaration of 'compon' [-Wimplicit-int] - 154 | extern compon(), stateon(), enton(); - | ^~~~~~ -genwin.h:154:18: warning: type defaults to 'int' in declaration of 'stateon' [-Wimplicit-int] - 154 | extern compon(), stateon(), enton(); - | ^~~~~~~ -genwin.h:154:29: warning: type defaults to 'int' in declaration of 'enton' [-Wimplicit-int] - 154 | extern compon(), stateon(), enton(); - | ^~~~~ -genwin.h:158:8: warning: type defaults to 'int' in declaration of 'closemat' [-Wimplicit-int] - 158 | extern closemat(); - | ^~~~~~~~ -genwin.h:160:8: warning: type defaults to 'int' in declaration of 'upper' [-Wimplicit-int] - 160 | extern upper(), lower(), findchar(); - | ^~~~~ seg.c:234:16: warning: implicit declaration of function 'findhi'; did you mean 'findchar'? [-Wimplicit-function-declaration] 234 | hii = findhi(i, last, H); | ^~~~~~ @@ -526,69 +625,6 @@ seg.c:945:1: warning: return type defaults to 'int' [-Wimplicit-int] 945 | usage() | ^~~~~ -genwin.h:160:17: warning: type defaults to 'int' in declaration of 'lower' [-Wimplicit-int] - 160 | extern upper(), lower(), findchar(); - | ^~~~~ -genwin.h:160:26: warning: type defaults to 'int' in declaration of 'findchar' [-Wimplicit-int] - 160 | extern upper(), lower(), findchar(); - | ^~~~~~~~ -genwin.c:62:1: warning: return type defaults to 'int' [-Wimplicit-int] - 62 | genwininit() - | ^~~~~~~~~~ -genwin.c: In function 'opendbase': -genwin.c:93:8: warning: implicit declaration of function 'blastdb' [-Wimplicit-function-declaration] - 93 | if (blastdb(name)) - | ^~~~~~~ -genwin.c: At top level: -genwin.c:144:8: warning: return type defaults to 'int' [-Wimplicit-int] - 144 | extern closedbase(dbase) - | ^~~~~~~~~~ -genwin.c:185:8: warning: return type defaults to 'int' [-Wimplicit-int] - 185 | extern closeseq(seq) - | ^~~~~~~~ -genwin.c:319:8: warning: return type defaults to 'int' [-Wimplicit-int] - 319 | extern closewin(win) - | ^~~~~~~~ -genwin.c:336:8: warning: return type defaults to 'int' [-Wimplicit-int] - 336 | extern compon(win) - | ^~~~~~ -genwin.c:364:8: warning: return type defaults to 'int' [-Wimplicit-int] - 364 | extern stateon(win) - | ^~~~~~~ -genwin.c:389:8: warning: return type defaults to 'int' [-Wimplicit-int] - 389 | extern enton(win) - | ^~~~~ -genwin.c: In function 'readentry': -genwin.c:510:9: warning: implicit declaration of function 'readhdr' [-Wimplicit-function-declaration] - 510 | if (!readhdr(seq)) - | ^~~~~~~ -genwin.c:528:4: warning: implicit declaration of function 'readseq' [-Wimplicit-function-declaration] - 528 | readseq(seq); - | ^~~~~~~ -genwin.c: At top level: -genwin.c:545:1: warning: return type defaults to 'int' [-Wimplicit-int] - 545 | readhdr(seq) - | ^~~~~~~ -genwin.c: In function 'readhdr': -genwin.c:670:10: warning: implicit declaration of function 'skipline' [-Wimplicit-function-declaration] - 670 | skipline(fp); - | ^~~~~~~~ -genwin.c: At top level: -genwin.c:684:1: warning: return type defaults to 'int' [-Wimplicit-int] - 684 | skipline(fp) - | ^~~~~~~~ -genwin.c:718:1: warning: return type defaults to 'int' [-Wimplicit-int] - 718 | readseq(seq) - | ^~~~~~~ -genwin.c:794:8: warning: return type defaults to 'int' [-Wimplicit-int] - 794 | extern upper(string, len) - | ^~~~~ -genwin.c:807:8: warning: return type defaults to 'int' [-Wimplicit-int] - 807 | extern lower(string, len) - | ^~~~~ -genwin.c:862:1: warning: return type defaults to 'int' [-Wimplicit-int] - 862 | tfree(ptr) - | ^~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/ncbi-seg-0.0.20000620=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wl,-z,relro -Wl,-z,now -o ncbi-seg seg.o genwin.o -lm make[1]: Leaving directory '/build/reproducible-path/ncbi-seg-0.0.20000620' dh_auto_test @@ -635,12 +671,14 @@ 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/383600/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/383600/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/2318985 and its subdirectories -I: Current time: Sun Mar 9 14:44:14 -12 2025 -I: pbuilder-time-stamp: 1741574654 +I: removing directory /srv/workspace/pbuilder/383600 and its subdirectories +I: Current time: Sun Apr 12 23:07:57 +14 2026 +I: pbuilder-time-stamp: 1775984877