Diff of the two buildlogs: -- --- b1/build.log 2025-02-05 15:00:09.844410196 +0000 +++ b2/build.log 2025-02-05 15:00:59.550159575 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 5 02:59:20 -12 2025 -I: pbuilder-time-stamp: 1738767560 +I: Current time: Wed Mar 11 11:23:13 +14 2026 +I: pbuilder-time-stamp: 1773177793 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2697555/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/837749/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 Mar 10 21:23 /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/837749/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/837749/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='0d429a3914f946dfbd16fba86f69a024' - 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='2697555' - PS1='# ' - PS2='> ' + INVOCATION_ID=020fcacdbfe34222b090a2ca9774bed8 + 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=837749 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.oCOOVSFl/pbuilderrc_k6Vw --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.oCOOVSFl/b1 --logfile b1/build.log repeatmasker-recon_1.08-8.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.oCOOVSFl/pbuilderrc_uIVs --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.oCOOVSFl/b2 --logfile b2/build.log repeatmasker-recon_1.08-8.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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) 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/2697555/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/837749/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ 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 (126 MB/s) +Fetched 20.1 MB in 0s (152 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 ... 19957 files and directories currently installed.) @@ -273,7 +305,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes +I: user script /srv/workspace/pbuilder/837749/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/837749/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable @@ -306,7 +342,7 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef -In file included from eledef.c:1: +In file included from imagespread.c:2: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { @@ -343,20 +379,7 @@ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -eledef.c: In function 'main': -eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | freopen(ele_name, "w", all_ele);\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -eledef.c:246:7: note: in expansion of macro 'DUMBBELL' - 246 | DUMBBELL; - | ^~~~~~~~ -eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | freopen(ele_name, "w", all_ele);\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -eledef.c:253:5: note: in expansion of macro 'DUMBBELL' - 253 | DUMBBELL; - | ^~~~~~~~ -In file included from imagespread.c:2: +In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { @@ -393,6 +416,19 @@ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c: In function 'main': +eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] + 95 | freopen(ele_name, "w", all_ele);\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c:246:7: note: in expansion of macro 'DUMBBELL' + 246 | DUMBBELL; + | ^~~~~~~~ +eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] + 95 | freopen(ele_name, "w", all_ele);\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c:253:5: note: in expansion of macro 'DUMBBELL' + 253 | DUMBBELL; + | ^~~~~~~~ In file included from ele.h:1, from eleredef.c:5: msps.h: In function 'scan_msp': @@ -429,7 +465,6 @@ In file included from ele.h:1, from edgeredef.c:1: msps.h: In function 'scan_msp': -eleredef.c: In function 'main': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ @@ -460,9 +495,18 @@ | | | | long int * int32_t * {aka int *} | %d +eleredef.c: In function 'main': +eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] + 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int long unsigned int + | %ld In file included from ele.h:1, from famdef.c:1: msps.h: In function 'scan_msp': +In file included from msps.h:4: +seqlist.h: In function 'GetSeqNames': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ @@ -481,12 +525,6 @@ | | | | long int * int32_t * {aka int *} | %d -eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] - 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); - | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | int long unsigned int - | %ld msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ @@ -504,14 +542,12 @@ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -edgeredef.c: In function 'general_edge_redef': -In file included from msps.h:4: -seqlist.h: In function 'GetSeqNames': -In file included from msps.h:4: -seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +edgeredef.c: In function 'general_edge_redef': +In file included from msps.h:4: +seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -565,8 +601,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_arm64.deb'. dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_arm64.deb'. +dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_arm64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -574,12 +610,14 @@ 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/837749/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/837749/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/2697555 and its subdirectories -I: Current time: Wed Feb 5 03:00:08 -12 2025 -I: pbuilder-time-stamp: 1738767608 +I: removing directory /srv/workspace/pbuilder/837749 and its subdirectories +I: Current time: Wed Mar 11 11:23:58 +14 2026 +I: pbuilder-time-stamp: 1773177838