Diff of the two buildlogs: -- --- b1/build.log 2025-01-27 04:51:35.503088703 +0000 +++ b2/build.log 2025-01-27 04:57:39.934638603 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 26 16:46:47 -12 2025 -I: pbuilder-time-stamp: 1737953207 +I: Current time: Mon Mar 2 01:14:39 +14 2026 +I: pbuilder-time-stamp: 1772363679 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking r-cran-glmmtmb_1.1.9+dfsg-3.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2696538/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1663649/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 1 11:14 /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/1663649/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1663649/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='cc6e98a99dca4b17ad1f416ef062709b' - 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='2696538' - PS1='# ' - PS2='> ' + INVOCATION_ID=d0ccca29a4454cdbbfc72d72e465d69a + 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=1663649 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.j9H3qFVP/pbuilderrc_IXQE --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.j9H3qFVP/b1 --logfile b1/build.log r-cran-glmmtmb_1.1.9+dfsg-3.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.j9H3qFVP/pbuilderrc_r5oB --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.j9H3qFVP/b2 --logfile b2/build.log r-cran-glmmtmb_1.1.9+dfsg-3.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/2696538/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1663649/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -337,7 +369,7 @@ Get: 212 http://deb.debian.org/debian trixie/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 r-cran-tmb arm64 1.9.15-1 [1089 kB] -Fetched 123 MB in 1s (235 MB/s) +Fetched 123 MB in 3s (48.4 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 ... 19970 files and directories currently installed.) @@ -1040,8 +1072,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 27 04:47:17 UTC 2025. -Universal Time is now: Mon Jan 27 04:47:17 UTC 2025. +Local time is now: Sun Mar 1 11:16:21 UTC 2026. +Universal Time is now: Sun Mar 1 11:16:21 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14+b1) ... @@ -1240,7 +1272,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/ && 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 > ../r-cran-glmmtmb_1.1.9+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1663649/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1663649/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/ && 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 > ../r-cran-glmmtmb_1.1.9+dfsg-3_source.changes dpkg-buildpackage: info: source package r-cran-glmmtmb dpkg-buildpackage: info: source version 1.1.9+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -1277,113 +1313,36 @@ using C++ compiler: 'g++ (Debian 14.2.0-12) 14.2.0' make[1]: Entering directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/src' g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/usr/lib/R/site-library/TMB/include' -I'/usr/lib/R/site-library/RcppEigen/include' -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c glmmTMB.cpp -o glmmTMB.o -g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/usr/lib/R/site-library/TMB/include' -I'/usr/lib/R/site-library/RcppEigen/include' -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cpp -o utils.o -g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o glmmTMB.so glmmTMB.o utils.o -fopenmp -L/usr/lib/R/lib -lR -"/usr/lib/R/bin/Rscript" -e "cat(as.character(packageVersion('TMB')), '\n', sep="", file='../inst/TMB-version')" -"/usr/lib/R/bin/Rscript" -e "cat(as.character(packageVersion('Matrix')), '\n', sep="", file='../inst/Matrix-version')" -make[1]: Leaving directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/src' -make[1]: Entering directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/src' -make[1]: Leaving directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/src' -installing to /build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg/debian/r-cran-glmmtmb/usr/lib/R/site-library/00LOCK-r-cran-glmmtmb-1.1.9+dfsg/00new/glmmTMB/libs -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (glmmTMB) -W: Ignoring specified R dependency: R (>= 3.6.0) -I: Using r-cran-glmmtmb for Recommends:glmmtmb -I: Using r-cran-knitr for Suggests:knitr -I: Using r-cran-rmarkdown for Suggests:rmarkdown -I: Using r-cran-testthat for Suggests:testthat -I: Using r-cran-mass for Suggests:MASS -I: Using r-cran-lattice for Suggests:lattice -I: Using r-cran-ggplot2 for Suggests:ggplot2 (>= 2.2.1) -I: Using r-cran-mlmrev for Suggests:mlmRev -I: Using r-cran-bbmle for Suggests:bbmle (>= 1.0.19) -I: Using r-cran-pscl for Suggests:pscl -I: Using r-cran-coda for Suggests:coda -I: Using r-cran-reshape2 for Suggests:reshape2 -I: Using r-cran-car for Suggests:car (>= 3.0.6) -I: Using r-cran-emmeans for Suggests:emmeans (>= 1.4) -I: Using r-cran-estimability for Suggests:estimability -W: Cannot find a debian package for Suggests:DHARMa -I: Using r-cran-multcomp for Suggests:multcomp -W: Cannot find a debian package for Suggests:MuMIn -I: Using r-cran-effects for Suggests:effects (>= 4.0-1) -W: Cannot find a debian package for Suggests:dotwhisker -I: Using r-cran-broom for Suggests:broom -W: Cannot find a debian package for Suggests:broom.mixed -I: Using r-cran-plyr for Suggests:plyr -I: Using r-cran-png for Suggests:png -I: Using r-cran-boot for Suggests:boot -W: Cannot find a debian package for Suggests:texreg -I: Using r-cran-xtable for Suggests:xtable -W: Cannot find a debian package for Suggests:huxtable -W: Cannot find a debian package for Suggests:mvabund -I: Using r-cran-blme for Suggests:blme -I: Using r-cran-purrr for Suggests:purrr -I: Using r-cran-dplyr for Suggests:dplyr -I: Using r-cran-tmb for Imports:TMB (>= 1.9.0) -I: Version replacement between package version 1.1-18.9000 and Debian version 1.1-35.5-1+b1 - suspicious. Do not replace anything. -I: Using r-cran-lme4 by changing version to (>= 1.1-18.9000) for Imports:lme4 (>= 1.1-18.9000) -I: Using r-cran-matrix by changing version to for Imports:Matrix -I: Using r-cran-nlme for Imports:nlme -I: Using r-cran-numderiv for Imports:numDeriv -I: Using r-cran-mgcv for Imports:mgcv -I: Using r-cran-tmb for LinkingTo:TMB -I: Using r-cran-rcppeigen for LinkingTo:RcppEigen -I: Use r-cran-glmmtmb as Debian binary package for variables substitution - dh_installdocs -O--buildsystem=R - dh_installchangelogs -O--buildsystem=R - dh_installsystemduser -O--buildsystem=R - dh_perl -O--buildsystem=R - dh_link -O--buildsystem=R - dh_strip_nondeterminism -O--buildsystem=R - dh_compress -O--buildsystem=R - dh_fixperms -O--buildsystem=R - dh_missing -O--buildsystem=R - dh_dwz -a -O--buildsystem=R - dh_strip -a -O--buildsystem=R - dh_makeshlibs -a -O--buildsystem=R - dh_shlibdeps -a -O--buildsystem=R -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 from: /lib/ld-linux-aarch64.so.1 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged - dh_installdeb -O--buildsystem=R - debian/rules override_dh_gencontrol -make[1]: Entering directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg' -tmbversion=`dpkg -l r-cran-tmb | grep 'ii' | sed 's/^.*r-cran-tmb[[:space:]]\+\([0-9.-]\+\)[[:space:]]\+.*/\1/'`; \ -sed -i "s/r-cran-tmb[^,]*/r-cran-tmb (>= ${tmbversion})/" debian/*substvars -dh_gencontrol -make[1]: Leaving directory '/build/reproducible-path/r-cran-glmmtmb-1.1.9+dfsg' - dh_md5sums -O--buildsystem=R - dh_builddeb -O--buildsystem=R -dpkg-deb: building package 'r-cran-glmmtmb' in '../r-cran-glmmtmb_1.1.9+dfsg-3_arm64.deb'. -dpkg-deb: building package 'r-cran-glmmtmb-dbgsym' in '../r-cran-glmmtmb-dbgsym_1.1.9+dfsg-3_arm64.deb'. - dpkg-genbuildinfo --build=binary -O../r-cran-glmmtmb_1.1.9+dfsg-3_arm64.buildinfo - dpkg-genchanges --build=binary -O../r-cran-glmmtmb_1.1.9+dfsg-3_arm64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +make[1]: *** wait: No child processes. Stop. +make[1]: *** Waiting for unfinished jobs.... +make[1]: *** wait: No child processes. Stop. +make: *** [debian/rules:10: binary] Terminated +Terminated I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/1663649/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Sun Mar 1 11:20:34 UTC 2026 +Filesystem Size Used Avail Use% Mounted on +tmpfs 30G 0 30G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/1663649/tmp/hooks/C01_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 +W: Stray processes left from build: +* system-pbuilder-build-r\x2dcran\x2dglmmtmb_1.1.9\x2bdfsg\x2d3-1663649.slice - Slice /system/pbuilder/build/r-cran-glmmtmb_1.1.9+dfsg-3/1663649 + Loaded: loaded + Active: active since Mon 2026-03-02 01:14:46 +14; 5min ago + Tasks: 1 + Memory: 1021.0M + CPU: 1min 10.033s + CGroup: /system.slice/system-pbuilder.slice/system-pbuilder-build.slice/system-pbuilder-build-r\x2dcran\x2dglmmtmb_1.1.9\x2bdfsg\x2d3.slice/system-pbuilder-build-r\x2dcran\x2dglmmtmb_1.1.9\x2bdfsg\x2d3-1663649.slice + `-run-ra03c5c9a1f28451db0c47c2a5d54c35e.scope + `-1694958 "[cc1plus]" + +Mar 02 01:14:46 codethink03-arm64 systemd[1]: Created slice system-pbuilder-build-r\x2dcran\x2dglmmtmb_1.1.9\x2bdfsg\x2d3-1663649.slice - Slice /system/pbuilder/build/r-cran-glmmtmb_1.1.9+dfsg-3/1663649. +Mar 02 01:20:35 codethink03-arm64 systemd[1]: system-pbuilder-build-r\x2dcran\x2dglmmtmb_1.1.9\x2bdfsg\x2d3-1663649.slice: A process of this unit has been killed by the OOM killer. I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2696538 and its subdirectories -I: Current time: Sun Jan 26 16:51:34 -12 2025 -I: pbuilder-time-stamp: 1737953494 +I: removing directory /srv/workspace/pbuilder/1663649 and its subdirectories