Diff of the two buildlogs: -- --- b1/build.log 2024-05-20 12:03:27.438085269 +0000 +++ b2/build.log 2024-05-20 12:11:49.552735019 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 22 06:18:16 -12 2025 -I: pbuilder-time-stamp: 1750616296 +I: Current time: Tue May 21 02:03:30 +14 2024 +I: pbuilder-time-stamp: 1716206610 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,51 +31,83 @@ dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3929485/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4157656/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +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 May 20 12:03 /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/4157656/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4157656/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='amd64' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fe1af5840c3e424f8d5634e5117eb37a' - 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='3929485' - PS1='# ' - PS2='> ' + INVOCATION_ID=5109ed32b76d4884b23fd3e67bf34495 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=4157656 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.DZ581OzE/pbuilderrc_POK5 --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.DZ581OzE/b1 --logfile b1/build.log primer3_2.6.1-4.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' + 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.DZ581OzE/pbuilderrc_kxKX --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.DZ581OzE/b2 --logfile b2/build.log primer3_2.6.1-4.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' I: uname -a - Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 22 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3929485/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 20 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4157656/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 33 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] -Fetched 19.2 MB in 0s (84.4 MB/s) +Fetched 19.2 MB in 0s (98.4 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 ... 19701 files and directories currently installed.) @@ -301,7 +333,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes +I: user script /srv/workspace/pbuilder/4157656/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4157656/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-4 dpkg-buildpackage: info: source distribution unstable @@ -433,16 +469,7 @@ cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c -ar rv libthalpara.a thal_parameters.o -ar: creating libthalpara.a -a - thal_parameters.o -ranlib libthalpara.a -ar rv liboligotm.a oligotm.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm -ar: creating liboligotm.a -a - oligotm.o -ranlib liboligotm.a -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] 6168 | else {free(tmp); return p;} @@ -450,15 +477,20 @@ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ -ar rv libmasker.a masker.o -ar: creating libmasker.a -a - masker.o -ranlib libmasker.a +ar rv libthalpara.a thal_parameters.o +ar: creating libthalpara.a +ar rv liboligotm.a oligotm.o +a - thal_parameters.o +ar: creating liboligotm.a +a - oligotm.o +ranlib libthalpara.a +ranlib liboligotm.a ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o @@ -472,6 +504,10 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' +ar rv libmasker.a masker.o +ar: creating libmasker.a +a - masker.o +ranlib libmasker.a In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: @@ -602,7 +638,7 @@ a3test.pl: testing ../src/amplicon3_core -START, Sun Jun 22 18:19:02 2025 +START, Mon May 20 12:04:31 2024 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -659,7 +695,7 @@ long_TBX18...0s [OK] long_RYK...0s [OK] long_WNT2...0s [OK] -long_ROCK2...0s [OK] +long_ROCK2...1s [OK] long_SFRP3...0s [OK] long_IFT20...0s [OK] long_DVL1...0s [OK] @@ -690,7 +726,7 @@ only_mv_IFT20...0s [OK] only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] -only_mv_FZD2...1s [OK] +only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] only_mv_WNT1...0s [OK] only_mv_MYH6...0s [OK] @@ -710,7 +746,7 @@ Tests in a3test.pl ran for 1 s (0.0166666666666667 min) -DONE Sun Jun 22 18:19:03 2025 Passed all tests - [OK] +DONE Mon May 20 12:04:32 2024 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -727,7 +763,7 @@ p3test.pl: testing ../src/primer3_core -START, Sun Jun 22 18:19:03 2025 +START, Mon May 20 12:04:32 2024 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -840,8 +876,8 @@ primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] primer_task_th...1s [OK] -primer_thal_args...0s [OK] -primer_thal_max_seq_error...1s [OK] +primer_thal_args...1s [OK] +primer_thal_max_seq_error...0s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] @@ -863,16 +899,16 @@ primer_ok_regions_formatted...0s [OK] primer_ok_regions2...3s [OK] primer_tm_lc_masking...0s [OK] -primer_tm_lc_masking_formatted...0s [OK] -primer_start_codon...1s [OK] +primer_tm_lc_masking_formatted...1s [OK] +primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] primer_new_tasks...0s [OK] -primer_new_tasks_formatted...0s [OK] +primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] -primer_annealing_temp...1s [OK] +primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] @@ -887,11 +923,11 @@ primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] -primer...1s [OK] +primer...2s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] -primer_mispriming...1s [OK] +primer_mispriming...0s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] @@ -899,8 +935,8 @@ primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...1s [OK] -primer_human...1s [OK] -long_seq...0s [OK] +primer_human...0s [OK] +long_seq...1s [OK] primer_position_penalty...0s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] @@ -913,21 +949,21 @@ primer_overhang...0s [OK] primer_overhang_th...11s [OK] primer_mispriming_th...8s [OK] -th-w-other-tasks...13s [OK] +th-w-other-tasks...12s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...13s [OK] -primer_sec_struct_thal...12s [OK] -primer_thermod_align...33s [OK] -primer_thermod_align_formatted...36s [OK] +primer_new_tasks_th...14s [OK] +primer_sec_struct_thal...11s [OK] +primer_thermod_align...35s [OK] +primer_thermod_align_formatted...35s [OK] primer1_th...83s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). -starting primer_lib_amb_codes at Sun Jun 22 18:22:53 2025...108s [OK] +starting primer_lib_amb_codes at Mon May 20 12:08:22 2024...107s [OK] -Tests in p3test.pl ran for 338 s (5.63333333333333 min) +Tests in p3test.pl ran for 337 s (5.61666666666667 min) -DONE Sun Jun 22 18:24:41 2025 Passed all tests - [OK] +DONE Mon May 20 12:10:09 2024 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -1027,8 +1063,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_amd64.deb'. -dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_amd64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. +dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_amd64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1036,12 +1072,14 @@ 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/4157656/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4157656/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/3929485 and its subdirectories -I: Current time: Sun Jun 22 06:26:26 -12 2025 -I: pbuilder-time-stamp: 1750616786 +I: removing directory /srv/workspace/pbuilder/4157656 and its subdirectories +I: Current time: Tue May 21 02:11:48 +14 2024 +I: pbuilder-time-stamp: 1716207108