Diff of the two buildlogs: -- --- b1/build.log 2025-10-19 01:07:31.897935947 +0000 +++ b2/build.log 2025-10-19 01:16:59.970564706 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 20 18:56:12 -12 2026 -I: pbuilder-time-stamp: 1795244172 +I: Current time: Sun Oct 19 15:07:33 +14 2025 +I: pbuilder-time-stamp: 1760836053 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -28,53 +28,85 @@ dpkg-source: info: applying gcc15.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2999846/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1285398/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Oct 19 01:07 /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/1285398/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1285398/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6fc12027d1374b149cff0ce4f992ea94' - 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='2999846' - PS1='# ' - PS2='> ' + INVOCATION_ID=4428b22b4f43485b99036f74217164ee + 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=1285398 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.eFJ1FB6z/pbuilderrc_OScQ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eFJ1FB6z/b1 --logfile b1/build.log primer3_2.6.1-6.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.eFJ1FB6z/pbuilderrc_ZFfJ --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eFJ1FB6z/b2 --logfile b2/build.log primer3_2.6.1-6.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2999846/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1285398/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -139,7 +171,7 @@ Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] -Fetched 11.2 MB in 0s (39.2 MB/s) +Fetched 11.2 MB in 0s (127 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 ... 19898 files and directories currently installed.) @@ -275,7 +307,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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_2.6.1-6_source.changes +I: user script /srv/workspace/pbuilder/1285398/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1285398/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_2.6.1-6_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-6 dpkg-buildpackage: info: source distribution unstable @@ -285,7 +321,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j42 clean + cd src && make -j40 clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ @@ -338,7 +374,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_build -- 'CPP=$(CXX)' - cd src && make -j42 INSTALL="install --strip-program=true" CPP=\$\(CXX\) + cd src && make -j40 INSTALL="install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows 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 primer3_boulder_main.c @@ -349,7 +385,6 @@ 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 p3_seq_lib.o p3_seq_lib.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 dpal_primer.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 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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_parameters.o thal_parameters.c cc -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c cc -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c @@ -357,6 +392,7 @@ 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 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_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 -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 +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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 format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] @@ -414,7 +450,6 @@ ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a -ar rv libmasker.a masker.o 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;} @@ -422,33 +457,24 @@ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ -ar: creating libmasker.a -a - masker.o -ranlib libmasker.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 ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o +ar rv libmasker.a masker.o +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 libmasker.a +ar: a - masker.o +creating liboligotm.a +a - oligotm.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 -ar rv libdpal.a dpal_primer.o -ar: creating libdpal.a -a - dpal_primer.o -ranlib libdpal.a +ranlib libmasker.a +ranlib liboligotm.a In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] - 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', @@ -457,8 +483,13 @@ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] + 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' -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 ntdpal ntdpal_main.o dpal.o +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' +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 In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: @@ -473,6 +504,10 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' +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 ntdpal ntdpal_main.o dpal.o +ar rv libdpal.a dpal_primer.o +ar: creating libdpal.a +a - dpal_primer.o In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, @@ -489,11 +524,12 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' +ranlib libdpal.a ar rv libthal.a thal_primer.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 ntthal thal_main.o thal.o thal_parameters.o -lm ar: creating libthal.a a - thal_primer.o ranlib libthal.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 ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o @@ -579,7 +615,7 @@ a3test.pl: testing ../src/amplicon3_core -START, Sat Nov 21 06:58:18 2026 +START, Sun Oct 19 01:08:27 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -587,7 +623,7 @@ plain_ROCK2...0s [OK] plain_SFRP3...0s [OK] plain_IFT20...0s [OK] -plain_DVL1...1s [OK] +plain_DVL1...0s [OK] plain_IFT88...0s [OK] plain_FZD2...0s [OK] plain_GAPDH...0s [OK] @@ -598,7 +634,7 @@ plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2...0s [OK] plain_on_command_line_ROCK2...0s [OK] -plain_on_command_line_SFRP3...0s [OK] +plain_on_command_line_SFRP3...1s [OK] plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1...0s [OK] plain_on_command_line_IFT88...0s [OK] @@ -627,7 +663,7 @@ heli_SFRP3...0s [OK] heli_IFT20...0s [OK] heli_DVL1...0s [OK] -heli_IFT88...1s [OK] +heli_IFT88...0s [OK] heli_FZD2...0s [OK] heli_GAPDH...0s [OK] heli_WNT1...0s [OK] @@ -665,7 +701,7 @@ only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] only_mv_IFT20...0s [OK] -only_mv_DVL1...1s [OK] +only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] @@ -685,9 +721,9 @@ no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] -Tests in a3test.pl ran for 3 s (0.05 min) +Tests in a3test.pl ran for 1 s (0.0166666666666667 min) -DONE Sat Nov 21 06:58:21 2026 Passed all tests - [OK] +DONE Sun Oct 19 01:08:28 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -704,7 +740,7 @@ p3test.pl: testing ../src/primer3_core -START, Sat Nov 21 06:58:21 2026 +START, Sun Oct 19 01:08:28 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -814,11 +850,11 @@ ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] -primer_must_use_th...1s [OK] +primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] -primer_task_th...3s [OK] +primer_task_th...0s [OK] primer_thal_args...1s [OK] -primer_thal_max_seq_error...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] @@ -826,19 +862,19 @@ dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] -primer_boundary_formatted...1s [OK] +primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] -primer3web_v3_0_0_default_settings...3s [OK] +primer3web_v3_0_0_default_settings...1s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] -primer_internal1_formatted...1s [OK] +primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] -primer_ok_regions2...24s [OK] +primer_ok_regions2...7s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] @@ -846,12 +882,12 @@ primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] -primer_new_tasks...1s [OK] +primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] -primer_annealing_temp...1s [OK] -primer_windows_newlines...3s [OK] -primer_must_overlap_point...2s [OK] +primer_annealing_temp...0s [OK] +primer_windows_newlines...1s [OK] +primer_must_overlap_point...1s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] @@ -864,47 +900,47 @@ primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] -primer...4s [OK] +primer...1s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] -primer_mispriming_formatted...1s [OK] +primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] -primer_mispriming_boundary2_formatted...1s [OK] +primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] -primer_rat...1s [OK] -primer_human...2s [OK] -long_seq...1s [OK] -primer_position_penalty...3s [OK] -primer_position_penalty_formatted...1s [OK] -p3-tmpl-mispriming...1s [OK] +primer_rat...0s [OK] +primer_human...1s [OK] +long_seq...0s [OK] +primer_position_penalty...1s [OK] +primer_position_penalty_formatted...0s [OK] +p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] -primer_obj_fn...7s [OK] +primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] -primer_masker...8s [OK] -primer_masker_formatted...6s [OK] -primer_overhang...1s [OK] -primer_overhang_th...39s [OK] -primer_mispriming_th...28s [OK] -th-w-other-tasks...46s [OK] +primer_masker...2s [OK] +primer_masker_formatted...2s [OK] +primer_overhang...0s [OK] +primer_overhang_th...10s [OK] +primer_mispriming_th...7s [OK] +th-w-other-tasks...13s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...50s [OK] -primer_sec_struct_thal...46s [OK] -primer_thermod_align...153s [OK] -primer_thermod_align_formatted...136s [OK] -primer1_th...377s [OK] +primer_new_tasks_th...14s [OK] +primer_sec_struct_thal...12s [OK] +primer_thermod_align...32s [OK] +primer_thermod_align_formatted...32s [OK] +primer1_th...76s [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 Sat Nov 21 07:14:20 2026...595s [OK] +starting primer_lib_amb_codes at Sun Oct 19 01:12:08 2025...168s [OK] -Tests in p3test.pl ran for 1554 s (25.9 min) +Tests in p3test.pl ran for 388 s (6.46666666666667 min) -DONE Sat Nov 21 07:24:15 2026 Passed all tests - [OK] +DONE Sun Oct 19 01:14:56 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -916,7 +952,7 @@ make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test - cd test && make -j42 clean + cd test && make -j40 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; @@ -963,7 +999,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_install -- PREFIX=debian/primer3/usr - cd src && make -j42 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" PREFIX=debian/primer3/usr + cd src && make -j40 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" PREFIX=debian/primer3/usr make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows install -d "debian/primer3/usr/bin" @@ -1017,12 +1053,14 @@ 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/1285398/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1285398/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/2999846 and its subdirectories -I: Current time: Fri Nov 20 19:30:30 -12 2026 -I: pbuilder-time-stamp: 1795246230 +I: removing directory /srv/workspace/pbuilder/1285398 and its subdirectories +I: Current time: Sun Oct 19 15:16:59 +14 2025 +I: pbuilder-time-stamp: 1760836619