Diff of the two buildlogs: -- --- b1/build.log 2024-05-08 07:28:05.763196526 +0000 +++ b2/build.log 2024-05-08 07:37:27.751274390 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 7 19:17:44 -12 2024 -I: pbuilder-time-stamp: 1715152665 +I: Current time: Wed Jun 11 03:51:11 +14 2025 +I: pbuilder-time-stamp: 1749563471 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4002661/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3896805/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Jun 10 13:51 /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/3896805/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3896805/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=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='11a8261771764baf88cf5ffbe060ddb1' - 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='4002661' - PS1='# ' - PS2='> ' + INVOCATION_ID=c7d899addd964bb2a5b266b20f863b15 + 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=3896805 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.eEaBFPeW/pbuilderrc_Sev2 --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.eEaBFPeW/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' - 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.eEaBFPeW/pbuilderrc_IxeP --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.eEaBFPeW/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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4002661/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3896805/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ 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 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (215 MB/s) +Fetched 18.7 MB in 0s (218 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 ... 19743 files and directories currently installed.) @@ -277,7 +309,11 @@ 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/3896805/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3896805/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 @@ -347,11 +383,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c format_output.c: In function 'print_seq': -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 -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL | ^~ @@ -366,6 +398,7 @@ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ format_output.c: In function 'format_oligos': format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) @@ -379,6 +412,7 @@ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ +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 -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ @@ -400,46 +434,47 @@ format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ -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 -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ +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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c +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;} + | ^ +libprimer3.cc:6168:15: note: call to 'void free(void*)' here + 6168 | else {free(tmp); return p;} + | ~~~~^~~~~ ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a -ar rv libdpal.a dpal_primer.o -ar: creating libdpal.a -a - dpal_primer.o -ranlib libdpal.a -ar rv libamplicontm.a amplicontm.o -ar: creating libamplicontm.a -a - amplicontm.o -ranlib libamplicontm.a -ar rv libmasker.a masker.o -ar: 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm -creating libmasker.a -a - masker.o -ranlib libmasker.a ar rv liboligotm.a oligotm.o ar: creating 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm 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 -mbranch-protection=standard -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;} - | ^ -libprimer3.cc:6168:15: note: call to 'void free(void*)' here - 6168 | else {free(tmp); return p;} - | ~~~~^~~~~ -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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.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 -mbranch-protection=standard -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 rv libmasker.a masker.o +ar: 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm +creating libmasker.a +a - masker.o +ranlib libmasker.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 -mbranch-protection=standard -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 In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', @@ -449,26 +484,27 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: 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', inlined from 'safe_malloc' at thal.c:804:7, - inlined from 'calc_hairpin' at thal.c:1922:19: + inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, - inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: + inlined from 'maxTM' at thal.c:1542:19, + inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o +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 'maxTM' at thal.c:1542:19, - inlined from 'fillMatrix' at thal.c:1473:16: + inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -488,11 +524,11 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:79:10: 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o 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 -mbranch-protection=standard -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 @@ -578,7 +614,7 @@ a3test.pl: testing ../src/amplicon3_core -START, Wed May 8 07:19:13 2024 +START, Tue Jun 10 13:51:50 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -588,7 +624,7 @@ plain_IFT20...0s [OK] plain_DVL1...0s [OK] plain_IFT88...0s [OK] -plain_FZD2...1s [OK] +plain_FZD2...0s [OK] plain_GAPDH...0s [OK] plain_WNT1...0s [OK] plain_MYH6...0s [OK] @@ -659,7 +695,7 @@ optimal_MYH6...0s [OK] only_mv_WNT9B...0s [OK] only_mv_TBX18...0s [OK] -only_mv_RYK...1s [OK] +only_mv_RYK...0s [OK] only_mv_WNT2...0s [OK] only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] @@ -684,9 +720,9 @@ 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 Wed May 8 07:19:16 2024 Passed all tests - [OK] +DONE Tue Jun 10 13:51:51 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -703,7 +739,7 @@ p3test.pl: testing ../src/primer3_core -START, Wed May 8 07:19:16 2024 +START, Tue Jun 10 13:51:51 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -815,28 +851,28 @@ [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] -primer_task_th...2s [OK] +primer_task_th...1s [OK] primer_thal_args...0s [OK] -primer_thal_max_seq_error...0s [OK] +primer_thal_max_seq_error...1s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] -primer_boundary...1s [OK] +primer_boundary...0s [OK] primer_boundary1...0s [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...1s [OK] +primer3web_v3_0_0_default_settings...2s [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...0s [OK] primer_ok_regions...0s [OK] -primer_ok_regions_formatted...1s [OK] +primer_ok_regions_formatted...0s [OK] primer_ok_regions2...6s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] @@ -845,12 +881,12 @@ primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] -primer_new_tasks...1s [OK] -primer_new_tasks_formatted...0s [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...0s [OK] -primer_must_overlap_point...1s [OK] +primer_annealing_temp...0s [OK] +primer_windows_newlines...1s [OK] +primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] @@ -874,11 +910,11 @@ primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] -primer_rat...0s [OK] -primer_human...1s [OK] -long_seq...0s [OK] -primer_position_penalty...1s [OK] -primer_position_penalty_formatted...0s [OK] +primer_rat...1s [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] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] @@ -888,22 +924,22 @@ primer_masker_formatted...2s [OK] primer_overhang...0s [OK] primer_overhang_th...12s [OK] -primer_mispriming_th...11s [OK] -th-w-other-tasks...14s [OK] +primer_mispriming_th...9s [OK] +th-w-other-tasks...13s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...17s [OK] -primer_sec_struct_thal...12s [OK] -primer_thermod_align...38s [OK] -primer_thermod_align_formatted...41s [OK] -primer1_th...121s [OK] +primer_new_tasks_th...15s [OK] +primer_sec_struct_thal...13s [OK] +primer_thermod_align...43s [OK] +primer_thermod_align_formatted...43s [OK] +primer1_th...113s [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 Wed May 8 07:24:08 2024...114s [OK] +starting primer_lib_amb_codes at Tue Jun 10 13:56:36 2025...123s [OK] -Tests in p3test.pl ran for 406 s (6.76666666666667 min) +Tests in p3test.pl ran for 408 s (6.8 min) -DONE Wed May 8 07:26:02 2024 Passed all tests - [OK] +DONE Tue Jun 10 13:58:39 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -1003,8 +1039,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_arm64.deb'. -dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. +dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1012,12 +1048,14 @@ 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/3896805/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3896805/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/4002661 and its subdirectories -I: Current time: Tue May 7 19:28:04 -12 2024 -I: pbuilder-time-stamp: 1715153284 +I: removing directory /srv/workspace/pbuilder/3896805 and its subdirectories +I: Current time: Wed Jun 11 04:00:26 +14 2025 +I: pbuilder-time-stamp: 1749564026