Diff of the two buildlogs: -- --- b1/build.log 2024-04-09 17:22:20.517485918 +0000 +++ b2/build.log 2024-04-09 17:39:12.514416447 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 12 11:13:16 -12 2025 -I: pbuilder-time-stamp: 1747091596 +I: Current time: Wed Apr 10 07:22:24 +14 2024 +I: pbuilder-time-stamp: 1712683344 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,54 +32,86 @@ dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/108110/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/42233/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Apr 9 17:22 /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/42233/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/42233/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='c9f84cd2328542a1ba6ef460d9211462' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='108110' - PS1='# ' - PS2='> ' + INVOCATION_ID=f6c8097c8cd74ffb85681cc62a8ae383 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=42233 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.JwxDVO7K/pbuilderrc_yBtg --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.JwxDVO7K/b1 --logfile b1/build.log primer3_2.6.1-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.JwxDVO7K/pbuilderrc_7xcO --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.JwxDVO7K/b2 --logfile b2/build.log primer3_2.6.1-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 11 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/108110/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 7 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/42233/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -145,7 +177,7 @@ Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] -Fetched 19.3 MB in 1s (34.9 MB/s) +Fetched 19.3 MB in 0s (60.2 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 ... 19875 files and directories currently installed.) @@ -280,7 +312,11 @@ 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/42233/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/42233/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 @@ -290,7 +326,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j22 clean + cd src && make -j7 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 ../*~ @@ -340,7 +376,7 @@ 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 -j22 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) + cd src && make -j7 "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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c @@ -350,15 +386,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c -cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c -cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL @@ -411,14 +438,10 @@ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.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;} @@ -426,18 +449,10 @@ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ -ranlib liboligotm.a -ar rv libamplicontm.a amplicontm.o -ar: creating libamplicontm.a -a - amplicontm.o -ar rv libmasker.a masker.o -ar: creating libmasker.a -a - masker.o -ranlib libamplicontm.a -ranlib libmasker.a -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c In file included from /usr/include/string.h:535, from thal.c:43: In function 'strcpy', @@ -447,9 +462,6 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' -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 'calc_bulge_internal.isra' at thal.c:2000:19: @@ -457,20 +469,44 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' -ranlib libdpal.a -In file included from /usr/include/string.h:535, - from thal.c:43: +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, - inlined from 'calc_hairpin' at thal.c:1922:19: + inlined from 'maxTM' at thal.c:1542:19, + inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/i386-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/i386-linux-gnu/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' +ar rv libdpal.a dpal_primer.o +ar: creating libdpal.a +a - dpal_primer.o +ranlib libdpal.a +ar rv libthalpara.a thal_parameters.o +ar: creating libthalpara.a +a - thal_parameters.o +ranlib libthalpara.a +ar rv liboligotm.a oligotm.o +ar: creating liboligotm.a +a - oligotm.o +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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm +ar rv libmasker.a masker.o +ar: creating libmasker.a +a - masker.o +ranlib libmasker.a +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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:535, + 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/i386-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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -490,11 +526,11 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/i386-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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -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, Mon May 12 23:14:03 2025 +START, Tue Apr 9 17:23:21 2024 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -620,7 +656,7 @@ classic_WNT1...0s [OK] classic_MYH6...0s [OK] heli_WNT9B...0s [OK] -heli_TBX18...1s [OK] +heli_TBX18...0s [OK] heli_RYK...0s [OK] heli_WNT2...0s [OK] heli_ROCK2...0s [OK] @@ -629,7 +665,7 @@ heli_DVL1...0s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] -heli_GAPDH...0s [OK] +heli_GAPDH...1s [OK] heli_WNT1...0s [OK] heli_MYH6...0s [OK] long_WNT9B...0s [OK] @@ -687,7 +723,7 @@ Tests in a3test.pl ran for 1 s (0.0166666666666667 min) -DONE Mon May 12 23:14:04 2025 Passed all tests - [OK] +DONE Tue Apr 9 17:23:22 2024 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, Mon May 12 23:14:04 2025 +START, Tue Apr 9 17:23:22 2024 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -814,10 +850,10 @@ ./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...4s [OK] -primer_thal_args...1s [OK] +primer_task_th...2s [OK] +primer_thal_args...0s [OK] primer_thal_max_seq_error...1s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] @@ -828,17 +864,17 @@ primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] -primer3_v1_1_4_default_settings...0s [OK] +primer3_v1_1_4_default_settings...1s [OK] primer3web_v0_4_0_default_settings...0s [OK] -primer3web_v3_0_0_default_settings...6s [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_internal1...1s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] -primer_ok_regions2...6s [OK] +primer_ok_regions2...13s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...1s [OK] @@ -848,11 +884,11 @@ primer_dmso_formamide...0s [OK] primer_new_tasks...1s [OK] primer_new_tasks_formatted...0s [OK] -primer_internal_position...0s [OK] +primer_internal_position...1s [OK] primer_annealing_temp...0s [OK] -primer_windows_newlines...4s [OK] -primer_must_overlap_point...1s [OK] -primer_overlap_junction...0s [OK] +primer_windows_newlines...2s [OK] +primer_must_overlap_point...0s [OK] +primer_overlap_junction...1s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] @@ -868,43 +904,43 @@ primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] -primer_mispriming...0s [OK] -primer_mispriming_formatted...1s [OK] +primer_mispriming...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...0s [OK] primer_mispriming_long_lib...0s [OK] -primer_rat...0s [OK] +primer_rat...1s [OK] primer_human...1s [OK] -long_seq...0s [OK] +long_seq...1s [OK] primer_position_penalty...1s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] -primer_obj_fn...2s [OK] +primer_obj_fn...3s [OK] p3_3_prime_n...0s [OK] -primer_masker...4s [OK] -primer_masker_formatted...3s [OK] +primer_masker...6s [OK] +primer_masker_formatted...6s [OK] primer_overhang...0s [OK] -primer_overhang_th...53s [OK] -primer_mispriming_th...41s [OK] -th-w-other-tasks...34s [OK] +primer_overhang_th...25s [OK] +primer_mispriming_th...19s [OK] +th-w-other-tasks...23s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...86s [OK] -primer_sec_struct_thal...34s [OK] -primer_thermod_align...151s [OK] -primer_thermod_align_formatted...151s [OK] -primer1_th...1020s [OK] +primer_new_tasks_th...36s [OK] +primer_sec_struct_thal...25s [OK] +primer_thermod_align...80s [OK] +primer_thermod_align_formatted...81s [OK] +primer1_th...230s [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 Mon May 12 23:40:55 2025...158s [OK] +starting primer_lib_amb_codes at Tue Apr 9 17:32:51 2024...207s [OK] -Tests in p3test.pl ran for 1769 s (29.4833333333333 min) +Tests in p3test.pl ran for 776 s (12.9333333333333 min) -DONE Mon May 12 23:43:33 2025 Passed all tests - [OK] +DONE Tue Apr 9 17:36:18 2024 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 -j22 clean + cd test && make -j7 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; @@ -959,7 +995,7 @@ 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 -j22 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 -j7 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" @@ -1003,9 +1039,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_i386.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_i386.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_i386.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_i386.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1013,12 +1049,14 @@ 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/42233/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/42233/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/108110 and its subdirectories -I: Current time: Mon May 12 11:45:17 -12 2025 -I: pbuilder-time-stamp: 1747093517 +I: removing directory /srv/workspace/pbuilder/42233 and its subdirectories +I: Current time: Wed Apr 10 07:39:11 +14 2024 +I: pbuilder-time-stamp: 1712684351