Diff of the two buildlogs: -- --- b1/build.log 2024-03-27 09:53:37.662611234 +0000 +++ b2/build.log 2024-03-27 10:48:13.321975424 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Mar 26 20:43:43 -12 2024 -I: pbuilder-time-stamp: 1711529023 +I: Current time: Wed Mar 27 23:55:27 +14 2024 +I: pbuilder-time-stamp: 1711533327 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/4117/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26216/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 27 09:56 /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/26216/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26216/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='cc1594ca115848879c2d5624dfae50b1' - 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='4117' - PS1='# ' - PS2='> ' + INVOCATION_ID=24d9d8442908400d8b06ea83b46d223c + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=26216 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.kXmMCwQ0/pbuilderrc_PThD --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.kXmMCwQ0/b1 --logfile b1/build.log primer3_2.6.1-4.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.kXmMCwQ0/pbuilderrc_NJzs --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.kXmMCwQ0/b2 --logfile b2/build.log primer3_2.6.1-4.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 24 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4117/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 25 11:27 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/26216/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 armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.14.1 [890 kB] -Fetched 18.3 MB in 1s (34.2 MB/s) +Fetched 18.3 MB in 1s (17.5 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 ... 19577 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/26216/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/26216/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 @@ -287,7 +323,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j5 clean + cd src && make -j4 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 ../*~ @@ -337,14 +373,13 @@ 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 -j5 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) + cd src && make -j4 "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 -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_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 -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o format_output.o format_output.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o read_boulder.o read_boulder.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o print_boulder.o print_boulder.c -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 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc 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 @@ -397,7 +432,9 @@ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ +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 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal_primer.o dpal.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;} @@ -405,15 +442,9 @@ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ -cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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', @@ -423,7 +454,7 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' -cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: @@ -439,6 +470,11 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' +cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 rv libdpal.a dpal_primer.o ar: creating libdpal.a @@ -460,9 +496,13 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o +ar rv libthal.a thal_primer.o +ar: creating libthal.a +a - thal_primer.o +ranlib libthal.a In file included from /usr/include/string.h:535, from thal.c:43: In function 'strcpy', @@ -487,10 +527,6 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:79:10: note: in a call to built-in function '__builtin___memcpy_chk' -ar rv libthal.a thal_primer.o -ar: creating libthal.a -a - thal_primer.o -ranlib libthal.a ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o @@ -576,11 +612,11 @@ a3test.pl: testing ../src/amplicon3_core -START, Wed Mar 27 08:47:07 2024 +START, Wed Mar 27 10:00:02 2024 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] -plain_WNT2...1s [OK] +plain_WNT2...0s [OK] plain_ROCK2...0s [OK] plain_SFRP3...0s [OK] plain_IFT20...0s [OK] @@ -599,7 +635,7 @@ plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1...0s [OK] plain_on_command_line_IFT88...0s [OK] -plain_on_command_line_FZD2...0s [OK] +plain_on_command_line_FZD2...1s [OK] plain_on_command_line_GAPDH...0s [OK] plain_on_command_line_WNT1...0s [OK] plain_on_command_line_MYH6...0s [OK] @@ -617,18 +653,18 @@ 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] heli_SFRP3...0s [OK] -heli_IFT20...1s [OK] -heli_DVL1...0s [OK] +heli_IFT20...0s [OK] +heli_DVL1...1s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] heli_GAPDH...0s [OK] heli_WNT1...0s [OK] -heli_MYH6...1s [OK] +heli_MYH6...0s [OK] long_WNT9B...0s [OK] long_TBX18...0s [OK] long_RYK...0s [OK] @@ -642,7 +678,7 @@ long_GAPDH...0s [OK] long_WNT1...0s [OK] long_MYH6...0s [OK] -optimal_WNT9B...0s [OK] +optimal_WNT9B...1s [OK] optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] @@ -662,7 +698,7 @@ 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] @@ -682,9 +718,9 @@ no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] -Tests in a3test.pl ran for 5 s (0.0833333333333333 min) +Tests in a3test.pl ran for 3 s (0.05 min) -DONE Wed Mar 27 08:47:12 2024 Passed all tests - [OK] +DONE Wed Mar 27 10:00:05 2024 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -701,7 +737,7 @@ p3test.pl: testing ../src/primer3_core -START, Wed Mar 27 08:47:12 2024 +START, Wed Mar 27 10:00:06 2024 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -811,97 +847,97 @@ ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] -primer_must_use_th...0s [OK] -primer_sec_struct_dpal...1s [OK] -primer_task_th...6s [OK] -primer_thal_args...3s [OK] +primer_must_use_th...1s [OK] +primer_sec_struct_dpal...0s [OK] +primer_task_th...5s [OK] +primer_thal_args...2s [OK] primer_thal_max_seq_error...2s [OK] -primer_first_base_index...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_boundary1...0s [OK] +primer_boundary...0s [OK] +primer_boundary1...1s [OK] primer_boundary_formatted...0s [OK] -primer_boundary1_formatted...1s [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...12s [OK] -primer3web_v4_0_0_default_settings...0s [OK] +primer3web_v3_0_0_default_settings...8s [OK] +primer3web_v4_0_0_default_settings...1s [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_regions2...65s [OK] -primer_tm_lc_masking...0s [OK] -primer_tm_lc_masking_formatted...1s [OK] -primer_start_codon...1s [OK] +primer_ok_regions_formatted...0s [OK] +primer_ok_regions2...38s [OK] +primer_tm_lc_masking...1s [OK] +primer_tm_lc_masking_formatted...0s [OK] +primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...1s [OK] -primer_new_tasks...2s [OK] +primer_new_tasks...1s [OK] primer_new_tasks_formatted...1s [OK] -primer_internal_position...1s [OK] -primer_annealing_temp...2s [OK] -primer_windows_newlines...6s [OK] -primer_must_overlap_point...3s [OK] +primer_internal_position...0s [OK] +primer_annealing_temp...0s [OK] +primer_windows_newlines...5s [OK] +primer_must_overlap_point...4s [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] primer_gc_end...0s [OK] -primer_check...1s [OK] -primer_must_use...0s [OK] +primer_check...0s [OK] +primer_must_use...1s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] -primer...6s [OK] +primer...3s [OK] primer_list_files...[OK] primer1...1s [OK] primer1_list_files...[OK] -primer_mispriming...2s [OK] -primer_mispriming_formatted...2s [OK] +primer_mispriming...1s [OK] +primer_mispriming_formatted...1s [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_long_lib...0s [OK] -primer_rat...2s [OK] -primer_human...6s [OK] +primer_mispriming_boundary2_formatted...0s [OK] +primer_mispriming_long_lib...1s [OK] +primer_rat...1s [OK] +primer_human...3s [OK] long_seq...1s [OK] -primer_position_penalty...4s [OK] -primer_position_penalty_formatted...4s [OK] +primer_position_penalty...2s [OK] +primer_position_penalty_formatted...2s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] -primer_obj_fn...13s [OK] -p3_3_prime_n...1s [OK] -primer_masker...13s [OK] -primer_masker_formatted...14s [OK] +primer_obj_fn...7s [OK] +p3_3_prime_n...0s [OK] +primer_masker...9s [OK] +primer_masker_formatted...8s [OK] primer_overhang...0s [OK] -primer_overhang_th...96s [OK] -primer_mispriming_th...71s [OK] -th-w-other-tasks...96s [OK] +primer_overhang_th...76s [OK] +primer_mispriming_th...55s [OK] +th-w-other-tasks...61s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...134s [OK] -primer_sec_struct_thal...95s [OK] -primer_thermod_align...318s [OK] -primer_thermod_align_formatted...317s [OK] -primer1_th...963s [OK] +primer_new_tasks_th...100s [OK] +primer_sec_struct_thal...61s [OK] +primer_thermod_align...234s [OK] +primer_thermod_align_formatted...237s [OK] +primer1_th...688s [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 Mar 27 09:25:08 2024...1102s [OK] +starting primer_lib_amb_codes at Wed Mar 27 10:27:14 2024...882s [OK] -Tests in p3test.pl ran for 3378 s (56.3 min) +Tests in p3test.pl ran for 2510 s (41.8333333333333 min) -DONE Wed Mar 27 09:43:30 2024 Passed all tests - [OK] +DONE Wed Mar 27 10:41:56 2024 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -913,7 +949,7 @@ 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 -j5 clean + cd test && make -j4 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; @@ -956,7 +992,7 @@ 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 -j5 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 -j4 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" @@ -1000,9 +1036,9 @@ 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_armhf.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_armhf.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_armhf.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_armhf.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1010,12 +1046,14 @@ 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/26216/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26216/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/4117 and its subdirectories -I: Current time: Tue Mar 26 21:53:33 -12 2024 -I: pbuilder-time-stamp: 1711533213 +I: removing directory /srv/workspace/pbuilder/26216 and its subdirectories +I: Current time: Thu Mar 28 00:48:09 +14 2024 +I: pbuilder-time-stamp: 1711536489