Diff of the two buildlogs: -- --- b1/build.log 2023-04-15 01:53:59.461333857 +0000 +++ b2/build.log 2023-04-15 01:55:57.464095640 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 14 13:52:24 -12 2023 -I: pbuilder-time-stamp: 1681523544 +I: Current time: Fri May 17 22:17:03 +14 2024 +I: pbuilder-time-stamp: 1715933823 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./snpomatic_1.0.orig.tar.gz] I: copying [./snpomatic_1.0-6.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Feb 28 19:06:14 2023 -12 +gpgv: Signature made Wed Mar 1 21:06:14 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,11 +30,20 @@ dpkg-source: info: applying build_all_binaries I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/32056/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/6673/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/6673/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/6673/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -44,38 +53,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='32056' + PPID='6673' PS1='# ' PS2='> ' 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.cJfLGQg1/pbuilderrc_Xq3D --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cJfLGQg1/b1 --logfile b1/build.log snpomatic_1.0-6.dsc' + 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.cJfLGQg1/pbuilderrc_4zvk --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cJfLGQg1/b2 --logfile b2/build.log --extrapackages usrmerge snpomatic_1.0-6.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 12 22:50 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/32056/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 17 09:10 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/6673/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -165,7 +174,7 @@ Get: 48 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 27.0 MB in 1s (46.6 MB/s) +Fetched 27.0 MB in 1s (38.2 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 ... 19616 files and directories currently installed.) @@ -386,8 +395,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/snpomatic-1.0/ && 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 > ../snpomatic_1.0-6_source.changes +I: user script /srv/workspace/pbuilder/6673/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/6673/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/snpomatic-1.0/ && 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 > ../snpomatic_1.0-6_source.changes dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-6 dpkg-buildpackage: info: source distribution unstable @@ -446,6 +464,31 @@ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o +src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)': +src/TChromosome.cpp:41:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] + 41 | if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); } + | ~^ ~~~~~~~~~~~~~~~~~ + | | | + | int std::__cxx11::basic_string::size_type {aka long unsigned int} + | %ld +src/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector&, bool)': +src/global_functions.cpp:146:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] + 146 | if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); } + | ~^ ~~~~~~~~~~~ + | | | + | int std::vector::size_type {aka long unsigned int} + | %ld +src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': +src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': +src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::init()': src/TChromosomeAlign.cpp:83:58: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 83 | fprintf ( sam , "@SQ\tSN:%s\tLN:%d\n" , (*chrs)[i].name.c_str() , (*chrs)[i].sequence.length() ) ; @@ -453,6 +496,30 @@ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld +src/global_functions.cpp:116:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 116 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)': +src/TChromosomalIndices.cpp:262:87: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] + 262 | if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ; + | ~^ ~~~~~~~~~~~~ + | | | + | int std::vector::size_type {aka long unsigned int} + | %ld +src/TChromosomalIndices.cpp:263:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] + 263 | else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ; + | ~^ ~~~~~~~~~~~~ + | | | + | int std::vector::size_type {aka long unsigned int} + | %ld +src/global_functions.cpp: In function 'void incorporate_all_gff(std::string, std::vector&)': +src/global_functions.cpp:165:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 165 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/global_functions.cpp: In function 'void incorporate_simple_snps(std::string, std::vector&)': +src/global_functions.cpp:220:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 220 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:956:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 956 | fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ; @@ -460,20 +527,6 @@ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %ld -src/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector&, bool)': -src/global_functions.cpp:146:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] - 146 | if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); } - | ~^ ~~~~~~~~~~~ - | | | - | int std::vector::size_type {aka long unsigned int} - | %ld -src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)': -src/TChromosome.cpp:41:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] - 41 | if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); } - | ~^ ~~~~~~~~~~~~~~~~~ - | | | - | int std::__cxx11::basic_string::size_type {aka long unsigned int} - | %ld src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_cigar_sqlite(const std::string&, const std::string&, uint, uint, char)': src/TChromosomeAlign.cpp:1583:43: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" , @@ -497,30 +550,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | std::__cxx11::basic_string::size_type {aka long unsigned int} -src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)': -src/TChromosomalIndices.cpp:262:87: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] - 262 | if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ; - | ~^ ~~~~~~~~~~~~ - | | | - | int std::vector::size_type {aka long unsigned int} - | %ld -src/TChromosomalIndices.cpp:263:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] - 263 | else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ; - | ~^ ~~~~~~~~~~~~ - | | | - | int std::vector::size_type {aka long unsigned int} - | %ld -src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)': -src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)': -src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)': src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; @@ -528,17 +557,6 @@ src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/global_functions.cpp:116:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 116 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/global_functions.cpp: In function 'void incorporate_all_gff(std::string, std::vector&)': -src/global_functions.cpp:165:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 165 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/global_functions.cpp: In function 'void incorporate_simple_snps(std::string, std::vector&)': -src/global_functions.cpp:220:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 220 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)': src/TChromosomalIndices.cpp:126:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 126 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; @@ -572,10 +590,6 @@ src/TChromosomalIndices.cpp:422:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 422 | fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/reassemble.cpp: In function 'void read_fastq(std::string, std::vector&, int)': -src/reassemble.cpp:319:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 319 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::string)': src/TChromosomeAlign.cpp:93:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; @@ -622,6 +636,10 @@ src/TChromosomeAlign.cpp:1655:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1655 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/reassemble.cpp: In function 'void read_fastq(std::string, std::vector&, int)': +src/reassemble.cpp:319:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 319 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble @@ -630,7 +648,7 @@ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap make[1]: Leaving directory '/build/snpomatic-1.0' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-NGPIqFsB + rm -fr -- /tmp/dh-xdg-rundir-lFbuGiYJ create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/snpomatic.substvars @@ -720,10 +738,10 @@ cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums dh_builddeb - dpkg-deb --root-owner-group --build debian/snpomatic .. dpkg-deb --root-owner-group --build debian/.debhelper/snpomatic/dbgsym-root .. -dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-6_arm64.deb'. + dpkg-deb --root-owner-group --build debian/snpomatic .. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-6_arm64.deb'. +dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-6_arm64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -731,12 +749,14 @@ 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/6673/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6673/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/32056 and its subdirectories -I: Current time: Fri Apr 14 13:53:58 -12 2023 -I: pbuilder-time-stamp: 1681523638 +I: removing directory /srv/workspace/pbuilder/6673 and its subdirectories +I: Current time: Fri May 17 22:18:56 +14 2024 +I: pbuilder-time-stamp: 1715933936