Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 20:34:10.339060227 +0000 +++ b2/build.log 2024-05-13 20:35:58.174473526 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 15 14:56:17 -12 2025 -I: pbuilder-time-stamp: 1750042577 +I: Current time: Tue May 14 10:34:14 +14 2024 +I: pbuilder-time-stamp: 1715632454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ 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/2731534/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3098951/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 May 13 20:34 /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/3098951/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3098951/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='9d597696534a4102ac44e146918e45dc' - 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='2731534' - PS1='# ' - PS2='> ' + INVOCATION_ID=52631870df4f49f9b5c92f5270f8ff3e + 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=3098951 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.J47xeZis/pbuilderrc_7xGG --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.J47xeZis/b1 --logfile b1/build.log snpomatic_1.0-7.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.J47xeZis/pbuilderrc_8Fqy --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.J47xeZis/b2 --logfile b2/build.log snpomatic_1.0-7.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 codethink01-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 Jun 13 17:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2731534/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3098951/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 48 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 27.4 MB in 0s (136 MB/s) +Fetched 27.4 MB in 0s (65.1 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 ... 19744 files and directories currently installed.) @@ -386,7 +418,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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_1.0-7_source.changes +I: user script /srv/workspace/pbuilder/3098951/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3098951/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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_1.0-7_source.changes dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-7 dpkg-buildpackage: info: source distribution unstable @@ -441,36 +477,30 @@ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -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: 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::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() ) ; @@ -478,13 +508,6 @@ | | | | 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/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() ) ; @@ -492,12 +515,23 @@ | | | | int std::__cxx11::basic_string::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} +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/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/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=] @@ -533,65 +567,27 @@ 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/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 ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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 ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:127:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::string)': -src/TChromosomalIndices.cpp:167:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 167 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::string)': -src/TChromosomalIndices.cpp:409:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 409 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:410:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 410 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:415:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 415 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:419:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 419 | fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:420:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 420 | fread ( &i.position , sizeof ( i.position ) , 1 , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/TChromosomalIndices.cpp:421:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 421 | fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ; - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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 ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:972:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 972 | fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ; | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::string, std::string, uint, uint, uint)': src/TChromosomeAlign.cpp:1070:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1070 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; @@ -629,6 +625,46 @@ 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/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 ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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 ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:127:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::string)': +src/TChromosomalIndices.cpp:167:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 167 | fgets ( dummy , READ_CHAR_BUFFER , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::string)': +src/TChromosomalIndices.cpp:409:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 409 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:410:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 410 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:415:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 415 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:419:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 419 | fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:420:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 420 | fread ( &i.position , sizeof ( i.position ) , 1 , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/TChromosomalIndices.cpp:421:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 421 | fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ; + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ) ; @@ -674,7 +710,7 @@ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/snpomatic-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/snpomatic-1.0' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-c4Am_PYD + rm -fr -- /tmp/dh-xdg-rundir-L8Vkf2F3 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/snpomatic.substvars @@ -766,8 +802,8 @@ 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_1.0-7_arm64.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-7_arm64.deb'. +dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-7_arm64.buildinfo dpkg-genchanges --build=binary -O../snpomatic_1.0-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -775,12 +811,14 @@ 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/3098951/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3098951/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/2731534 and its subdirectories -I: Current time: Sun Jun 15 14:57:08 -12 2025 -I: pbuilder-time-stamp: 1750042628 +I: removing directory /srv/workspace/pbuilder/3098951 and its subdirectories +I: Current time: Tue May 14 10:35:56 +14 2024 +I: pbuilder-time-stamp: 1715632556