Diff of the two buildlogs: -- --- b1/build.log 2024-05-06 02:44:18.965214403 +0000 +++ b2/build.log 2024-05-06 02:45:45.585530717 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 5 14:43:04 -12 2024 -I: pbuilder-time-stamp: 1714963384 +I: Current time: Sun Jun 8 23:07:25 +14 2025 +I: pbuilder-time-stamp: 1749373645 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying stdgnu++11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/230241/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1367878/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 8 09:07 /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/1367878/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1367878/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='d5d8a3417cfe485aa5e507a1297cc396' - 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='230241' - PS1='# ' - PS2='> ' + INVOCATION_ID=9df2e00e37fb4a76ba2683ced141aaa8 + 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=1367878 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.CUwa8C3Y/pbuilderrc_4JkZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CUwa8C3Y/b1 --logfile b1/build.log rsem_1.3.3+dfsg-3.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.CUwa8C3Y/pbuilderrc_5rvO --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CUwa8C3Y/b2 --logfile b2/build.log rsem_1.3.3+dfsg-3.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 codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/230241/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1367878/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -202,7 +234,7 @@ Get: 72 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.4+20240414-1 [336 kB] -Fetched 46.1 MB in 1s (63.1 MB/s) +Fetched 46.1 MB in 0s (188 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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.) @@ -462,8 +494,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon May 6 02:43:24 UTC 2024. -Universal Time is now: Mon May 6 02:43:24 UTC 2024. +Local time is now: Sun Jun 8 09:07:44 UTC 2025. +Universal Time is now: Sun Jun 8 09:07:44 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -525,7 +557,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && 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 > ../rsem_1.3.3+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1367878/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1367878/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rsem-1.3.3+dfsg/ && 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 > ../rsem_1.3.3+dfsg-3_source.changes dpkg-buildpackage: info: source package rsem dpkg-buildpackage: info: source version 1.3.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -580,15 +616,25 @@ /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ +In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, + from /usr/include/boost/math/special_functions/math_fwd.hpp:29, + from /usr/include/boost/math/special_functions/erf.hpp:13, + from /usr/include/boost/math/distributions/normal.hpp:19, + from LenDist.h:10, + from SingleModel.h:17, + from simulation.cpp:22: +/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] + 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" + | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o getUnique.o getUnique.cpp -In file included from wiggle.cpp:8: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp +In file included from BamConverter.h:12, + from tbam2gbam.cpp:8: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o samValidator.o samValidator.cpp -In file included from BamConverter.h:12, - from tbam2gbam.cpp:8: +In file included from wiggle.cpp:8: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | if (b->m_data < b->l_data) { @@ -599,17 +645,6 @@ sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ -In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, - from /usr/include/boost/math/special_functions/math_fwd.hpp:29, - from /usr/include/boost/math/special_functions/erf.hpp:13, - from /usr/include/boost/math/distributions/normal.hpp:19, - from LenDist.h:10, - from SingleModel.h:17, - from simulation.cpp:22: -/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] - 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" - | ^~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp BamConverter.h: In constructor 'BamConverter::BamConverter(const char*, const char*, const char*, Transcripts&, int, const std::string&)': BamConverter.h:70:22: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | sam_hdr_write(out, out_header); @@ -628,6 +663,13 @@ BamConverter.h:212:43: warning: ignoring return value of 'int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 212 | sam_write1(out, out_header, tmp_b2); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o scanForPairedEndReads.o scanForPairedEndReads.cpp +In file included from getUnique.cpp:10: +sam_utils.h: In function 'void expand_data_size(bam1_t*)': +sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 34 | if (b->m_data < b->l_data) { + | ~~~~~~~~~~^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp In file included from samValidator.cpp:11: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] @@ -657,6 +699,14 @@ | ~~~~~~~~~~~~~ | | | hts_pos_t {aka long int} +getUnique.cpp: In function 'void output()': +getUnique.cpp:29:59: warning: ignoring return value of 'int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +getUnique.cpp: In function 'int main(int, char**)': +getUnique.cpp:45:22: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | sam_hdr_write(out, header); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~ samValidator.cpp: In function 'int main(int, char**)': samValidator.cpp:145:82: warning: format '%d' expects argument of type 'int', but argument 3 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 145 | printf("\nPaired-end read %s aligns to [%d, %d) of transcript %s, which exceeds the transcript's boundary [0, %d)!\n", @@ -683,11 +733,16 @@ sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ -In file included from getUnique.cpp:10: -sam_utils.h: In function 'void expand_data_size(bam1_t*)': -sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 34 | if (b->m_data < b->l_data) { - | ~~~~~~~~~~^~~~~~~~~~~ +In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, + from /usr/include/boost/math/special_functions/math_fwd.hpp:29, + from /usr/include/boost/math/special_functions/erf.hpp:13, + from /usr/include/boost/math/distributions/normal.hpp:19, + from LenDist.h:10, + from SingleModel.h:17, + from Gibbs.cpp:15: +/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] + 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" + | ^~~~~~~ scanForPairedEndReads.cpp: In function 'int main(int, char**)': scanForPairedEndReads.cpp:66:22: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | sam_hdr_write(out, header); @@ -722,33 +777,13 @@ scanForPairedEndReads.cpp:120:25: warning: ignoring return value of 'int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | sam_write1(out, header, b); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -getUnique.cpp: In function 'void output()': -getUnique.cpp:29:59: warning: ignoring return value of 'int sam_write1(samFile*, const sam_hdr_t*, const bam1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | for (size_t i = 0; i < arr.size(); ++i) sam_write1(out, header, arr[i]); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -getUnique.cpp: In function 'int main(int, char**)': -getUnique.cpp:45:22: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | sam_hdr_write(out, header); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o Gibbs.o Gibbs.cpp -In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, - from /usr/include/boost/math/special_functions/math_fwd.hpp:29, - from /usr/include/boost/math/special_functions/erf.hpp:13, - from /usr/include/boost/math/distributions/normal.hpp:19, - from LenDist.h:10, - from SingleModel.h:17, - from Gibbs.cpp:15: -/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] - 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" - | ^~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from BamWriter.h:14, from EM.cpp:45: sam_utils.h: In function 'void expand_data_size(bam1_t*)': sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 34 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rsem-1.3.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -ffast-math -c -o calcCI.o calcCI.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, @@ -759,9 +794,6 @@ /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz BamWriter.h: In constructor 'BamWriter::BamWriter(const char*, const char*, const char*, Transcripts&, int)': BamWriter.h:70:16: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | sam_hdr_write(out, out_header); @@ -781,13 +813,17 @@ EM.cpp:635:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 635 | system(command); | ~~~~~~^~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz +g++ -Wl,-z,relro -Wl,-z,now -o rsem-preref preRef.o +g++ -Wl,-z,relro -Wl,-z,now -o rsem-build-read-index buildReadIndex.o +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2wig bam2wig.o wiggle.o -lhts -lz +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-bam2readdepth bam2readdepth.o wiggle.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-get-unique getUnique.o -lhts -lz +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-sam-validator samValidator.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-scan-for-paired-end-reads scanForPairedEndReads.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-tbam2gbam tbam2gbam.o SamHeader.o -lhts -lz +g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-parse-alignments parseIt.o -lhts -lz g++ -Wl,-z,relro -Wl,-z,now -o rsem-synthesis-reference-transcripts synthesisRef.o -g++ -Wl,-z,relro -Wl,-z,now -o rsem-extract-reference-transcripts extractRef.o In file included from simulation.cpp:13: utils.h: In member function 'void PairedEndModel::estimateFromReads(const char*)': utils.h:146:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] @@ -937,6 +973,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +utils.h: In member function 'void SingleModel::estimateFromReads(const char*)': +utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] + 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void genReadFileNames(const char*, int, int, int&, char (*)[10005])' at utils.h:142:10, + inlined from 'void SingleModel::estimateFromReads(const char*)' at SingleModel.h:284:20: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 30019) into a destination of size 20010 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +utils.h: In member function 'void SingleQModel::estimateFromReads(const char*)': +utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] + 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void genReadFileNames(const char*, int, int, int&, char (*)[10005])' at utils.h:142:10, + inlined from 'void SingleQModel::estimateFromReads(const char*)' at SingleQModel.h:294:20: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 30019) into a destination of size 20010 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from calcCI.cpp:11: utils.h: In member function 'void PairedEndModel::estimateFromReads(const char*)': utils.h:146:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] @@ -997,6 +1061,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o utils.h: In member function 'void SingleModel::estimateFromReads(const char*)': utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); @@ -1011,20 +1076,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -utils.h: In member function 'void SingleQModel::estimateFromReads(const char*)': -utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] - 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void genReadFileNames(const char*, int, int, int&, char (*)[10005])' at utils.h:142:10, - inlined from 'void SingleQModel::estimateFromReads(const char*)' at SingleQModel.h:294:20: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 30019) into a destination of size 20010 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ In file included from EM.cpp:47: WriteResults.h: In function 'void writeResultsEM(int, const char*, const char*, Transcripts&, std::vector&, std::vector&, double*, bool)': WriteResults.h:138:28: warning: '.grp' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] @@ -1094,30 +1145,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]': -calcCI.cpp:183:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] - 183 | sprintf(inpF, "%s%d", cvsF, i); - | ^~ -calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] - 183 | sprintf(inpF, "%s%d", cvsF, i); - | ^~~~~~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]' at calcCI.cpp:183:10: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -o rsem-simulate-reads simulation.o -utils.h: In member function 'void SingleModel::estimateFromReads(const char*)': +utils.h: In member function 'void SingleQModel::estimateFromReads(const char*)': utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void genReadFileNames(const char*, int, int, int&, char (*)[10005])' at utils.h:142:10, - inlined from 'void SingleModel::estimateFromReads(const char*)' at SingleModel.h:284:20: + inlined from 'void SingleQModel::estimateFromReads(const char*)' at SingleQModel.h:294:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 30019) into a destination of size 20010 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1125,14 +1159,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -utils.h: In member function 'void SingleQModel::estimateFromReads(const char*)': -utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] - 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); - | ^~ +calcCI.cpp: In function 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]': +calcCI.cpp:183:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] + 183 | sprintf(inpF, "%s%d", cvsF, i); + | ^~ +calcCI.cpp:183:31: note: directive argument in the range [0, 2147483646] + 183 | sprintf(inpF, "%s%d", cvsF, i); + | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'void genReadFileNames(const char*, int, int, int&, char (*)[10005])' at utils.h:142:10, - inlined from 'void SingleQModel::estimateFromReads(const char*)' at SingleQModel.h:294:20: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 30019) into a destination of size 20010 + inlined from 'void sample_theta_vectors_from_count_vectors() [with ModelType = PairedEndQModel]' at calcCI.cpp:183:10: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 10015 bytes into a destination of size 10005 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, @@ -1187,6 +1223,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts utils.h: In member function 'void SingleModel::estimateFromReads(const char*)': utils.h:142:40: warning: '%s' directive writing up to 30014 bytes into a region of size 20009 [-Wformat-overflow=] 142 | sprintf(readFs[0], "%s_%s.%s", readFN, tags[tagType], suffix); @@ -1215,7 +1252,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-run-gibbs Gibbs.o -lhts +g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = PairedEndRead; HitType = PairedEndHit; ModelType = PairedEndModel]': EM.cpp:127:26: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); @@ -1282,7 +1319,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -pthread -o rsem-calculate-credibility-intervals calcCI.o -lhts EM.cpp: In function 'void init(ReadReader**&, HitContainer**&, double**&, ModelType**&) [with ReadType = SingleReadQ; HitType = SingleHit; ModelType = SingleQModel]': EM.cpp:127:26: warning: '.dat' directive writing 4 bytes into a region of size between 1 and 10005 [-Wformat-overflow=] 127 | sprintf(datF, "%s.dat", imdName); @@ -1575,8 +1611,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_arm64.deb'. dpkg-deb: building package 'rsem-dbgsym' in '../rsem-dbgsym_1.3.3+dfsg-3_arm64.deb'. +dpkg-deb: building package 'rsem' in '../rsem_1.3.3+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rsem_1.3.3+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../rsem_1.3.3+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1584,12 +1620,14 @@ 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/1367878/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1367878/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/230241 and its subdirectories -I: Current time: Sun May 5 14:44:17 -12 2024 -I: pbuilder-time-stamp: 1714963457 +I: removing directory /srv/workspace/pbuilder/1367878 and its subdirectories +I: Current time: Sun Jun 8 23:08:44 +14 2025 +I: pbuilder-time-stamp: 1749373724