Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 21:30:00.050135275 +0000 +++ b2/build.log 2024-04-30 21:33:56.420056364 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 2 15:48:00 -12 2025 -I: pbuilder-time-stamp: 1748922480 +I: Current time: Wed May 1 11:30:02 +14 2024 +I: pbuilder-time-stamp: 1714512602 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 typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/940796/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2840631/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 30 21:30 /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/2840631/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2840631/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4cedb47303fb4e1ca84d2e465f2224b6' - 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='940796' - PS1='# ' - PS2='> ' + INVOCATION_ID=0ba2dbe505d54e908fb3b6fcd80631f3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2840631 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.NSZNuiqu/pbuilderrc_owxb --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.NSZNuiqu/b1 --logfile b1/build.log seer_1.1.4-7.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.NSZNuiqu/pbuilderrc_PfE0 --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.NSZNuiqu/b2 --logfile b2/build.log seer_1.1.4-7.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 19:07 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/940796/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 22 12:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2840631/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -405,7 +437,7 @@ Get: 146 http://deb.debian.org/debian trixie/main amd64 libdlib-dev amd64 19.24+dfsg-1.1 [2054 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libgzstream0 amd64 1.5+git20171107.9a20658-2 [7228 B] Get: 148 http://deb.debian.org/debian trixie/main amd64 libgzstream-dev amd64 1.5+git20171107.9a20658-2 [7380 B] -Fetched 197 MB in 8s (25.7 MB/s) +Fetched 197 MB in 3s (56.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. @@ -907,8 +939,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 3 03:49:57 UTC 2025. -Universal Time is now: Tue Jun 3 03:49:57 UTC 2025. +Local time is now: Tue Apr 30 21:32:12 UTC 2024. +Universal Time is now: Tue Apr 30 21:32:12 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -1045,7 +1077,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/seer-1.1.4/ && 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 > ../seer_1.1.4-7_source.changes +I: user script /srv/workspace/pbuilder/2840631/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2840631/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/seer-1.1.4/ && 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 > ../seer_1.1.4-7_source.changes dpkg-buildpackage: info: source package seer dpkg-buildpackage: info: source version 1.1.4-7 dpkg-buildpackage: info: source distribution unstable @@ -1055,7 +1091,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make clean make[2]: Entering directory '/build/reproducible-path/seer-1.1.4/src' @@ -1075,7 +1111,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' dh_auto_build -- LDFLAGS+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial - make -j42 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial + make -j20 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' @@ -1100,39 +1136,25 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o fasta.o fasta.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapMain.o mapMain.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.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 seercommon.hpp:30, - from kmds.hpp:9, - from kmdsCmdLine.cpp:8: + from linkFunction.hpp:6, + from seer.hpp:10, + from seerMain.cpp:8: /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/armadillo:26, - from kmer.hpp:9, - from kmer.cpp:8: -/usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' - 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") - | ^ -/usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' - 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") - | ^ -/usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' - 329 | #pragma message ("INFO: see the documentation for details") - | ^ 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 seercommon.hpp:30, - from seerCommon.cpp:9: + from linkFunction.hpp:6, + from seer.hpp:10, + from seerBinaryAssoc.cpp:8: /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)" | ^~~~~~~ @@ -1142,7 +1164,8 @@ from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, - from logitFunction.cpp:8: + from seer.hpp:10, + from seerStats.cpp:8: /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)" | ^~~~~~~ @@ -1151,8 +1174,7 @@ from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, - from kmds.hpp:9, - from kmdsMain.cpp:8: + from seerCommon.cpp:9: /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)" | ^~~~~~~ @@ -1170,9 +1192,8 @@ from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, - from linkFunction.hpp:6, - from seer.hpp:10, - from seerCmdLine.cpp:9: + from kmds.hpp:9, + from kmdsStruct.cpp:8: /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)" | ^~~~~~~ @@ -1181,9 +1202,7 @@ from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, - from linkFunction.hpp:6, - from seer.hpp:10, - from seerStats.cpp:8: + from seerIO.cpp:12: /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)" | ^~~~~~~ @@ -1192,7 +1211,8 @@ from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, - from seerErr.cpp:8: + from kmds.hpp:9, + from kmdsMain.cpp:8: /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)" | ^~~~~~~ @@ -1203,27 +1223,39 @@ from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, - from seerMain.cpp:8: + from seerContinuousAssoc.cpp:8: /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/armadillo:26, + from kmer.hpp:9, + from kmer.cpp:8: +/usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' + 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") + | ^ +/usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' + 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") + | ^ +/usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' + 329 | #pragma message ("INFO: see the documentation for details") + | ^ 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 seercommon.hpp:30, - from seerIO.cpp:12: + from seerErr.cpp:8: /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/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.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 seercommon.hpp:30, from linkFunction.hpp:6, - from seer.hpp:10, - from seerContinuousAssoc.cpp:8: + from linearFunction.cpp:8: /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)" | ^~~~~~~ @@ -1233,7 +1265,7 @@ from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, - from linearFunction.cpp:8: + from logitFunction.cpp:8: /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)" | ^~~~~~~ @@ -1244,7 +1276,7 @@ from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, - from seerBinaryAssoc.cpp:8: + from seerCmdLine.cpp:9: /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)" | ^~~~~~~ @@ -1254,10 +1286,12 @@ from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from kmds.hpp:9, - from kmdsStruct.cpp:8: + from kmdsCmdLine.cpp:8: /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/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' @@ -1280,6 +1314,7 @@ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' @@ -1291,7 +1326,6 @@ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o filter_seer In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' @@ -1380,6 +1414,7 @@ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' @@ -1414,6 +1449,7 @@ 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o combineKmers +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o filter_seer g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o map_back g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o seer g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial -o kmds @@ -1423,7 +1459,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' if dh_auto_test ; then echo Test passed ; else echo '****************************** TEST FAILED. Please contact upstream *******************************' ; fi - make -j42 test + make -j20 test make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' @@ -1449,7 +1485,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' dh_auto_install -- PREFIX=/build/reproducible-path/seer-1.1.4/debian/seer/usr - make -j42 install DESTDIR=/build/reproducible-path/seer-1.1.4/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/seer-1.1.4/debian/seer/usr + make -j20 install DESTDIR=/build/reproducible-path/seer-1.1.4/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/seer-1.1.4/debian/seer/usr make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' @@ -1501,12 +1537,14 @@ 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/2840631/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2840631/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/940796 and its subdirectories -I: Current time: Mon Jun 2 15:52:58 -12 2025 -I: pbuilder-time-stamp: 1748922778 +I: removing directory /srv/workspace/pbuilder/2840631 and its subdirectories +I: Current time: Wed May 1 11:33:55 +14 2024 +I: pbuilder-time-stamp: 1714512835