Diff of the two buildlogs: -- --- b1/build.log 2024-11-13 06:39:04.857722502 +0000 +++ b2/build.log 2024-11-13 06:41:09.725255459 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 16 00:59:06 -12 2025 -I: pbuilder-time-stamp: 1765889946 +I: Current time: Wed Nov 13 20:39:07 +14 2024 +I: pbuilder-time-stamp: 1731479947 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,54 +33,86 @@ dpkg-source: info: applying set_path.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/103268/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Nov 13 06:39 /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/30597/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30597/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='955072740b6343a4b33ce7dd358b9931' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='103268' - PS1='# ' - PS2='> ' + INVOCATION_ID=b62cdfc252e1414f919870970a68170d + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=30597 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.zpE282tY/pbuilderrc_IDaW --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.zpE282tY/b1 --logfile b1/build.log fastqtl_2.184+v7+dfsg-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.zpE282tY/pbuilderrc_0wi9 --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.zpE282tY/b2 --logfile b2/build.log fastqtl_2.184+v7+dfsg-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos6-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/103268/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -275,7 +307,7 @@ Get: 133 http://deb.debian.org/debian unstable/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.20+ds-2 [1693 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 r-mathlib i386 4.4.2-1 [2598 kB] -Fetched 75.1 MB in 6s (12.6 MB/s) +Fetched 75.1 MB in 1s (58.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19955 files and directories currently installed.) @@ -729,8 +761,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 16 13:00:06 UTC 2025. -Universal Time is now: Tue Dec 16 13:00:06 UTC 2025. +Local time is now: Wed Nov 13 06:39:41 UTC 2024. +Universal Time is now: Wed Nov 13 06:39:41 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -846,7 +878,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fastqtl-2.184+v7+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 > ../fastqtl_2.184+v7+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/30597/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fastqtl-2.184+v7+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 > ../fastqtl_2.184+v7+dfsg-4_source.changes dpkg-buildpackage: info: source package fastqtl dpkg-buildpackage: info: source version 2.184+v7+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -856,7 +892,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j22 clean + make -j10 clean make[1]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg' rm -f obj/*.o bin/fastQTL make[1]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg' @@ -871,7 +907,7 @@ mkdir -p /build/reproducible-path/fastqtl-2.184+v7+dfsg/obj/ mkdir -p /build/reproducible-path/fastqtl-2.184+v7+dfsg/bin/ dh_auto_build -- CXXFLAGS='-g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14' - make -j22 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14" + make -j10 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14" make[2]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg' g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc @@ -883,31 +919,39 @@ g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/commands.o -c src/commands.cpp -Isrc g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/df.o -c src/df.cpp -Isrc g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/fastQTL.o -c src/fastQTL.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/tabix.o -c src/utils/tabix.cpp -Isrc -g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc -src/utils/tabix.cpp: In constructor 'Tabix::Tabix(std::string&)': -src/utils/tabix.cpp:17:22: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] - 17 | if ( bgzf_is_bgzf(cfilename)!=1 ) - | ~~~~~~~~~~~~^~~~~~~~~~~ -In file included from src/utils/tabix.hpp:12, - from src/utils/tabix.cpp:6: -/usr/include/htslib/bgzf.h:270:9: note: declared here - 270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); - | ^~~~~~~~~~~~ +In file included from src/analysisMapping.cpp:17: +src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': +src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] + 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; +src/data.h:181:9: note: here + 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; + | ^~~~ +src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=] + 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; +src/data.h:182:9: note: here + 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; + | ^~~~ +src/analysisPermutationInteraction.cpp: In member function 'void data::runPermutationInteraction(std::string, int)': +src/analysisPermutationInteraction.cpp:48:39: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 48 | random_shuffle(permuted_phenotypes[perm].begin(), permuted_phenotypes[perm].end()); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/algorithm:61, + from src/utils/utils.h:54, + from src/data.h:25, + from src/analysisPermutationInteraction.cpp:17: +/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here + 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ src/analysisPermutation.cpp: In member function 'void data::runPermutation(std::string, std::vector)': src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 75 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/analysisPermutationInteraction.cpp:76:47: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 76 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end()); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here + 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from src/utils/utils.h:54, from src/data.h:25, @@ -915,6 +959,7 @@ /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ +In file included from src/analysisPermutationPerGroup.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -926,7 +971,7 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ -In file included from src/analysisPermutationSequence.cpp:17: +In file included from src/analysisNominal.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -938,7 +983,7 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ -In file included from src/management.cpp:20: +In file included from src/analysisPermutationSequence.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -962,45 +1007,6 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ -src/analysisPermutationInteraction.cpp: In member function 'void data::runPermutationInteraction(std::string, int)': -src/analysisPermutationInteraction.cpp:48:39: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 48 | random_shuffle(permuted_phenotypes[perm].begin(), permuted_phenotypes[perm].end()); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/algorithm:61, - from src/utils/utils.h:54, - from src/data.h:25, - from src/analysisPermutationInteraction.cpp:17: -/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here - 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -src/analysisPermutationInteraction.cpp:76:47: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 76 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end()); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here - 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -src/utils/utils.cpp: In function 'void putils::random_shuffle(std::vector >&)': -src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 133 | random_shuffle(O.begin(), O.end()); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/algorithm:61, - from src/utils/utils.h:54, - from src/utils/utils.cpp:17: -/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here - 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': -src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] - 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; -src/data.h:181:9: note: here - 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; - | ^~~~ -src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=] - 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; -src/data.h:182:9: note: here - 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; - | ^~~~ -In file included from src/analysisNominal.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1012,7 +1018,6 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ -In file included from src/analysisPermutationPerGroup.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1024,7 +1029,17 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ -In file included from src/analysisMapping.cpp:17: +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc +In file included from src/management.cpp:20: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1036,6 +1051,27 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/tabix.o -c src/utils/tabix.cpp -Isrc +g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc +src/utils/tabix.cpp: In constructor 'Tabix::Tabix(std::string&)': +src/utils/tabix.cpp:17:22: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] + 17 | if ( bgzf_is_bgzf(cfilename)!=1 ) + | ~~~~~~~~~~~~^~~~~~~~~~~ +In file included from src/utils/tabix.hpp:12, + from src/utils/tabix.cpp:6: +/usr/include/htslib/bgzf.h:270:9: note: declared here + 270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); + | ^~~~~~~~~~~~ +src/utils/utils.cpp: In function 'void putils::random_shuffle(std::vector >&)': +src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 133 | random_shuffle(O.begin(), O.end()); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/algorithm:61, + from src/utils/utils.h:54, + from src/utils/utils.cpp:17: +/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here + 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ g++ -std=c++11 -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o obj/analysisNominal.o obj/analysisNominalBest.o obj/analysisPermutation.o obj/analysisPermutationInteraction.o obj/analysisPermutationPerGroup.o obj/analysisPermutationSequence.o obj/commands.o obj/df.o obj/fastQTL.o obj/management.o obj/mle.o obj/readCovariates.o obj/readGenotypes.o obj/readGroups.o obj/readInclusionsExclusions.o obj/readInteractions.o obj/readPhenotypes.o obj/readThresholds.o obj/residualizer.o obj/tabix.o obj/utils.o -lRmath -lhts -lm -lz -lbz2 -lboost_iostreams -lboost_program_options -lgslcblas -lgsl -lblas -o bin/fastQTL make[2]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg' cd /build/reproducible-path/fastqtl-2.184+v7+dfsg/example/ && \ @@ -1056,11 +1092,11 @@ dh_installchangelogs dh_installman dh_python3 -I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_chunk.py -I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_FastQTL_threaded.py I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/annotate_outputs.py -I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/sort_index_pairs.py I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/merge_chunks.py +I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_FastQTL_threaded.py +I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_chunk.py +I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/sort_index_pairs.py dh_lintian dh_perl dh_link @@ -1081,9 +1117,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-4_i386.deb'. dpkg-deb: building package 'fastqtl-dbgsym' in '../fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb'. dpkg-deb: building package 'fastqtl-doc' in '../fastqtl-doc_2.184+v7+dfsg-4_all.deb'. -dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../fastqtl_2.184+v7+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../fastqtl_2.184+v7+dfsg-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1091,12 +1127,14 @@ 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/30597/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30597/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/103268 and its subdirectories -I: Current time: Tue Dec 16 01:02:02 -12 2025 -I: pbuilder-time-stamp: 1765890122 +I: removing directory /srv/workspace/pbuilder/30597 and its subdirectories +I: Current time: Wed Nov 13 20:41:09 +14 2024 +I: pbuilder-time-stamp: 1731480069