Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 05:09:47.724490267 +0000 +++ b2/build.log 2024-12-20 05:27:38.483473968 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 21 23:29:42 -12 2026 -I: pbuilder-time-stamp: 1769081382 +I: Current time: Fri Dec 20 19:09:53 +14 2024 +I: pbuilder-time-stamp: 1734671393 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2144547/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1105373/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 Dec 20 05:10 /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/1105373/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1105373/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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='90ec236cfbc542a2a2705aac6227df70' - 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='2144547' - PS1='# ' - PS2='> ' + INVOCATION_ID=9d3d498977524ba6971e07a244031ee9 + 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=1105373 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.2lIDhcDr/pbuilderrc_JlXH --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.2lIDhcDr/b1 --logfile b1/build.log gemma_0.98.5+dfsg-3.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.2lIDhcDr/pbuilderrc_lsRh --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.2lIDhcDr/b2 --logfile b2/build.log gemma_0.98.5+dfsg-3.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 ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2144547/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1105373/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -195,7 +227,7 @@ Get: 64 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 65 http://deb.debian.org/debian trixie/main amd64 shunit2 all 2.1.8-4 [33.9 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 58.1 MB in 1s (63.9 MB/s) +Fetched 58.1 MB in 2s (28.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19959 files and directories currently installed.) @@ -489,7 +521,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gemma-0.98.5+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 > ../gemma_0.98.5+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/1105373/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1105373/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gemma-0.98.5+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 > ../gemma_0.98.5+dfsg-3_source.changes dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -499,7 +535,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+dfsg' rm -vf ./src/*.o rm -vf ./src/*~ @@ -532,7 +568,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j20 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp @@ -614,57 +650,61 @@ rm -vf output/* ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log -Run options: --seed 15435 +Run options: --seed 2617 # Running: -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** INFO: no intercept term is found in the cvt file: a column of 1s is added. -## number of total individuals = 198 -## number of analyzed individuals = 67 -## number of covariates = 3 +**** TEST MODE: trim individuals from 1940 to 400 +**** TEST MODE: trim individuals from 1940 to 400 +## number of total individuals = 400 +## number of analyzed individuals = 247 +## number of covariates = 1 ## number of phenotypes = 1 -## number of total SNPs/var = 7320 -## number of analyzed SNPs = 7317 +## leave one chromosome out (LOCO) = 1 +## number of total SNPs/var = 12226 +## number of considered SNPS = 1000 +## number of SNPS for K = 11182 +## number of SNPS for GWAS = 1044 +## number of analyzed SNPs = 889 Calculating Relatedness Matrix ... - 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% -**** WARNING: Mismatch coordinates (194,0)0:0! -K is not symmetric! in src/gemma.cpp at line 1913 in BatchRun + 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** INFO: no intercept term is found in the cvt file: a column of 1s is added. -## number of total individuals = 198 -## number of analyzed individuals = 67 -## number of covariates = 3 +**** TEST MODE: trim individuals from 1940 to 400 +**** TEST MODE: trim individuals from 1940 to 400 +## number of total individuals = 400 +## number of analyzed individuals = 247 +## number of covariates = 1 ## number of phenotypes = 1 -## number of total SNPs/var = 7320 -## number of analyzed SNPs = 7317 +## leave one chromosome out (LOCO) = 1 +## number of total SNPs/var = 12226 +## number of considered SNPS = 1000 +## number of SNPS for K = 11182 +## number of SNPS for GWAS = 1044 +## number of analyzed SNPs = 889 Start Eigen-Decomposition... -pve estimate =0.00100086 -se(pve) =0.204165 - 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% +pve estimate =0.678775 +se(pve) =0.0717914 + 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. -GSL_RNG_SEED=100 +.GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** INFO: no intercept term is found in the cvt file: a column of 1s is added. -## number of total individuals = 198 -## number of analyzed individuals = 67 -## number of covariates = 3 +## number of total individuals = 1940 +## number of analyzed individuals = 1410 +## number of covariates = 1 ## number of phenotypes = 1 -## number of total SNPs/var = 7320 -## number of analyzed SNPs = 7317 -Start Eigen-Decomposition... -pve estimate =0.00100086 -se(pve) =0.204165 - 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% +## number of total SNPs/var = 12226 +## number of analyzed SNPs = 10768 + 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. .GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 @@ -699,63 +739,55 @@ GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -## number of total individuals = 1940 -## number of analyzed individuals = 1410 -## number of covariates = 1 +**** INFO: no intercept term is found in the cvt file: a column of 1s is added. +## number of total individuals = 198 +## number of analyzed individuals = 67 +## number of covariates = 3 ## number of phenotypes = 1 -## number of total SNPs/var = 12226 -## number of analyzed SNPs = 10768 - 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% +## number of total SNPs/var = 7320 +## number of analyzed SNPs = 7317 +Calculating Relatedness Matrix ... + 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. -.GSL_RNG_SEED=100 +GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** TEST MODE: trim individuals from 1940 to 400 -**** TEST MODE: trim individuals from 1940 to 400 -## number of total individuals = 400 -## number of analyzed individuals = 247 -## number of covariates = 1 +**** INFO: no intercept term is found in the cvt file: a column of 1s is added. +## number of total individuals = 198 +## number of analyzed individuals = 67 +## number of covariates = 3 ## number of phenotypes = 1 -## leave one chromosome out (LOCO) = 1 -## number of total SNPs/var = 12226 -## number of considered SNPS = 1000 -## number of SNPS for K = 11182 -## number of SNPS for GWAS = 1044 -## number of analyzed SNPs = 889 -Calculating Relatedness Matrix ... - 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% -Mismatch coordinates (4,0)0:0! -**** WARNING: K is not symmetric! in src/gemma.cpp at line 1913 in BatchRun +## number of total SNPs/var = 7320 +## number of analyzed SNPs = 7317 +Start Eigen-Decomposition... +pve estimate =0.00100086 +se(pve) =0.204165 + 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. -GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 +GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... -**** TEST MODE: trim individuals from 1940 to 400 -**** TEST MODE: trim individuals from 1940 to 400 -## number of total individuals = 400 -## number of analyzed individuals = 247 -## number of covariates = 1 +**** INFO: no intercept term is found in the cvt file: a column of 1s is added. +## number of total individuals = 198 +## number of analyzed individuals = 67 +## number of covariates = 3 ## number of phenotypes = 1 -## leave one chromosome out (LOCO) = 1 -## number of total SNPs/var = 12226 -## number of considered SNPS = 1000 -## number of SNPS for K = 11182 -## number of SNPS for GWAS = 1044 -## number of analyzed SNPs = 889 +## number of total SNPs/var = 7320 +## number of analyzed SNPs = 7317 Start Eigen-Decomposition... -pve estimate =0.678775 -se(pve) =0.0717914 - 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% +pve estimate =0.00100086 +se(pve) =0.204165 + 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. . -Finished in 101.221524s, 0.0395 runs/s, 0.2075 assertions/s. +Finished in 672.722539s, 0.0059 runs/s, 0.0312 assertions/s. 4 runs, 21 assertions, 0 failures, 0 errors, 0 skips make[2]: Leaving directory '/build/reproducible-path/gemma-0.98.5+dfsg' - rm -fr -- /tmp/dh-xdg-rundir-IUQk64ID + rm -fr -- /tmp/dh-xdg-rundir-rFtAX302 rm -rf output make[1]: Leaving directory '/build/reproducible-path/gemma-0.98.5+dfsg' create-stamp debian/debhelper-build-stamp @@ -780,10 +812,10 @@ chmod -R u\+rw,go=rX debian/gemma-doc/usr/share/doc install -p -m0644 debian/copyright debian/gemma-doc/usr/share/doc/gemma-doc/copyright dh_installchangelogs - install -m0755 -d debian/gemma-doc/usr/share/doc/gemma-doc - install -p -m0644 debian/.debhelper/generated/gemma-doc/dh_installchangelogs.dch.trimmed debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian install -m0755 -d debian/gemma/usr/share/doc/gemma install -p -m0644 debian/.debhelper/generated/gemma/dh_installchangelogs.dch.trimmed debian/gemma/usr/share/doc/gemma/changelog.Debian + install -m0755 -d debian/gemma-doc/usr/share/doc/gemma-doc + install -p -m0644 debian/.debhelper/generated/gemma-doc/dh_installchangelogs.dch.trimmed debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian dh_perl dh_link dh_strip_nondeterminism @@ -793,21 +825,21 @@ dh_compress cd debian/gemma cd debian/gemma-doc - chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian chmod a-x usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt - gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian + chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian gzip -9nf usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt + gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian cd '/build/reproducible-path/gemma-0.98.5+dfsg' cd '/build/reproducible-path/gemma-0.98.5+dfsg' dh_fixperms find debian/gemma ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a @@ -839,27 +871,27 @@ echo misc:Pre-Depends= >> debian/gemma.substvars install -m0755 -d debian/.debhelper/gemma/dbgsym-root/DEBIAN dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -cdebian/control -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=6000ceb20d17477dc8f0a2d88a7851c92d515ace -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/gemma-doc/DEBIAN/control chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -cdebian/control -Pdebian/gemma + chmod 0644 -- debian/gemma-doc/DEBIAN/control chmod 0644 -- debian/gemma/DEBIAN/control dh_md5sums - install -m0755 -d debian/gemma-doc/DEBIAN install -m0755 -d debian/gemma/DEBIAN cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/gemma-doc/DEBIAN cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma/DEBIAN/md5sums install -m0755 -d debian/.debhelper/gemma/dbgsym-root/DEBIAN cd debian/.debhelper/gemma/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/gemma-doc/DEBIAN/md5sums + chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/gemma .. dpkg-deb --root-owner-group --build debian/.debhelper/gemma/dbgsym-root .. dpkg-deb --root-owner-group --build debian/gemma-doc .. dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.5+dfsg-3_amd64.deb'. -dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-3_amd64.deb'. dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.5+dfsg-3_all.deb'. +dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gemma_0.98.5+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../gemma_0.98.5+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -867,12 +899,14 @@ 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/1105373/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1105373/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/2144547 and its subdirectories -I: Current time: Wed Jan 21 23:32:46 -12 2026 -I: pbuilder-time-stamp: 1769081566 +I: removing directory /srv/workspace/pbuilder/1105373 and its subdirectories +I: Current time: Fri Dec 20 19:27:37 +14 2024 +I: pbuilder-time-stamp: 1734672457