Diff of the two buildlogs: -- --- b1/build.log 2024-05-16 23:07:40.279445342 +0000 +++ b2/build.log 2024-05-16 23:08:39.012949235 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 11:05:46 -12 2024 -I: pbuilder-time-stamp: 1715900746 +I: Current time: Thu Jun 19 19:30:41 +14 2025 +I: pbuilder-time-stamp: 1750311041 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying dont-hardcode-glibc-version.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/45804/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/60529/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-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 Jun 19 05:30 /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/60529/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/60529/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=11 ' - 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]="21" [3]="1" [4]="release" [5]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + 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='4e9f9853e2784b0b966e48f2029cc801' - 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='45804' - PS1='# ' - PS2='> ' + INVOCATION_ID=05c2f9b09e184c388c68d2e3ea80194a + 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=60529 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.JYVQWefV/pbuilderrc_YUGg --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.JYVQWefV/b1 --logfile b1/build.log bolt-lmm_2.4.1+dfsg-2.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://46.16.76.132:3128' + 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.JYVQWefV/pbuilderrc_dzKM --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.JYVQWefV/b2 --logfile b2/build.log bolt-lmm_2.4.1+dfsg-2.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://213.165.73.152:3128 I: uname -a - Linux ionos12-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 15 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/45804/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 18 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/60529/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -189,7 +221,7 @@ Get: 55 http://deb.debian.org/debian unstable/main i386 libopenblas-dev i386 0.3.27+ds-2 [52.3 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.5+dfsg2-2 [346 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] -Fetched 65.8 MB in 1s (52.2 MB/s) +Fetched 65.8 MB in 1s (62.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19704 files and directories currently installed.) @@ -440,7 +472,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bolt-lmm-2.4.1+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 > ../bolt-lmm_2.4.1+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/60529/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/60529/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bolt-lmm-2.4.1+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 > ../bolt-lmm_2.4.1+dfsg-2_source.changes dpkg-buildpackage: info: source package bolt-lmm dpkg-buildpackage: info: source version 2.4.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -450,7 +486,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j11 clean + cd src && make -j21 clean make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' rm -f *.o rm -f bolt @@ -501,64 +537,64 @@ run_example_reml2.sh make[1]: Leaving directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg' dh_auto_build -O--sourcedirectory=src -Nbolt-lmm-example - cd src && make -j11 "INSTALL=install --strip-program=true" + cd src && make -j21 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bolt-lmm-2.4.1+dfsg/src' g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltMain.o -c BoltMain.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Bolt.o -c Bolt.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltParams.o -c BoltParams.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o BoltReml.o -c BoltReml.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o CovariateBasis.o -c CovariateBasis.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o DataMatrix.o -c DataMatrix.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o FileUtils.o -c FileUtils.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Jackknife.o -c Jackknife.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o LDscoreCalibration.o -c LDscoreCalibration.cpp -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MapInterpolater.o -c MapInterpolater.cpp +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MatrixUtils.o -c MatrixUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MatrixUtils.o -c MatrixUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -FileUtils.cpp: In function 'int FileUtils::checkBgenSample(const std::string&, const std::string&, int)': -FileUtils.cpp:338:14: warning: unused variable 'destLen' [-Wunused-variable] - 338 | uLongf destLen = D, bufLen = D, zBufLen = C-4; - | ^~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o MemoryUtils.o -c MemoryUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o NumericUtils.o -c NumericUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o PhenoBuilder.o -c PhenoBuilder.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o RestrictSnpSet.o -c RestrictSnpSet.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -NonlinearOptMulti.cpp: In function 'std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)': -NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type 'class nlopt::roundoff_limited' by value [-Wcatch-value=] - 230 | catch (nlopt::roundoff_limited) { - | ^~~~~~~~~~~~~~~~ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SnpData.o -c SnpData.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SnpInfo.o -c SnpInfo.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o SpectrumTools.o -c SpectrumTools.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o StatsUtils.o -c StatsUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o StringUtils.o -c StringUtils.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o Timer.o -c Timer.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/bolt-lmm-2.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/n/data1/bwh/medicine/loh/ploh/external_software/zstd-1.5.2/lib -o memcpy.o -c memcpy.cpp cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +FileUtils.cpp: In function 'int FileUtils::checkBgenSample(const std::string&, const std::string&, int)': +FileUtils.cpp:338:14: warning: unused variable 'destLen' [-Wunused-variable] + 338 | uLongf destLen = D, bufLen = D, zBufLen = C-4; + | ^~~~~~~ +NonlinearOptMulti.cpp: In function 'std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)': +NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type 'class nlopt::roundoff_limited' by value [-Wcatch-value=] + 230 | catch (nlopt::roundoff_limited) { + | ^~~~~~~~~~~~~~~~ In file included from Bolt.cpp:56: In member function 'LMM::Bolt::VarCompData& LMM::Bolt::VarCompData::operator=(const LMM::Bolt::VarCompData&)', inlined from 'double LMM::Bolt::estLogDelta(double*, double*, const std::vector&, int, double, int, double, int, bool) const' at Bolt.cpp:2219:16: @@ -605,8 +641,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.4.1+dfsg-2_all.deb'. dpkg-deb: building package 'bolt-lmm-dbgsym' in '../bolt-lmm-dbgsym_2.4.1+dfsg-2_i386.deb'. +dpkg-deb: building package 'bolt-lmm-example' in '../bolt-lmm-example_2.4.1+dfsg-2_all.deb'. dpkg-deb: building package 'bolt-lmm' in '../bolt-lmm_2.4.1+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../bolt-lmm_2.4.1+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../bolt-lmm_2.4.1+dfsg-2_i386.changes @@ -615,12 +651,14 @@ 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/60529/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/60529/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/45804 and its subdirectories -I: Current time: Thu May 16 11:07:39 -12 2024 -I: pbuilder-time-stamp: 1715900859 +I: removing directory /srv/workspace/pbuilder/60529 and its subdirectories +I: Current time: Thu Jun 19 19:31:37 +14 2025 +I: pbuilder-time-stamp: 1750311097