Diff of the two buildlogs: -- --- b1/build.log 2024-12-19 03:54:06.095430764 +0000 +++ b2/build.log 2024-12-19 03:58:26.079641533 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 18 15:48:20 -12 2024 -I: pbuilder-time-stamp: 1734580100 +I: Current time: Thu Dec 19 17:54:30 +14 2024 +I: pbuilder-time-stamp: 1734580470 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18962/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15263/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 19 03:54 /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/15263/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15263/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='98a39b936a334db795eb7a74fa8a03a2' - 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='18962' - PS1='# ' - PS2='> ' + INVOCATION_ID=e22aa78610ab414f8e8d3f3408117636 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=15263 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.Ql5faG1K/pbuilderrc_dnT7 --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.Ql5faG1K/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.Ql5faG1K/pbuilderrc_OMtQ --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.Ql5faG1K/b2 --logfile b2/build.log muscle_5.1.0-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18962/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/15263/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] -Fetched 19.1 MB in 0s (40.8 MB/s) +Fetched 19.1 MB in 1s (28.5 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 ... 19674 files and directories currently installed.) @@ -271,7 +303,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes +I: user script /srv/workspace/pbuilder/15263/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/15263/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable @@ -281,7 +317,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j3 clean + cd src && make -j4 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' @@ -295,13 +331,13 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' - cd src && make -j3 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) + cd src && make -j4 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash -Repo not found, git hash set to zero mkdir -p Linux/ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp +Repo not found, git hash set to zero g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp @@ -323,11 +359,11 @@ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp derep.cpp: In member function 'uint Derep::CalcHash(const Sequence*) const': derep.cpp:15:19: warning: conversion from 'long long unsigned int' to 'uint64' {aka 'long unsigned int'} changes value from '14695981039346656037' to '2216829733' [-Woverflow] 15 | uint64 hash = 0xcbf29ce484222325uL; | ^~~~~~~~~~~~~~~~~~~~ -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp @@ -339,6 +375,7 @@ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from myutils.h:32, @@ -421,6 +458,9 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from myutils.h:32, @@ -435,7 +475,6 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -444,8 +483,9 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:780:6: @@ -506,10 +546,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/help.o help.cpp @@ -532,6 +568,7 @@ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ @@ -550,12 +587,11 @@ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp myutils.cpp: In function 'void IncrementRand()': myutils.cpp:2268:32: warning: right shift count >= width of type [-Wshift-count-overflow] 2268 | g_X[4] = (uint32) (Sum >> 32); | ~~~~^~~~~ -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp @@ -647,12 +683,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/15263/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15263/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/18962 and its subdirectories -I: Current time: Wed Dec 18 15:54:02 -12 2024 -I: pbuilder-time-stamp: 1734580442 +I: removing directory /srv/workspace/pbuilder/15263 and its subdirectories +I: Current time: Thu Dec 19 17:58:21 +14 2024 +I: pbuilder-time-stamp: 1734580701