Diff of the two buildlogs: -- --- b1/build.log 2024-12-10 01:45:25.344187428 +0000 +++ b2/build.log 2024-12-10 01:47:19.423008407 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 11 20:06:15 -12 2026 -I: pbuilder-time-stamp: 1768205175 +I: Current time: Mon Jan 12 22:08:28 +14 2026 +I: pbuilder-time-stamp: 1768205308 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3385801/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3708482/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Jan 12 08:08 /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/3708482/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3708482/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='fb127660e7da4d55911490ed5e9cc857' - 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='3385801' - PS1='# ' - PS2='> ' + INVOCATION_ID=a527ea6d264042a6b1825a5f0a67f7f9 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3708482 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.0LCVuCA3/pbuilderrc_56pA --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0LCVuCA3/b1 --logfile b1/build.log hilive_2.0a-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.0LCVuCA3/pbuilderrc_vAyO --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0LCVuCA3/b2 --logfile b2/build.log hilive_2.0a-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3385801/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3708482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -270,7 +302,7 @@ Get: 119 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 liblz4-dev arm64 1.9.4-3+b1 [79.1 kB] Get: 121 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] -Fetched 76.4 MB in 1s (149 MB/s) +Fetched 76.4 MB in 0s (165 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 20083 files and directories currently installed.) @@ -769,7 +801,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hilive-2.0a/ && 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 > ../hilive_2.0a-5_source.changes +I: user script /srv/workspace/pbuilder/3708482/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/3708482/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hilive-2.0a/ && 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 > ../hilive_2.0a-5_source.changes dpkg-buildpackage: info: source package hilive dpkg-buildpackage: info: source version 2.0a-5 dpkg-buildpackage: info: source distribution experimental @@ -807,7 +843,7 @@ -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found SeqAn: /usr/include (found version "2.5.0") --- Configuring done (2.7s) +-- Configuring done (2.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -838,25 +874,25 @@ make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' [ 6%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/tools_static.cpp -[ 12%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o +[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o +[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o +[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o +[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o +[ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o +[ 43%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o +[ 50%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o +[ 56%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/tools.cpp -[ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnread.cpp -[ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp -[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnout.cpp -[ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -[ 43%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/kindex.cpp -[ 50%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/parallel.cpp -[ 56%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/argument_parser.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, - from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, - from /build/reproducible-path/hilive-2.0a/lib/parallel.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:6, + from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -868,7 +904,7 @@ from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/parallel.h:4: + from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -891,7 +927,8 @@ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ -In file included from /build/reproducible-path/hilive-2.0a/lib/tools_static.cpp:1: +In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, + from /build/reproducible-path/hilive-2.0a/lib/tools.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -927,8 +964,8 @@ 1043 | not1(const _Predicate& __pred) | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, - from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, - from /build/reproducible-path/hilive-2.0a/lib/kindex.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, + from /build/reproducible-path/hilive-2.0a/lib/parallel.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -940,7 +977,7 @@ from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/kindex.h:4: + from /build/reproducible-path/hilive-2.0a/lib/parallel.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -965,8 +1002,8 @@ | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnread.h:6, - from /build/reproducible-path/hilive-2.0a/lib/alnread.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/alnout.h:7, + from /build/reproducible-path/hilive-2.0a/lib/alnout.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -978,7 +1015,7 @@ from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/alnread.h:4: + from /build/reproducible-path/hilive-2.0a/lib/alnout.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1002,20 +1039,18 @@ 1043 | not1(const _Predicate& __pred) | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, - from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:6, - from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, + from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:5, + from /build/reproducible-path/hilive-2.0a/lib/argument_parser.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:4: + from /usr/include/boost/program_options/errors.hpp:12, + from /usr/include/boost/program_options/options_description.hpp:12, + from /usr/include/boost/program_options.hpp:15, + from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:1: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1040,14 +1075,8 @@ | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnout.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnout.cpp:1: -/build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': -/build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] - 304 | std::not1(std::ptr_fun(std::isspace)))); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, - from /build/reproducible-path/hilive-2.0a/lib/tools.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:7, + from /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -1059,21 +1088,7 @@ from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/tools_static.h:10: -/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here - 1123 | ptr_fun(_Result (*__x)(_Arg)) - | ^~~~~~~ -/build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:22: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] - 304 | std::not1(std::ptr_fun(std::isspace)))); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/alnout.h:4: + from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1087,14 +1102,33 @@ /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here + 1123 | ptr_fun(_Result (*__x)(_Arg)) + | ^~~~~~~ +/build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:22: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] + 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ +In file included from /build/reproducible-path/hilive-2.0a/lib/tools_static.cpp:1: +/build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': +/build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] + 304 | std::not1(std::ptr_fun(std::isspace)))); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, + from /build/reproducible-path/hilive-2.0a/lib/tools_static.h:10: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ -/build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:22: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] - 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); +/build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:22: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] + 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) @@ -1114,8 +1148,8 @@ | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/alnread.h:6, + from /build/reproducible-path/hilive-2.0a/lib/alnread.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); @@ -1127,7 +1161,7 @@ from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, - from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:4: + from /build/reproducible-path/hilive-2.0a/lib/alnread.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1151,18 +1185,20 @@ 1043 | not1(const _Predicate& __pred) | ^~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, - from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, - from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:5, - from /build/reproducible-path/hilive-2.0a/lib/argument_parser.cpp:1: + from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, + from /build/reproducible-path/hilive-2.0a/lib/kindex.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, - from /usr/include/boost/program_options/errors.hpp:12, - from /usr/include/boost/program_options/options_description.hpp:12, - from /usr/include/boost/program_options.hpp:15, - from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:1: + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, + from /build/reproducible-path/hilive-2.0a/lib/kindex.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1217,20 +1253,20 @@ make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' cd /build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu /build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu /build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu/CMakeFiles/hilive-out.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' +make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' -make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' -make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build +make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu' [ 81%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -[ 81%] Building CXX object CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o [ 81%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.cpp.o +[ 81%] Building CXX object CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o +/usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-aarch64-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection 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-ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++17 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_OPENMP=1 -fopenmp -MD -MT CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -MF CMakeFiles/hilive-build.dir/tools/build_index.cpp.o.d -o CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/build_index.cpp In file included from /build/reproducible-path/hilive-2.0a/tools/../lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/tools/../lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/tools/hilive.cpp:4: @@ -1398,12 +1434,14 @@ 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 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