Diff of the two buildlogs: -- --- b1/build.log 2024-11-26 23:12:45.688445410 +0000 +++ b2/build.log 2024-11-26 23:14:18.584245063 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 26 11:10:58 -12 2024 -I: pbuilder-time-stamp: 1732662658 +I: Current time: Tue Dec 30 19:35:47 +14 2025 +I: pbuilder-time-stamp: 1767072947 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -32,53 +32,85 @@ 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/22037/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/23535/tmp/hooks/D01_modify_environment starting +debug: Running on infom08-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 Dec 30 05:35 /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/23535/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/23535/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=6 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='74c42794e1294ad890187d122738118c' - 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='22037' - PS1='# ' - PS2='> ' + INVOCATION_ID=e978b78351624dc4a0982ec1886a301e + 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=23535 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.9BfxC5My/pbuilderrc_eHve --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.9BfxC5My/b1 --logfile b1/build.log hilive_2.0a-5.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.9BfxC5My/pbuilderrc_xmG1 --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.9BfxC5My/b2 --logfile b2/build.log hilive_2.0a-5.dsc' + SUDO_GID=111 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom07-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/22037/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/23535/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -272,7 +304,7 @@ Get: 119 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.20+ds-2 [1693 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 liblz4-dev i386 1.9.4-3+b1 [84.8 kB] Get: 121 http://deb.debian.org/debian experimental/main i386 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] -Fetched 81.5 MB in 8s (10.8 MB/s) +Fetched 81.5 MB in 1s (113 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19959 files and directories currently installed.) @@ -771,7 +803,11 @@ 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/23535/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/23535/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 @@ -809,7 +845,7 @@ -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found SeqAn: /usr/include (found version "2.5.0") --- Configuring done (1.1s) +-- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -826,7 +862,7 @@ -- Build files have been written to: /build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/hilive-2.0a' dh_auto_build - cd obj-i686-linux-gnu && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j5 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hilive-2.0a -B/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -838,21 +874,17 @@ make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' make -f CMakeFiles/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/build make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' -[ 6%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -[ 12%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -[ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -[ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o +[ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o +[ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o +[ 18%] 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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/alnread.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 -/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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/alnstream.cpp.o -/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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: +[ 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 +/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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)))); @@ -864,7 +896,7 @@ 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/illumina_parsers.h:4: + 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)) | ^~~~~~~ @@ -888,9 +920,7 @@ 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/alnstream.h:7, - from /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:1: + 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)))); @@ -902,7 +932,7 @@ 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/tools_static.h:10: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -926,7 +956,9 @@ 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/tools.cpp:1: + 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: /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)))); @@ -938,7 +970,7 @@ 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: + 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)) | ^~~~~~~ @@ -963,8 +995,8 @@ | ^~~~ 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/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)))); @@ -976,7 +1008,7 @@ 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/alnstream.h:4: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -999,7 +1031,10 @@ /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/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)))); @@ -1011,7 +1046,7 @@ 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: + 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)) | ^~~~~~~ @@ -1034,10 +1069,30 @@ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ +/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'uint64_t oAlnStream::lz4write(const char*, uint64_t)': +/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:23:43: warning: 'int LZ4_compress(const char*, char*, int)' is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] + 23 | uint32_t compressed_size = LZ4_compress (source, buf.data(), size); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/hilive-2.0a/lib/headers.h:5: +/usr/include/lz4.h:765:75: note: declared here + 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); + | ^~~~~~~~~~~~ +/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'ReadAlignment* iAlnStream::get_alignment()': +/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:359:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 359 | fread(buffer.data(),1,buf_size,fstream); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:389:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 389 | fread(buffer.data(),1,buf_size,fstream); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o +/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[ 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 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: + 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)))); @@ -1049,7 +1104,7 @@ 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/alnout.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)) | ^~~~~~~ @@ -1072,25 +1127,6 @@ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ -/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'uint64_t oAlnStream::lz4write(const char*, uint64_t)': -/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:23:43: warning: 'int LZ4_compress(const char*, char*, int)' is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] - 23 | uint32_t compressed_size = LZ4_compress (source, buf.data(), size); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/hilive-2.0a/lib/headers.h:5: -/usr/include/lz4.h:765:75: note: declared here - 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); - | ^~~~~~~~~~~~ -[ 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 -/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'ReadAlignment* iAlnStream::get_alignment()': -/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:359:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 359 | fread(buffer.data(),1,buf_size,fstream); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:389:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 389 | fread(buffer.data(),1,buf_size,fstream); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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, @@ -1219,20 +1255,20 @@ make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' cd /build/reproducible-path/hilive-2.0a/obj-i686-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-i686-linux-gnu /build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu /build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu/CMakeFiles/hilive-out.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-i686-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[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-i686-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-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' +make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build +make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-i686-linux-gnu' +[ 68%] 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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-out.dir/tools/hilive_out.cpp.o -MF CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o.d -o CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp [ 75%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -[ 75%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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.dir/tools/hilive.cpp.o -MF CMakeFiles/hilive.dir/tools/hilive.cpp.o.d -o CMakeFiles/hilive.dir/tools/hilive.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive.cpp /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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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-out.dir/tools/hilive_out.cpp.o -MF CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o.d -o CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp +[ 81%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.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-i686-linux-gnu -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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.dir/tools/hilive.cpp.o -MF CMakeFiles/hilive.dir/tools/hilive.cpp.o.d -o CMakeFiles/hilive.dir/tools/hilive.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive.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: @@ -1272,7 +1308,7 @@ | ^~~~ 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_out.cpp:5: + from /build/reproducible-path/hilive-2.0a/tools/build_index.cpp:5: /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../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)))); @@ -1281,7 +1317,7 @@ 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/tools/hilive_out.cpp:1: + from /build/reproducible-path/hilive-2.0a/tools/build_index.cpp:1: /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ @@ -1291,13 +1327,6 @@ /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/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/build_index.cpp:5: -/build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': -/build/reproducible-path/hilive-2.0a/tools/../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)))); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../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()); @@ -1305,20 +1334,27 @@ /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/tools/../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/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_out.cpp:5: +/build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': +/build/reproducible-path/hilive-2.0a/tools/../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/tools/build_index.cpp:1: + from /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp:1: /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/tools/../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) - | ^~~~ /build/reproducible-path/hilive-2.0a/tools/../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)))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1396,12 +1432,14 @@ 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/23535/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/23535/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/22037 and its subdirectories -I: Current time: Tue Nov 26 11:12:44 -12 2024 -I: pbuilder-time-stamp: 1732662764 +I: removing directory /srv/workspace/pbuilder/23535 and its subdirectories +I: Current time: Tue Dec 30 19:37:16 +14 2025 +I: pbuilder-time-stamp: 1767073036