Diff of the two buildlogs: -- --- b1/build.log 2024-11-30 09:15:37.464849939 +0000 +++ b2/build.log 2024-11-30 09:24:57.303595215 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 29 21:04:28 -12 2024 -I: pbuilder-time-stamp: 1732957468 +I: Current time: Sat Nov 30 23:16:27 +14 2024 +I: pbuilder-time-stamp: 1732958187 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying use_debian_packaged_googletest.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/5982/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10527/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 Nov 30 09:16 /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/10527/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10527/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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + 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=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='0da34ada352540d5956e5bc044608c8f' - 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='5982' - PS1='# ' - PS2='> ' + INVOCATION_ID=d46dd7d661624c28851e9d960153bc3a + 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=10527 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.NVLoztjW/pbuilderrc_9VZO --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.NVLoztjW/b1 --logfile b1/build.log idba_1.1.3-8.dsc' - SUDO_GID='112' - SUDO_UID='106' - 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.NVLoztjW/pbuilderrc_tXk2 --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.NVLoztjW/b2 --logfile b2/build.log idba_1.1.3-8.dsc' + SUDO_GID=110 + SUDO_UID=103 + 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 virt32b 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/5982/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/10527/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -170,7 +202,7 @@ Get: 51 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf googletest all 1.15.2-1 [514 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libgtest-dev armhf 1.15.2-1 [246 kB] -Fetched 26.3 MB in 1s (43.6 MB/s) +Fetched 26.3 MB in 1s (38.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (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 ... 19683 files and directories currently installed.) @@ -364,8 +396,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 30 09:05:12 UTC 2024. -Universal Time is now: Sat Nov 30 09:05:12 UTC 2024. +Local time is now: Sat Nov 30 09:17:24 UTC 2024. +Universal Time is now: Sat Nov 30 09:17:24 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -411,7 +443,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/idba-1.1.3/ && 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 > ../idba_1.1.3-8_source.changes +I: user script /srv/workspace/pbuilder/10527/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/10527/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/idba-1.1.3/ && 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 > ../idba_1.1.3-8_source.changes dpkg-buildpackage: info: source package idba dpkg-buildpackage: info: source version 1.1.3-8 dpkg-buildpackage: info: source distribution unstable @@ -655,7 +691,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' make all-recursive make[2]: Entering directory '/build/reproducible-path/idba-1.1.3' @@ -664,6 +700,7 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp In file included from ../src/container/hash_map.h:14, from ../src/misc/hash_aligner.h:14, from ../src/misc/hash_aligner.cpp:9: @@ -724,6 +761,16 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()': +../src/misc/log.cpp:78:13: warning: 'throw' will always call 'terminate' [-Wterminate] + 78 | throw runtime_error("cannot kill log process"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../src/misc/log.cpp:78:13: note: in C++11 destructors default to 'noexcept' +../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)': +../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] + 122 | write(log_thread.out_fd, line, len); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from ../src/basic/math.cpp:3: @@ -764,17 +811,6 @@ /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++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp -../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()': -../src/misc/log.cpp:78:13: warning: 'throw' will always call 'terminate' [-Wterminate] - 78 | throw runtime_error("cannot kill log process"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../src/misc/log.cpp:78:13: note: in C++11 destructors default to 'noexcept' -../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)': -../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] - 122 | write(log_thread.out_fd, line, len); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp @@ -1032,11 +1068,11 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp ../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque&, std::deque&)': ../src/graph/contig_graph.cpp:1391:30: warning: variable 'end' set but not used [-Wunused-but-set-variable] 1391 | ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component); | ^~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/graph/hash_graph_branch_group.h:14, @@ -1101,17 +1137,16 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp -In file included from ../src/container/hash_table.h:23, - from ../src/graph/hash_graph.h:22, - from ../src/assembly/local_assembler.h:15, - from ../src/assembly/local_assembler.cpp:9: +In file included from ../src/container/hash_map.h:14, + from ../src/graph/contig_graph.h:19, + from ../src/assembly/assembly_utility.cpp:14: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, from ../src/assembly/assembly_utility.h:17, - from ../src/assembly/local_assembler.h:13: + from ../src/assembly/assembly_utility.cpp:9: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1163,23 +1198,17 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)': -../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable] - 488 | bool flag = false; - | ^~~~ -../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable] - 489 | int aligned[2] = {0}; - | ^~~~~~~ -In file included from ../src/container/hash_map.h:14, - from ../src/graph/contig_graph.h:19, - from ../src/assembly/assembly_utility.cpp:14: +In file included from ../src/container/hash_table.h:23, + from ../src/graph/hash_graph.h:22, + from ../src/assembly/local_assembler.h:15, + from ../src/assembly/local_assembler.cpp:9: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, from ../src/assembly/assembly_utility.h:17, - from ../src/assembly/assembly_utility.cpp:9: + from ../src/assembly/local_assembler.h:13: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1231,6 +1260,13 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)': +../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable] + 488 | bool flag = false; + | ^~~~ +../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable] + 489 | int aligned[2] = {0}; + | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc In file included from ../gtest_src/gtest/gtest-all.cc:39: @@ -1255,16 +1291,17 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, - from ../src/release/idba_tran.cpp:22: + from ../src/release/idba_ud.cpp:21: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ../src/release/idba_tran.cpp:11: + from ../src/release/idba_ud.cpp:11: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1316,16 +1353,15 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -In file included from ../src/container/hash_table.h:23, - from ../src/graph/hash_graph.h:22, - from ../src/assembly/local_assembler.h:15, - from ../src/release/idba_ud.cpp:21: +In file included from ../src/container/hash_map.h:14, + from ../src/graph/contig_graph.h:19, + from ../src/release/idba.cpp:23: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ../src/release/idba_ud.cpp:11: + from ../src/release/idba.cpp:11: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1377,15 +1413,16 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -In file included from ../src/container/hash_map.h:14, - from ../src/graph/contig_graph.h:19, - from ../src/release/idba.cpp:23: +In file included from ../src/container/hash_table.h:23, + from ../src/graph/hash_graph.h:22, + from ../src/assembly/local_assembler.h:15, + from ../src/release/idba_tran.cpp:22: ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ../src/release/idba.cpp:11: + from ../src/release/idba_tran.cpp:11: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1437,15 +1474,6 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque&, ContigGraph&, std::deque&)': -../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 241 | if (flag && path.size() > option.min_transcript) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)': -../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 523 | if (transcripts[i].size() >= option.min_transcript) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, @@ -1507,6 +1535,14 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque&, ContigGraph&, std::deque&)': +../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 241 | if (flag && path.size() > option.min_transcript) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)': +../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 523 | if (transcripts[i].size() >= option.min_transcript) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp In file included from ../src/container/hash_table.h:23, @@ -1571,18 +1607,35 @@ 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp ../src/tools/validate_component.cpp: In function 'int main(int, char**)': ../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable] 141 | int ref_id = dict[record.ref_name]; | ^~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp ../src/tools/validate_rna.cpp: In function 'int main(int, char**)': ../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 396 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp +../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)': +../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 218 | fgets(line, MaxLine, fcoord); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 219 | fgets(line, MaxLine, fcoord); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 220 | fgets(line, MaxLine, fcoord); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fgets(line, MaxLine, fcoord); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 222 | fgets(line, MaxLine, fcoord); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/tools/print_graph.cpp:9: @@ -1643,25 +1696,6 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)': -../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 218 | fgets(line, MaxLine, fcoord); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 219 | fgets(line, MaxLine, fcoord); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 220 | fgets(line, MaxLine, fcoord); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fgets(line, MaxLine, fcoord); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 222 | fgets(line, MaxLine, fcoord); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/assembly/local_assembler.h:15, @@ -1723,6 +1757,8 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp @@ -1745,13 +1781,14 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp ../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive 6 | #include "graph/contig_graph.h"; | ^ ../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive 7 | #include "sequence/sequence.h"; | ^ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/tools/test.cpp:6: @@ -1816,27 +1853,27 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp In file included from /usr/include/c++/14/vector:72, from ../src/tools/validate_reads_blat.cpp:16: /usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at ../src/tools/validate_reads_blat.cpp:71:24: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp ../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)': ../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 388 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp ../src/release/parallel_blat.cpp: In function 'void CreateFile(const std::string&)': ../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 47 | system(cmd.c_str()); @@ -1853,12 +1890,11 @@ ../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp ../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)': ../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 89 | fscanf(flist, "%s %lf", buf, &weight[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic @@ -1872,7 +1908,6 @@ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic -g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic @@ -1881,8 +1916,8 @@ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic -g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic +g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic @@ -1891,6 +1926,7 @@ g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic +g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' Making all in test make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' @@ -1907,7 +1943,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' # /usr/bin/make unittest -export PATH=/build/reproducible-path/idba-1.1.3/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games && cd test && /usr/bin/make check +export PATH=/build/reproducible-path/idba-1.1.3/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path && cd test && /usr/bin/make check make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/test' /usr/bin/make compact_sequence_unittest hash_table_unittest bit_edges_unittest kmer_unittest hash_set_unittest atomic_integer_unittest vertex_status_unittest histgram_unittest managed_list_unittest sequence_unittest short_sequence_unittest hash_map_unittest make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/test' @@ -2289,7 +2325,7 @@ dh_prep dh_installdirs dh_auto_install - make -j3 install DESTDIR=/build/reproducible-path/idba-1.1.3/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/idba-1.1.3/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/idba-1.1.3' Making install in lib make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/lib' @@ -2357,24 +2393,24 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/idba/usr/bin/idba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_psl contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_hybrid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_ud contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_tran contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_hybrid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/idba/usr/bin/idba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/parallel_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/parallel_rna_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_psl contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/parallel_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'idba' in '../idba_1.1.3-8_armhf.deb'. dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_armhf.deb'. dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_armhf.deb'. +dpkg-deb: building package 'idba' in '../idba_1.1.3-8_armhf.deb'. dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../idba_1.1.3-8_armhf.buildinfo dpkg-genchanges --build=binary -O../idba_1.1.3-8_armhf.changes @@ -2383,12 +2419,14 @@ 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/10527/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10527/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/5982 and its subdirectories -I: Current time: Fri Nov 29 21:15:32 -12 2024 -I: pbuilder-time-stamp: 1732958132 +I: removing directory /srv/workspace/pbuilder/10527 and its subdirectories +I: Current time: Sat Nov 30 23:24:53 +14 2024 +I: pbuilder-time-stamp: 1732958693