Diff of the two buildlogs: -- --- b1/build.log 2024-04-07 16:10:41.220183932 +0000 +++ b2/build.log 2024-04-07 16:12:56.238436699 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 7 04:06:43 -12 2024 -I: pbuilder-time-stamp: 1712506003 +I: Current time: Sun May 11 12:33:42 +14 2025 +I: pbuilder-time-stamp: 1746916422 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,54 +33,86 @@ 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/33790/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10204/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 10 22:33 /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/10204/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10204/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=8 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='3a3fd5c58dee4dea88a8159ab8d74c8e' - 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='33790' - PS1='# ' - PS2='> ' + INVOCATION_ID=64e8d9fdd8a24314b274484aaa779f43 + 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=10204 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.KypboSZj/pbuilderrc_5jm0 --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.KypboSZj/b1 --logfile b1/build.log idba_1.1.3-8.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.KypboSZj/pbuilderrc_IfSu --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.KypboSZj/b2 --logfile b2/build.log idba_1.1.3-8.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 7 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/33790/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 9 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/10204/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -165,7 +197,7 @@ Get: 43 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 googletest all 1.14.0-1 [512 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libgtest-dev i386 1.14.0-1+b1 [263 kB] -Fetched 26.1 MB in 2s (16.1 MB/s) +Fetched 26.1 MB in 0s (93.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19876 files and directories currently installed.) @@ -324,8 +356,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 7 16:07:19 UTC 2024. -Universal Time is now: Sun Apr 7 16:07:19 UTC 2024. +Local time is now: Sat May 10 22:34:01 UTC 2025. +Universal Time is now: Sat May 10 22:34:01 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -368,7 +400,11 @@ 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/10204/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/10204/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 @@ -612,7 +648,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' dh_auto_build - make -j8 + make -j21 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' @@ -626,6 +662,29 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc +../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 -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 -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 ../src/container/hash_map.h:14, from ../src/misc/hash_aligner.h:14, from ../src/misc/hash_aligner.cpp:9: @@ -686,23 +745,6 @@ /usr/include/c++/13/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' -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp -../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 -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 -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/graph/contig_graph_branch_group.h:15, @@ -764,8 +806,6 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/graph/contig_graph.cpp:9: @@ -826,66 +866,6 @@ /usr/include/c++/13/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/graph/hash_graph.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++/13/bits/refwrap.h:39, - from /usr/include/c++/13/deque:67, - from ../src/graph/hash_graph.h:15: -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 25 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 32 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 39 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 46 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 53 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 60 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 67 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 74 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/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/graph/scaffold_graph.h:19, @@ -951,11 +931,19 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../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 -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 -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp +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++/13/bits/refwrap.h:39, + from /usr/include/c++/13/deque:67, + from ../src/assembly/assembly_utility.h:17, + from ../src/assembly/assembly_utility.cpp:9: +/usr/include/c++/13/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/graph/hash_graph_branch_group.h:14, @@ -963,6 +951,12 @@ ../src/basic/hash.h:18:26: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 18 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 25 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from ../src/graph/hash_graph.h:15: @@ -981,33 +975,75 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 32 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 39 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 46 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 53 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 60 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 67 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 74 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1017,7 +1053,6 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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, @@ -1080,16 +1115,19 @@ /usr/include/c++/13/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/assembly/assembly_utility.cpp:14: +../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); + | ^~~ +In file included from ../src/container/hash_table.h:23, + from ../src/graph/hash_graph.h:22, + from ../src/graph/hash_graph.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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/assembly/assembly_utility.h:17, - from ../src/assembly/assembly_utility.cpp:9: + from ../src/graph/hash_graph.h:15: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1148,8 +1186,6 @@ ../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 -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 -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 -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 -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: ../gtest_src/gtest/gtest.h: In static member function 'static const char* testing::internal::String::CloneCString(const char*)': ../gtest_src/gtest/gtest.h:2672:17: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] @@ -1177,16 +1213,38 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.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: +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 +g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -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 -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 -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"; + | ^ +In file included from ../src/container/hash_map.h:14, + from ../src/graph/contig_graph.h:19, + from ../src/tools/test.cpp:6: ../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++/13/bits/refwrap.h:39, - from /usr/include/c++/13/deque:67, - from ../src/release/idba_tran.cpp:11: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from ../src/tools/test.cpp:1: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1208,7 +1266,6 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ @@ -1239,20 +1296,35 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const std::string&)': +../src/tools/parallel_rna_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()); + | ~~~~~~^~~~~~~~~~~~~ +../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const std::string&)': +../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 53 | system(cmd.c_str()); + | ~~~~~~^~~~~~~~~~~~~ +../src/tools/parallel_rna_blat.cpp: In function 'void Append(const std::string&, const std::string&)': +../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 59 | system(cmd.c_str()); + | ~~~~~~^~~~~~~~~~~~~ +../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const std::string&)': +../src/tools/parallel_rna_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()); + | ~~~~~~^~~~~~~~~~~~~ ../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]; | ^~~~~~ -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_hybrid.cpp:21: +In file included from ../src/container/hash_map.h:14, + from ../src/graph/contig_graph.h:19, + from ../src/tools/print_graph.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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/release/idba_hybrid.cpp:11: + from ../src/graph/contig_graph.h:14: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1307,13 +1379,13 @@ 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: + from ../src/tools/idba_tran_test.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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/release/idba_ud.cpp:11: + from ../src/tools/idba_tran_test.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1368,13 +1440,13 @@ 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/tools/scaffold.cpp:21: + 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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/tools/scaffold.cpp:11: + from ../src/release/idba_ud.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1384,97 +1456,94 @@ /usr/include/c++/13/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_hybrid.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 + | ^~~~~~~~~~~~~~ ../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 39 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/deque:67, + from ../src/release/idba_hybrid.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 46 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ +../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 25 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 53 | struct Hash: public std::unary_function +../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 60 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 67 | struct Hash: public std::unary_function +../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 32 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 74 | struct Hash: public std::unary_function +../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/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) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -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++/13/bits/refwrap.h:39, - from /usr/include/c++/13/deque:67, - from ../src/release/idba.cpp:11: -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 25 | struct Hash: public std::unary_function - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ -../src/basic/hash.h:32:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 32 | struct Hash: public std::unary_function +../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ ../src/basic/hash.h:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ +../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 60 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ ../src/basic/hash.h:46:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 46 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 67 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../src/basic/hash.h:60:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 60 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ +../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] + 74 | struct Hash: public std::unary_function + | ^~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here + 117 | struct unary_function + | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1490,41 +1559,16 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../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 -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 -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_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]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../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 -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 -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.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: +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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/graph/contig_graph.h:14: + from ../src/release/idba_tran.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1576,18 +1620,38 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.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 -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 -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.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 -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 -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.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/tools/idba_tran_test.cpp:21: + from ../src/tools/scaffold.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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, - from ../src/tools/idba_tran_test.cpp:11: + from ../src/tools/scaffold.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1639,50 +1703,25 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -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 -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 -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 -../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const std::string&)': -../src/tools/parallel_rna_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()); - | ~~~~~~^~~~~~~~~~~~~ -../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const std::string&)': -../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 53 | system(cmd.c_str()); - | ~~~~~~^~~~~~~~~~~~~ -../src/tools/parallel_rna_blat.cpp: In function 'void Append(const std::string&, const std::string&)': -../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 59 | system(cmd.c_str()); - | ~~~~~~^~~~~~~~~~~~~ -../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const std::string&)': -../src/tools/parallel_rna_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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.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 -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 -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 -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 -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 -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 -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 +../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 -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 -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, - from ../src/tools/test.cpp:6: + 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++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from ../src/tools/test.cpp:1: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/deque:67, + from ../src/release/idba.cpp:11: /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1734,16 +1773,11 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -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 -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 -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 -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 -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 -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 -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 -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 -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 -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/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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.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()); @@ -1760,41 +1794,43 @@ ../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()); | ~~~~~~^~~~~~~~~~~~~ -../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 -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 -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 -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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic +../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++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold 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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.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 -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 -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 -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 -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 -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 -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 g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic +../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++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -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 -g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/idba-1.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.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 -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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.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 -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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold 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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.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 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.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 -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 @@ -1812,7 +1848,7 @@ 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' @@ -2062,7 +2098,7 @@ dh_prep dh_installdirs dh_auto_install - make -j8 install DESTDIR=/build/reproducible-path/idba-1.1.3/debian/tmp AM_UPDATE_INFO_DIR=no + make -j21 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' @@ -2130,8 +2166,8 @@ dh_builddeb dpkg-deb: building package 'idba' in '../idba_1.1.3-8_i386.deb'. dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_i386.deb'. -dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_i386.deb'. dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_i386.deb'. +dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_i386.deb'. dpkg-genbuildinfo --build=binary -O../idba_1.1.3-8_i386.buildinfo dpkg-genchanges --build=binary -O../idba_1.1.3-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2139,12 +2175,14 @@ 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/10204/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10204/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/33790 and its subdirectories -I: Current time: Sun Apr 7 04:10:40 -12 2024 -I: pbuilder-time-stamp: 1712506240 +I: removing directory /srv/workspace/pbuilder/10204 and its subdirectories +I: Current time: Sun May 11 12:35:53 +14 2025 +I: pbuilder-time-stamp: 1746916553