Diff of the two buildlogs: -- --- b1/build.log 2025-03-18 19:52:21.928231531 +0000 +++ b2/build.log 2025-03-18 19:57:09.719229154 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Mar 18 07:50:47 -12 2025 -I: pbuilder-time-stamp: 1742327447 +I: Current time: Tue Apr 21 16:15:25 +14 2026 +I: pbuilder-time-stamp: 1776737725 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,51 +28,83 @@ 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/1604387/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1086845/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 Apr 21 02:15 /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/1086845/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1086845/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='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e4ebf16019a14cca8652011cf40ba6af' - 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='1604387' - PS1='# ' - PS2='> ' + INVOCATION_ID=d6149d0d675f4477a42d50ceeee4ff5d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=1086845 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.wsUcDSeH/pbuilderrc_ErcJ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wsUcDSeH/b1 --logfile b1/build.log idba_1.1.3-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.wsUcDSeH/pbuilderrc_UwGL --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wsUcDSeH/b2 --logfile b2/build.log idba_1.1.3-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-32-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1604387/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1086845/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -158,7 +190,7 @@ Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 googletest all 1.16.0-1 [517 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.16.0-1 [259 kB] -Fetched 28.2 MB in 0s (110 MB/s) +Fetched 28.2 MB in 1s (48.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19784 files and directories currently installed.) @@ -324,8 +356,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Mar 18 19:51:12 UTC 2025. -Universal Time is now: Tue Mar 18 19:51:12 UTC 2025. +Local time is now: Tue Apr 21 02:16:01 UTC 2026. +Universal Time is now: Tue Apr 21 02:16:01 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -369,7 +401,11 @@ 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/1086845/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1086845/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 @@ -634,6 +670,11 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.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' In file included from ../src/container/hash_map.h:14, from ../src/misc/hash_aligner.h:14, from ../src/misc/hash_aligner.cpp:9: @@ -694,11 +735,6 @@ /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); @@ -849,7 +885,6 @@ /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 -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 -fcf-protection -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc ../src/basic/hash.h:25:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 25 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ @@ -898,6 +933,7 @@ /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 -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 -fcf-protection -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc In file included from ../src/container/hash_table.h:23, from ../src/graph/hash_graph.h:22, from ../src/graph/hash_graph.cpp:9: @@ -1020,6 +1056,10 @@ /usr/include/c++/14/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); + | ^~~ In file included from ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/assembly/assembly_utility.cpp:14: @@ -1075,10 +1115,6 @@ /usr/include/c++/14/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); - | ^~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ @@ -1243,24 +1279,16 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../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]; - | ^~~~~~ -../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]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ../src/tools/idba_tran_test.cpp:11: + from ../src/tools/scaffold.cpp:11: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1312,16 +1340,24 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +../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]; + | ^~~~~~ +../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]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_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 | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, - from ../src/tools/scaffold.cpp:11: + from ../src/release/idba_hybrid.cpp:11: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ @@ -1337,12 +1373,6 @@ /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: -../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:39:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 39 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ @@ -1361,24 +1391,12 @@ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct 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: -/usr/include/c++/14/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++/14/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++/14/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 | ^~~~~~~~~~~~~~ @@ -1391,6 +1409,25 @@ /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/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++/14/bits/refwrap.h:39, + from /usr/include/c++/14/deque:67, + from ../src/tools/idba_tran_test.cpp:11: +/usr/include/c++/14/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++/14/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 | ^~~~~~~~~~~~~~ @@ -1433,16 +1470,15 @@ /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_hybrid.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_hybrid.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 | ^~~~~~~~~~~~~~ @@ -1497,13 +1533,13 @@ 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_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 | ^~~~~~~~~~~~~~ @@ -1534,38 +1570,21 @@ ../src/basic/hash.h:53:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 53 | struct Hash: public std::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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp /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/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++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../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/basic/hash.h:67:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 67 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ -../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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -../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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/basic/hash.h:74:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 74 | struct Hash: public std::unary_function | ^~~~~~~~~~~~~~ @@ -1575,13 +1594,13 @@ 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/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_ud.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 | ^~~~~~~~~~~~~~ @@ -1633,6 +1652,23 @@ /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 -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 -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.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] @@ -1651,29 +1687,9 @@ ../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive 6 | #include "graph/contig_graph.h"; | ^ -../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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../src/container/hash_map.h:14, from ../src/graph/contig_graph.h:19, from ../src/tools/test.cpp:6: @@ -1738,13 +1754,33 @@ /usr/include/c++/14/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()); + | ~~~~~~^~~~~~~~~~~~~ +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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp +../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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -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 -fcf-protection -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.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] @@ -1784,17 +1820,17 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic @@ -1808,14 +1844,13 @@ make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3' -make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3' make[1]: Leaving directory '/build/reproducible-path/idba-1.1.3' 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' @@ -2071,8 +2106,8 @@ Making install in bin make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/bin' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/bin' -make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' +make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/bin' @@ -2086,8 +2121,8 @@ Making install in script make[2]: Entering directory '/build/reproducible-path/idba-1.1.3/script' make[3]: Entering directory '/build/reproducible-path/idba-1.1.3/script' -make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' +make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/build/reproducible-path/idba-1.1.3/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' make[2]: Leaving directory '/build/reproducible-path/idba-1.1.3/script' @@ -2126,8 +2161,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_amd64.deb'. -dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_amd64.deb'. dpkg-deb: building package 'idba' in '../idba_1.1.3-8_amd64.deb'. +dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_amd64.deb'. dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../idba_1.1.3-8_amd64.buildinfo dpkg-genchanges --build=binary -O../idba_1.1.3-8_amd64.changes @@ -2136,12 +2171,14 @@ 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/1086845/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1086845/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/1604387 and its subdirectories -I: Current time: Tue Mar 18 07:52:21 -12 2025 -I: pbuilder-time-stamp: 1742327541 +I: removing directory /srv/workspace/pbuilder/1086845 and its subdirectories +I: Current time: Tue Apr 21 16:20:08 +14 2026 +I: pbuilder-time-stamp: 1776738008