Diff of the two buildlogs: -- --- b1/build.log 2025-10-18 00:03:49.304475766 +0000 +++ b2/build.log 2025-10-18 00:11:05.413016898 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 17 11:56:47 -12 2025 -I: pbuilder-time-stamp: 1760745407 +I: Current time: Fri Nov 20 20:26:51 +14 2026 +I: pbuilder-time-stamp: 1795156011 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying networkx_update.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/745455/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3388096/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 Nov 20 06:27 /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/3388096/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3388096/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=16 ' + 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='66e54285250543658f71e5430fcfe060' - 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='745455' - PS1='# ' - PS2='> ' + INVOCATION_ID=7a85ec8afa794d05ba6620fa1e53f6b9 + 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=3388096 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.gGXfJbLD/pbuilderrc_NTa9 --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.gGXfJbLD/b1 --logfile b1/build.log hinge_0.5.0-8.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.gGXfJbLD/pbuilderrc_oYAr --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.gGXfJbLD/b2 --logfile b2/build.log hinge_0.5.0-8.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/745455/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3388096/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -411,7 +443,7 @@ Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-pbcore all 2.1.2+dfsg-13 [2832 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-ujson amd64 5.11.0-2 [26.5 kB] -Fetched 265 MB in 9s (29.4 MB/s) +Fetched 265 MB in 3s (76.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19856 files and directories currently installed.) @@ -1279,8 +1311,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Oct 18 00:00:46 UTC 2025. -Universal Time is now: Sat Oct 18 00:00:46 UTC 2025. +Local time is now: Fri Nov 20 06:30:35 UTC 2026. +Universal Time is now: Fri Nov 20 06:30:35 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... @@ -1513,7 +1545,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hinge-0.5.0/ && 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 > ../hinge_0.5.0-8_source.changes +I: user script /srv/workspace/pbuilder/3388096/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3388096/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hinge-0.5.0/ && 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 > ../hinge_0.5.0-8_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-8 dpkg-buildpackage: info: source distribution unstable @@ -1624,7 +1660,7 @@ to work with policies introduced by or earlier. --- Configuring done (1.5s) +-- Configuring done (2.4s) CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy @@ -1665,7 +1701,7 @@ /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp This warning is for project developers. Use -Wno-dev to suppress it. --- Generating done (0.1s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -1682,7 +1718,7 @@ -- Build files have been written to: /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/hinge-0.5.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1692,16 +1728,16 @@ make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake "--color=" +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake "--color=" +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake "--color=" @@ -1710,44 +1746,46 @@ make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build +make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 6%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o -[ 6%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o -[ 10%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -[ 13%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o +[ 6%] Generating hinge.1 +[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o +[ 17%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o +[ 17%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/reproducible-path/hinge-0.5.0/src/hinge.1.md -o hinge.1 +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DB.c +[ 20%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/ini.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/align.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DW_banded.c -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/ini.c -[ 17%] Generating hinge.1 -[ 20%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o [ 24%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/reproducible-path/hinge-0.5.0/src/hinge.1.md -o hinge.1 -[ 27%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/paf.c -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DB.c [ 31%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +[ 31%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/paf.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 31%] Built target man /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); @@ -1758,37 +1796,35 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 31%] Built target man -[ 34%] Linking C static library libPAF.a +[ 34%] Linking C static library libDW_banded.a +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake +[ 37%] Linking C static library libPAF.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 -/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o -/usr/bin/ranlib libPAF.a -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] 533 | free(reads); | ^~~~~~~~~~~ In function 'Malloc', inlined from 'Open_DB' at /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:525:29: -[ 34%] Built target PAF /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ -[ 37%] Linking C static library libDW_banded.a -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake -[ 41%] Linking C static library libkmer_lookup.a -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a +/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o +/usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 41%] Linking C static library libkmer_lookup.a +[ 41%] Built target DW_banded +[ 41%] Built target PAF +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 41%] Built target DW_banded [ 41%] Built target kmer_lookup make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' @@ -1807,27 +1843,27 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ -[ 48%] Linking CXX static library libini.a +[ 48%] Linking C static library libfalcon.a +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 +[ 51%] Linking CXX static library libini.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 -/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o -/usr/bin/ranlib libini.a -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 51%] Linking C static library libDB.a +[ 55%] Linking C static library libDB.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 -[ 51%] Built target ini -[ 55%] Linking C static library libfalcon.a -/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o -/usr/bin/ranlib libDB.a -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 -[ 55%] Built target DB /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 55%] Built target falcon +/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o +/usr/bin/ranlib libDB.a +/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o +/usr/bin/ranlib libini.a +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 55%] Built target DB +[ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LA.dir/link.txt --verbose=1 @@ -1861,9 +1897,9 @@ make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/filter /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake "--color=" -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/maximal /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' @@ -1875,28 +1911,28 @@ make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 79%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o [ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -[ 72%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +[ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o +[ 82%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +[ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_GRAPH_NO_LIB -DBOOST_REGEX_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/filter/filter.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/maximal/maximal.cpp -[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -[ 79%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_GRAPH_NO_LIB -DBOOST_REGEX_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp -[ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp +cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp [ 86%] Linking CXX executable consensus cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/consensus.dir/link.d CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a @@ -1929,7 +1965,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/hinge/ - cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1940,61 +1976,61 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter @@ -2028,8 +2064,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-8_amd64.deb'. dpkg-deb: building package 'hinge' in '../hinge_0.5.0-8_amd64.deb'. +dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../hinge_0.5.0-8_amd64.buildinfo dpkg-genchanges --build=binary -O../hinge_0.5.0-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2037,12 +2073,14 @@ 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/3388096/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3388096/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/745455 and its subdirectories -I: Current time: Fri Oct 17 12:03:48 -12 2025 -I: pbuilder-time-stamp: 1760745828 +I: removing directory /srv/workspace/pbuilder/3388096 and its subdirectories +I: Current time: Fri Nov 20 20:34:04 +14 2026 +I: pbuilder-time-stamp: 1795156444