Diff of the two buildlogs: -- --- b1/build.log 2025-09-15 08:42:28.164237093 +0000 +++ b2/build.log 2025-09-15 08:45:24.040457655 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 18 03:02:50 -12 2026 -I: pbuilder-time-stamp: 1792335770 +I: Current time: Mon Sep 15 22:42:30 +14 2025 +I: pbuilder-time-stamp: 1757925750 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying tests-2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2728054/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/793934/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +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 Sep 15 08:42 /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/793934/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/793934/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='arm64' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='487cd83be6804034b75ae8d26d542333' - 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='2728054' - PS1='# ' - PS2='> ' + INVOCATION_ID=4b04f289eba54571a2ee61792ca24c78 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=793934 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.OK1wgmVL/pbuilderrc_P9Xe --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OK1wgmVL/b1 --logfile b1/build.log kissplice_2.6.7-2.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' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OK1wgmVL/pbuilderrc_Asu4 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OK1wgmVL/b2 --logfile b2/build.log kissplice_2.6.7-2.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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2728054/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/793934/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -255,7 +287,7 @@ Get: 133 http://deb.debian.org/debian forky/main arm64 texlive-base all 2025.20250727-3 [23.1 MB] Get: 134 http://deb.debian.org/debian forky/main arm64 texlive-latex-base all 2025.20250727-3 [1318 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] -Fetched 109 MB in 1s (105 MB/s) +Fetched 109 MB in 0s (228 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 20020 files and directories currently installed.) @@ -709,8 +741,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Oct 18 15:03:22 UTC 2026. -Universal Time is now: Sun Oct 18 15:03:22 UTC 2026. +Local time is now: Mon Sep 15 08:43:01 UTC 2025. +Universal Time is now: Mon Sep 15 08:43:01 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -839,7 +871,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kissplice-2.6.7/ && 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 > ../kissplice_2.6.7-2_source.changes +I: user script /srv/workspace/pbuilder/793934/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/793934/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kissplice-2.6.7/ && 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 > ../kissplice_2.6.7-2_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.7-2 dpkg-buildpackage: info: source distribution unstable @@ -882,7 +918,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex --- Configuring done (0.6s) +-- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -904,78 +940,78 @@ make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake "--color=" +make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend +make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" +make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" -make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake "--color=" +make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.7 /build/reproducible-path/kissplice-2.6.7/doc /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build +make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build -[ 3%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build -[ 5%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -[ 3%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -MF CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o.d -o CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/ErrorRemoval.cpp +[ 1%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/commons.cpp make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build -[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/commons.cpp -[ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp -[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +[ 5%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[ 10%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/commons.cpp -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/extension_algorithm.cpp +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[ 13%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -[ 15%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CleanDuplicates.cpp -[ 17%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -MF CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp -[ 18%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -MF CMakeFiles/ks_run_modules.dir/run.cpp.o.d -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/run.cpp -[ 20%] Generating user_guide.pdf +[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o +[ 8%] Generating user_guide.pdf cd /build/reproducible-path/kissplice-2.6.7/doc && /build/reproducible-path/kissplice-2.6.7/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc/user_guide.tex +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/extension_algorithm.cpp +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc/user_guide.tex +[ 10%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -MF CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +[ 13%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o +[ 12%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. +[ 15%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -MF CMakeFiles/ks_print_bcc.dir/Utils.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -MF CMakeFiles/ks_run_modules.dir/run.cpp.o.d -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/run.cpp +[ 17%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CleanDuplicates.cpp +[ 18%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -MF CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o.d -o CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/ErrorRemoval.cpp +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/commons.cpp entering extended mode (/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc/user_guide. @@ -1012,28 +1048,28 @@ (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/dvips.def))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) -(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def[ 22%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -) -(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -MF CMakeFiles/ks_print_bcc.dir/Utils.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp - +(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/enumerate.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) -(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) +(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)[ 22%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o + (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty -(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) +(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp + (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty -(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) -(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty[ 24%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/interface_libchash.cpp +(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))[ 24%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/interface_libchash.cpp ) +(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) @@ -1042,49 +1078,18 @@ (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def -(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1047 | fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1094 | fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty[ 25%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) -(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) +(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty[ 27%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp +) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty -(/usr/share/texlive/texmf-dist/tex/latex/listings/lstpatch.sty)[ 25%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/extension_algorithm.cpp - +(/usr/share/texlive/texmf-dist/tex/latex/listings/lstpatch.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) -(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp +(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)[ 29%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o No file user_guide.aux. *geometry* driver: auto-detecting @@ -1123,8 +1128,13 @@ (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] -) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty -(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) +) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.stycd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp + +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/extension_algorithm.cpp +[ 32%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp + (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) No file user_guide.toc. @@ -1132,16 +1142,42 @@ [1 Non-PDF special ignored! papersize=614.295pt,794.96999pt -{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}][ 29%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp - +{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Underfull \hbox (badness 10000) in paragraph at lines 58--60 Underfull \hbox (badness 10000) in paragraph at lines 61--63 -[2]/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': +[2] +[3] +Overfull \hbox (24.58913pt too wide) in paragraph at lines 151--160 +[]\T1/cmr/m/n/12 The \T1/cmtt/m/n/12 sample_example \T1/cmr/m/n/12 di-rec-tory +con-tains four files \T1/cmtt/m/n/12 mock1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 m +ock2.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 virus1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/ +12 virus2.fq + +LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 171 +. + + +Overfull \hbox (24.90025pt too wide) in paragraph at lines 189--189 +[]\T1/cmr/m/n/12 Figure 1: []Content of the file \T1/cmtt/m/n/12 results_mock1_ +mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , + +LaTeX Warning: Reference `fig:extype1_C0' on page 4 undefined on input line 199 +. + + +[4 <./MBTD1_C2.pngIn file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:61: +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 84 | fscanf(info_file, "%d \n",&bcc_size ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 85 | fscanf(info_file, "%d \n",&records_per_file ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1151,6 +1187,41 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1074:4: note: in expansion of macro 'LOAD_AND_RETURN' 1074 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:60: +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:198:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 198 | fgets(buffer, 100 * MAX, node_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:277:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 277 | fgets(buffer, 100 * MAX, edge_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -1231,27 +1302,48 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ - -[3] -Overfull \hbox (24.58913pt too wide) in paragraph at lines 151--160 -[]\T1/cmr/m/n/12 The \T1/cmtt/m/n/12 sample_example \T1/cmr/m/n/12 di-rec-tory -con-tains four files \T1/cmtt/m/n/12 mock1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 m -ock2.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 virus1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/ -12 virus2.fq - -LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 171 -. - - -Overfull \hbox (24.90025pt too wide) in paragraph at lines 189--189 -[]\T1/cmr/m/n/12 Figure 1: []Content of the file \T1/cmtt/m/n/12 results_mock1_ +>] +Overfull \hbox (24.90025pt too wide) in paragraph at lines 203--203 +[]\T1/cmr/m/n/12 Figure 2: []Content of the file \T1/cmtt/m/n/12 results_mock1_ mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , -LaTeX Warning: Reference `fig:extype1_C0' on page 4 undefined on input line 199 +LaTeX Warning: Reference `fig:extype1_C2' on page 5 undefined on input line 210 . -[4 <./MBTD1_C2.pngIn file included from /build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp:51: +[5 <./MBTD1_C0.png/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1047 | fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1094 | fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp:51: /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = Printer; TNodeFunctor = Printer]': /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(info_file, "%d \n",&bcc_size ); @@ -1287,75 +1379,17 @@ /build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:61: -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 84 | fscanf(info_file, "%d \n",&bcc_size ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 85 | fscanf(info_file, "%d \n",&records_per_file ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:60: -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ->]/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:198:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 198 | fgets(buffer, 100 * MAX, node_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:277:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 277 | fgets(buffer, 100 * MAX, edge_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Overfull \hbox (24.90025pt too wide) in paragraph at lines 203--203 -[]\T1/cmr/m/n/12 Figure 2: []Content of the file \T1/cmtt/m/n/12 results_mock1_ -mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , - -LaTeX Warning: Reference `fig:extype1_C2' on page 5 undefined on input line 210 -. - - -[5 <./MBTD1_C0.png[ 31%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o ->]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp -[ 32%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o - +[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/interface_libchash.cpp +>] LaTeX Warning: Reference `fig:quantif' on page 6 undefined on input line 273. -[6 <./quantifModel.pngcd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp -[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/interface_libchash.cpp -[ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/outputs.cpp ->] +[6 <./quantifModel.png>] Overfull \hbox (1.2115pt too wide) in paragraph at lines 327--328 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes \T1/cmr/m/n/12 for the nodes @@ -1397,9 +1431,7 @@ []\T1/cmtt/m/n/12 KisSplice \T1/cmr/m/n/12 also cre-ates a sum-mary log file in the re-sults di-rec-tory named -[8][ 37%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp - +[8] [9] Underfull \hbox (badness 10000) in paragraph at lines 408--409 @@ -1411,19 +1443,57 @@ (/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/doc/user_guide. aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 -[ 39%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_print_bcc +[ 36%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp +[ 37%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_print_bcc cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 -[ 41%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp -[ 43%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp +[ 39%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_print_bcc.dir/link.d CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_print_bcc make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +[ 41%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_error_removal +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 +[ 43%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/CGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp [ 43%] Built target ks_print_bcc -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/coherent_algorithm.cpp -[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp +[ 44%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp +[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1047 | fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1094 | fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_error_removal.dir/link.d CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_error_removal +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -1434,6 +1504,7 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1074:4: note: in expansion of macro 'LOAD_AND_RETURN' 1074 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ +[ 46%] Built target ks_error_removal /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -1514,15 +1585,13 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ +[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/outputs.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 -[ 48%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/CGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf[ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/couple.cpp -) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf @@ -1532,23 +1601,23 @@ [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] -[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] -[248] [249] [250] [251] [252] [253] [254] [255]) + Ok [224][ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/coherent_algorithm.cpp + [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] +[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246][ 51%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o + [247] +[248]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp + [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143[ 51%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -] [144] [145] [146]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp - [147] [148] [149] [150] [151] +[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] -[183] [184] [185] [186][ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o - [187] [188]) +[183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf - Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_index.cpp - [125] + Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] @@ -1562,8 +1631,10 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf - Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] -[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77][ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o + [78] +[79] [80] [81] [82] [83] [84] [85] [86]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/couple.cpp + [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] @@ -1575,6 +1646,8 @@ Font metrics written on ectt1095.tfm. Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. +[ 55%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1095.600pk: successfully generated. @@ -1593,68 +1666,11 @@ kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var /fonts/pk/ljfour/jknappen/ec/ectt1095.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 -[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -MF CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o.d -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/SplitBcc.cpp -[ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/outputs.cpp -[ 58%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_error_removal -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 -[ 60%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -MF CMakeFiles/ks_run_modules.dir/Utils.cpp.o.d -o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp -mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 -This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) - -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf - Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217] [218] [219] [220] [221] [222] [223]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] -[236] [237] [238] [239] [240] [241]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_error_removal.dir/link.d CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_error_removal - [242]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' - [243] [244] [245] [246] [247] -[248] [249] [250] [251] [252] [253] [254] [255]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf - Ok [128] [129][ 60%] Built target ks_error_removal - [130] [131] [132] [133] [134] [135] [136] [137][ 62%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o - [138]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CycleCompression.cpp - [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149][ 63%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o - [150]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp - [151] -[152] [153] [154] [155] [156] [157]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171][ 65%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o - [172] [173] [174] [175]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/CGraph.cpp - [176] [177] [178] [179] [180] [181] [182] -[183] [184] [185] [186] [187] [188]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf - Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] -[95] [127] [32]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf - Ok [14] [15] [19][ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o - [20] [13]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/kissReads.cpp - [18] [33] [39] [42] [43] [44] [46] [47] [58] -[59] [61] [96] [189] [17] [45] [16] [21] [22]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf - Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf - Ok [24] [34] [35] [36] [37] [64] [191] [159]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28] [27] [29] [30] [31]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf - Ok [38][ 68%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o - [63] [190]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mfcd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp - - Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74]/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +[ 56%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp +[ 58%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp +/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1686,41 +1702,105 @@ /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [75] [76] [77] [78] +[ 60%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp +[ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/outputs.cpp +[ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/LabelledCEdge.cpp +mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 +This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) + +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf + Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] +[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] +[216] [217] [218] [219[ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_index.cpp +] [220] [221] [222] [223]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf + Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] +[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] +[248] [249] [250] [251] [252] [253] [254] [255]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf + Ok [128[ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/kissReads.cpp +] [129] [130] [131] [132][ 68%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o + [133]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -MF CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o.d -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/SplitBcc.cpp + [134] [135] [136] [137] [138] [139] +[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150[ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/coherent_algorithm.cpp + [151] +[152] [153] [154] [155] [156] [157]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf + Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] +[183] [184] [185] [186] [187] [188]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf + Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] +[95] [127] [32]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf + Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] +[59] [61] [96] [189] [17] [45] [16] [21[ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o +] [22]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mfcd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/couple.cpp + + Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf + Ok [24] [34] [35] [36] [37] [64] [191] [159]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf + Ok [25] [26] [28] [27] [29] [30] [31]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf + Ok [38] [63] [190]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf - Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) + Ok [48] [49] [50] [51[ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o +] [52] [53] [54] [55][ 75%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o + [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf - Ok) ) ) ) + Ok)cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/kissReads.cpp + ) ) ) Font metrics written on ectt1440.tfm. Output written on ectt1440.600gf (256 characters, 61024 bytes). Transcript written on ectt1440.log. +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_index.cpp +[ 77%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/list.cpp mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 -[ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o +[ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/list.cpp -[ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o +[ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/tree.cpp -[ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/coherent_algorithm.cpp +[ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_info.cpp +[ 84%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/Utils.cpp +[ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/tree.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf[ 75%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o - +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mfcd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp - + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf @@ -1730,19 +1810,13 @@ [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] -[150] [151] [152] [153] [154] [155] [156] [157] [158[ 77%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/couple.cpp - [159][ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o - [160] [161] -[162] [163] [164] [165] [166] [167] [168] [169]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_info.cpp - [171] [172] [173] [174] +[150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] +[162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf - Ok [48] [49][ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o - [50] [51] [52] [53] [54] [55] [56] [57]) + Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf - Ok [185]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_index.cpp - [178] [179] [170] [186]) + Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) @@ -1754,40 +1828,12 @@ debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour /jknappen/ec/tcrm1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 -[ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/kissReads.cpp -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1047 | fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1094 | fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 87%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_info.cpp +[ 89%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -MF CMakeFiles/ks_run_modules.dir/Utils.cpp.o.d -o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/modules/Utils.cpp +[ 91%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/Utils.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -1800,42 +1846,41 @@ Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217][ 84%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o - [218]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/list.cpp - [219] [220] [221] [222] [223]) +[216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] -[248] [249] [250] [251] [252][ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/Utils.cpp - [253] [254] [255]) +[248] [249] [250] [251] [252] [253] [254[ 93%] Linking CXX executable ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSNPS +]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 + [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161] [162] [163] [164] [165][ 87%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o - [166]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/tree.cpp - [167] [168] [169] [170] -[171] [172] [173] [174][ 89%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++14 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/fragment_info.cpp - [175] [176] [177] [178] [179] [180] [181] [182] + Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] -[59] [61] [96] [189] [17] [45] [16] [21] [22]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf +[59] [61] [96] [189] [17] [45]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_kissreadsSNPS.dir/link.d CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -o ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSNPS /usr/lib/aarch64-linux-gnu/libz.so -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a + [16] [21] [22]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mfmake[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' + Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28] [27] [29] [30] [31]) + Ok [25] [26][ 93%] Built target ks_kissreadsSNPS + [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf - Ok [38] [63] [190]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf + Ok [38[ 94%] Linking CXX executable ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSplice +] [63] [190]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mfcd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf @@ -1850,12 +1895,13 @@ Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. -[ 91%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +n/ec/ecbx1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_kissreadsSplice.dir/link.d CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -o ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSplice /usr/lib/aarch64-linux-gnu/libz.so -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +[ 94%] Built target ks_kissreadsSplice mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -1879,9 +1925,7 @@ [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176][ 93%] Linking CXX executable ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSNPS - [177] [178] [179] [180] [181]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 - [182] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] @@ -1912,21 +1956,11 @@ Font metrics written on ecbx1440.tfm. Output written on ecbx1440.600gf (256 characters, 70764 bytes). Transcript written on ecbx1440.log. -[ 94%] Linking CXX executable ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSplice -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_kissreadsSNPS.dir/link.d CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -o ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSNPS /usr/lib/aarch64-linux-gnu/libz.so -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[ 94%] Built target ks_kissreadsSNPS -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_kissreadsSplice.dir/link.d CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -o ../../../lib/aarch64-linux-gnu/kissplice/ks_kissreadsSplice /usr/lib/aarch64-linux-gnu/libz.so -lm /usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[ 94%] Built target ks_kissreadsSplice -[ 96%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_bubble_enumeration -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -1944,16 +1978,17 @@ Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf[ 96%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_run_modules +cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_bubble_enumeration.dir/link.d CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_bubble_enumeration - [215] -[216] [217]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' - [218] [219] [220] [221] [222] [223]) +[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] +[216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf - Ok [128][ 96%] Built target ks_bubble_enumeration - [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] + Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] +[140] [141] [142] [143] [144][ 98%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_bubble_enumeration + [145]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 + [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] @@ -1962,12 +1997,15 @@ Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf - Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf + Ok [0] [1] [2] [3] [4] [5]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_run_modules.dir/link.d CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_run_modules + [6] [7] [8] [9] [10] [11] [12]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mfmake[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' + Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilig.mf Ok [25] [26] [27] [28] [29] [30] [31]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf[ 98%] Built target ks_run_modules + Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] @@ -1989,6 +2027,9 @@ ted/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.60 0pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_bubble_enumeration.dir/link.d CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_bubble_enumeration +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' +[ 98%] Built target ks_bubble_enumeration mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -2056,7 +2097,9 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] + Ok [192] [193] [194] [195] [196] [197] [198] [199][100%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_clean_duplicates + [200]cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 + [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf @@ -2066,9 +2109,12 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] -[152] [153] [154] [155] [156] [157]) +[152] [153] [154]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_clean_duplicates.dir/link.d CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_clean_duplicates + [155] [156]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' + [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] + Ok [158] [160] [161] [162] [163] [164] [165] [166][100%] Built target ks_clean_duplicates + [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf @@ -2104,11 +2150,6 @@ uild/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home /.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1728.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 -[ 98%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_run_modules -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_run_modules.dir/link.d CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_run_modules -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[ 98%] Built target ks_run_modules mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -2163,16 +2204,11 @@ Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. -[100%] Linking CXX executable ../lib/aarch64-linux-gnu/kissplice/ks_clean_duplicates -cd /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ks_clean_duplicates.dir/link.d CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/aarch64-linux-gnu/kissplice/ks_clean_duplicates -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' -[100%] Built target ks_clean_duplicates mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1728 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -2807,14 +2843,14 @@ 1: --type1-only Only quantify Type 1 bubbles (alternative splicing 1: events, MAJOR SPEED UP with -b > 10 BUT all other 1: bubbles will not appear in the result file). -1/8 Test #1: KisspliceBasicTest ............... Passed 0.08 sec +1/8 Test #1: KisspliceBasicTest ............... Passed 0.07 sec test 2 Start 2: KisspliceDBGTest 2: Test command: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceDBGTest.py "/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin" 2: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests 2: Test timeout computed to be: 10000000 -2/8 Test #2: KisspliceDBGTest ................. Passed 4.46 sec +2/8 Test #2: KisspliceDBGTest ................. Passed 5.00 sec test 3 Start 3: KisspliceTwoSequencesTest @@ -2822,9 +2858,9 @@ 3: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests 3: Test timeout computed to be: 10000000 3: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta -C 0 -3: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-09_518565\n\n\n[03:05:09 18/10/2026] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[03:05:13 18/10/2026] --> Done!\nElapsed time: 3.7 seconds\nElapsed time: 0.0 seconds\n\n[03:05:13 18/10/2026] --> Finding the BCCs...\n[03:05:13 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[03:05:13 18/10/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:05:13 18/10/2026] --> Done!\nElapsed time: 0.4 seconds\n\n[03:05:13 18/10/2026] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[03:05:13 18/10/2026] --> Sampling bubbles by type...\n[03:05:13 18/10/2026] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[03:05:13 18/10/2026] --> Removing low-complexity/redundant bubbles...\n[03:05:13 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[03:05:14 18/10/2026] --> Computing read coherence and coverage...\n[03:05:14 18/10/2026] --> Done!\n[03:05:14 18/10/2026] --> Sorting all bubbles...\n[03:05:14 18/10/2026] --> Done!\nElapsed time: 0.9 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 8 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-09_518565**********\n' +3: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-07_495624\n\n\n[22:45:07 15/09/2025] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[22:45:11 15/09/2025] --> Done!\nElapsed time: 3.8 seconds\nElapsed time: 0.0 seconds\n\n[22:45:11 15/09/2025] --> Finding the BCCs...\n[22:45:11 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[22:45:11 15/09/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:45:11 15/09/2025] --> Done!\nElapsed time: 0.4 seconds\n\n[22:45:11 15/09/2025] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[22:45:11 15/09/2025] --> Sampling bubbles by type...\n[22:45:11 15/09/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[22:45:11 15/09/2025] --> Removing low-complexity/redundant bubbles...\n[22:45:11 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[22:45:11 15/09/2025] --> Computing read coherence and coverage...\n[22:45:12 15/09/2025] --> Done!\n[22:45:12 15/09/2025] --> Sorting all bubbles...\n[22:45:12 15/09/2025] --> Done!\nElapsed time: 0.8 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 8 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-07_495624**********\n' 3: kisspliceTwoSequencesTest.py: test SUCCESSFUL -3/8 Test #3: KisspliceTwoSequencesTest ........ Passed 5.16 sec +3/8 Test #3: KisspliceTwoSequencesTest ........ Passed 5.18 sec test 4 Start 4: KisspliceGraphAndSequenceTest @@ -2832,9 +2868,9 @@ 4: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests 4: Test timeout computed to be: 10000000 4: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -C 0 -4: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -C 0\n-r and -g options used together: \nthe graph will be used to find events, while reads files are used for checking read-coherency and coverage\nUsing the read files: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-14_707790\n\n\nElapsed time: 0.0 seconds\n\n[03:05:14 18/10/2026] --> Finding the BCCs...\n[03:05:14 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[03:05:14 18/10/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.3 seconds\n\n[03:05:15 18/10/2026] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[03:05:15 18/10/2026] --> Sampling bubbles by type...\n[03:05:15 18/10/2026] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[03:05:15 18/10/2026] --> Removing low-complexity/redundant bubbles...\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[03:05:15 18/10/2026] --> Computing read coherence and coverage...\n[03:05:15 18/10/2026] --> Done!\n[03:05:15 18/10/2026] --> Sorting all bubbles...\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.4 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-14_707790**********\n' +4: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta -C 0\n-r and -g options used together: \nthe graph will be used to find events, while reads files are used for checking read-coherency and coverage\nUsing the read files: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-12_892723\n\n\nElapsed time: 0.0 seconds\n\n[22:45:12 15/09/2025] --> Finding the BCCs...\n[22:45:12 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[22:45:12 15/09/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:45:13 15/09/2025] --> Done!\nElapsed time: 0.4 seconds\n\n[22:45:13 15/09/2025] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[22:45:13 15/09/2025] --> Sampling bubbles by type...\n[22:45:13 15/09/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[22:45:13 15/09/2025] --> Removing low-complexity/redundant bubbles...\n[22:45:13 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[22:45:13 15/09/2025] --> Computing read coherence and coverage...\n[22:45:13 15/09/2025] --> Done!\n[22:45:13 15/09/2025] --> Sorting all bubbles...\n[22:45:13 15/09/2025] --> Done!\nElapsed time: 0.4 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-12_892723**********\n' 4: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -4/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 0.92 sec +4/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 1.03 sec test 5 Start 5: KisspliceGraphTest @@ -2842,9 +2878,9 @@ 5: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests 5: Test timeout computed to be: 10000000 5: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -C 0 -5: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -C 0\nUsing the read files: None\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-15_580888\n\n\nElapsed time: 0.0 seconds\n\n[03:05:15 18/10/2026] --> Finding the BCCs...\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[03:05:15 18/10/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.3 seconds\n\n[03:05:15 18/10/2026] --> Starting Bubble Output Module\n[03:05:15 18/10/2026] --> Sampling bubbles by type...\n[03:05:15 18/10/2026] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[03:05:15 18/10/2026] --> Removing low-complexity/redundant bubbles...\n[03:05:15 18/10/2026] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-10-18_03-05-15_580888**********\n' +5: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -C 0\nUsing the read files: None\nResults will be stored in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-13_803255\n\n\nElapsed time: 0.0 seconds\n\n[22:45:13 15/09/2025] --> Finding the BCCs...\n[22:45:13 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[22:45:13 15/09/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:45:14 15/09/2025] --> Done!\nElapsed time: 0.4 seconds\n\n[22:45:14 15/09/2025] --> Starting Bubble Output Module\n[22:45:14 15/09/2025] --> Sampling bubbles by type...\n[22:45:14 15/09/2025] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[22:45:14 15/09/2025] --> Removing low-complexity/redundant bubbles...\n[22:45:14 15/09/2025] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-09-15_22-45-13_803255**********\n' 5: kisspliceGraphTest.py: test SUCCESSFUL -5/8 Test #5: KisspliceGraphTest ............... Passed 0.45 sec +5/8 Test #5: KisspliceGraphTest ............... Passed 0.60 sec test 6 Start 6: ksBubbleEnumerationTest @@ -2854,7 +2890,7 @@ 6: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/lib/aarch64-linux-gnu/kissplice/ks_bubble_enumeration /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_info_bcc /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_contents_edges_bcc /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_contents_nodes_bcc /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_all_edges_bcc /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_all_nodes_bcc 2 25 /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_bubble_enumeration_output 3 bcc_test 0 -u 1000 -L 49 -l 42 -M 10000 -b 5 6: b'\t Enumerating bubbles with at most 5 branching nodes in each path!\n============================================================================\nSummary of results\n============================================================================\nNo of bubbles: 4\n============================================================================\n' 6: Ks_Bubble_Enumeration_Test: test SUCCESSFUL -6/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.04 sec +6/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.08 sec test 7 Start 7: ksRunModulesTest @@ -2864,7 +2900,7 @@ 7: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/lib/aarch64-linux-gnu/kissplice/ks_run_modules /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes 25 /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_run_modules_output_graph 7: b'Searching biconnected components...\nNumber of biconnected components found: 109\n\nProcessing component 1...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 2...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 3...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 4...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 5...\nInitial size: 9 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 8 nodes.\nDone!\n\nProcessing component 6...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 7...\nInitial size: 41 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 11.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 30 nodes.\nDone!\n\nProcessing component 8...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 9...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 10...\nInitial size: 68 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 4.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 64 nodes.\nDone!\n\nProcessing component 11...\nInitial size: 54 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 5.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 49 nodes.\nDone!\n\nProcessing component 12...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 13...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 14...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 15...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 16...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 17...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 18...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 19...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 20...\nInitial size: 37 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 37 nodes.\nDone!\n\nProcessing component 21...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 22...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 23...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 24...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 25...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 26...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 27...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 28...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 29...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 30...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 31...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 32...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 33...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 34...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 35...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 6 nodes.\nDone!\n\nProcessing component 36...\nInitial size: 9 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 8 nodes.\nDone!\n\nProcessing component 37...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 38...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 39...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 40...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 41...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 42...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 43...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 44...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 45...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 46...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 47...\nInitial size: 13 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 8.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 48...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 49...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 50...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 51...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 52...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 53...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 54...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 55...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 56...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 57...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 58...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 59...\nInitial size: 8 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 6 nodes.\nDone!\n\nProcessing component 60...\nInitial size: 9 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 8 nodes.\nDone!\n\nProcessing component 61...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 62...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 63...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 64...\nInitial size: 8 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 7 nodes.\nDone!\n\nProcessing component 65...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 66...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 67...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 68...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 69...\nInitial size: 3 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 1 nodes.\nDone!\n\nProcessing component 70...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 4.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 1 nodes.\nDone!\n\nProcessing component 71...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 72...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 73...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 74...\nInitial size: 29 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 8.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 21 nodes.\nDone!\n\nProcessing component 75...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 76...\nInitial size: 8 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 3.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 3.\nFinal size: 1 nodes.\nDone!\n\nProcessing component 77...\nInitial size: 6 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 6 nodes.\nDone!\n\nProcessing component 78...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 79...\nInitial size: 7 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 3.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 80...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 81...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 82...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 83...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 84...\nInitial size: 8 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 8 nodes.\nDone!\n\nProcessing component 85...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 86...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 87...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 88...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 89...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 90...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 91...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 92...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 93...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 94...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 95...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 96...\nInitial size: 33 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 5.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 28 nodes.\nDone!\n\nProcessing component 97...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 98...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 99...\nInitial size: 5 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 5 nodes.\nDone!\n\nProcessing component 100...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 101...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 102...\nInitial size: 14 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 14 nodes.\nDone!\n\nProcessing component 103...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 104...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 105...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 4 nodes.\nDone!\n\nProcessing component 106...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 107...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 108...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\nProcessing component 109...\nInitial size: 4 nodes.\nCompressing linear paths...\nNumber of compressed nodes: 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal size: 3 nodes.\nDone!\n\n' 7: ks_run_modules: test SUCCESSFUL -7/8 Test #7: ksRunModulesTest ................. Passed 0.05 sec +7/8 Test #7: ksRunModulesTest ................. Passed 0.12 sec test 8 Start 8: ksErrorRemovalTest @@ -2874,11 +2910,11 @@ 8: /build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu/lib/aarch64-linux-gnu/kissplice/ks_error_removal /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance 0.02/build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_error_removal_output 8: b'252 out of 5336 edges removed\n' 8: ks_error_removal: test SUCCESSFUL -8/8 Test #8: ksErrorRemovalTest ............... Passed 0.04 sec +8/8 Test #8: ksErrorRemovalTest ............... Passed 0.07 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 11.21 sec +Total Test time (real) = 12.13 sec make[2]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.7' create-stamp debian/debhelper-build-stamp @@ -2945,12 +2981,14 @@ 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/793934/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/793934/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/2728054 and its subdirectories -I: Current time: Sun Oct 18 03:05:26 -12 2026 -I: pbuilder-time-stamp: 1792335926 +I: removing directory /srv/workspace/pbuilder/793934 and its subdirectories +I: Current time: Mon Sep 15 22:45:23 +14 2025 +I: pbuilder-time-stamp: 1757925923