Diff of the two buildlogs: -- --- b1/build.log 2024-11-26 09:24:53.681779642 +0000 +++ b2/build.log 2024-11-26 09:30:21.670920251 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 29 03:41:43 -12 2025 -I: pbuilder-time-stamp: 1767022903 +I: Current time: Tue Nov 26 23:24:55 +14 2024 +I: pbuilder-time-stamp: 1732613095 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ 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/3218117/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2247549/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 26 09:25 /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/2247549/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2247549/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5e221e826cb84c2983ef030d9435eef5' - 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='3218117' - PS1='# ' - PS2='> ' + INVOCATION_ID=2e01ae7c63e44c5ca27814b69c85cbb5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2247549 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.04czow18/pbuilderrc_3sW2 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.04czow18/b1 --logfile b1/build.log kissplice_2.6.7-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.04czow18/pbuilderrc_eWoA --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.04czow18/b2 --logfile b2/build.log kissplice_2.6.7-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3218117/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2247549/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -264,7 +296,7 @@ Get: 140 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 141 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] -Fetched 113 MB in 38s (2985 kB/s) +Fetched 113 MB in 19s (6104 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) @@ -741,8 +773,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 29 15:46:31 UTC 2025. -Universal Time is now: Mon Dec 29 15:46:31 UTC 2025. +Local time is now: Tue Nov 26 09:27:36 UTC 2024. +Universal Time is now: Tue Nov 26 09:27:36 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -880,7 +912,11 @@ 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_2.6.7-1_source.changes +I: user script /srv/workspace/pbuilder/2247549/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2247549/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_2.6.7-1_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.7-1 dpkg-buildpackage: info: source distribution unstable @@ -923,7 +959,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex --- Configuring done (2.1s) +-- Configuring done (3.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -936,143 +972,99 @@ -- Build files have been written to: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.7' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kissplice-2.6.7 -B/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake "--color=" 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[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend -make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake "--color=" +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build +make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +[ 1%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 3%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o +[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend +[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" -[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -[ 17%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -[ 41%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -[ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -[ 18%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 8%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build +[ 10%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o +[ 13%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 15%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 18%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o +[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o +[ 22%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 24%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +[ 25%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -[ 55%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -[ 55%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -[ 55%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -[ 56%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -[ 56%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -[ 58%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -[ 60%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -[ 62%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 63%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 29%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +[ 31%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 65%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 67%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -[ 68%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 70%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 72%] Generating user_guide.pdf +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 +[ 32%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 34%] 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-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.tex /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) @@ -1167,7 +1159,32 @@ /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]); | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': +entering extended mode + +(/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.t +ex +LaTeX2e <2024-11-01> +L3 programming layer <2024-11-02> +(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls +Document Class: article 2024/06/29 v1.4n Standard LaTeX document class +(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) +(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) +(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) +(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty +(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) +(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty +(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) +(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty[ 36%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o + +(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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/generic/babel-english/english.ldf)) +(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) +(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty +For additional information on amsmath, use the `?' option. +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1177,7 +1194,9 @@ /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)); | ^~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': + +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1187,7 +1206,8 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro 'LOAD_AND_RETURN' 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': + +(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1257,66 +1277,28 @@ /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]); | ^~~~~~~ -entering extended mode - -(/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.t -ex -LaTeX2e <2024-11-01> -L3 programming layer <2024-11-02> -(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls -Document Class: article 2024/06/29 v1.4n Standard LaTeX document class -(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) -(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) -(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty -(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) -(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty -(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) -(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty -(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) -(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty -(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) -(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) -(/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) -(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty -For additional information on amsmath, use the `?' option. -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) -(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) -(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty[ 74%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o - -(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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/latex/graphics/graphicx.sty +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) -(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)[ 77%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -[ 77%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 - -(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/dvips.defcd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 79%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -)cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -)[ 81%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -)cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -[ 82%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -[ 84%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -[ 87%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -[ 87%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 - -(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.stycd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 - +(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) +(/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) (/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/amscls/amsthm.sty[ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +)cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + (/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/hyperref/hyperref.sty[ 41%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + (/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/pdfescape/pdfescape.sty @@ -1332,11 +1314,15 @@ (/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) -(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def[ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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/tex/latex/url/url.sty) (/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/base/atbegshi-ltx.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty @@ -1345,8 +1331,14 @@ (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/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) +(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o + +(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.defcd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +)[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + No file user_guide.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex @@ -1385,62 +1377,31 @@ (/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/latexconfig/epstopdf-sys.cfg))[ 51%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) -(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)[ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + No file user_guide.toc. [1 Non-PDF special ignored! papersize=614.295pt,794.96999pt -{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]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 ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/PrintBcc.cpp:50: -/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 = Printer]': -/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/PrintBcc.cpp: In member function 'void Printer::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp:64:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 64 | fgets(buffer, 100 * MAX, in_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 = Printer]': -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - +{/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] -[3] +[2[ 55%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o +]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + +[3][ 56%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + 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 @@ -1459,102 +1420,10 @@ . -[4 <./MBTD1_C2.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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[4 <./MBTD1_C2.png[ 58%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 >] 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_ @@ -1607,6 +1476,8 @@ /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 >] LaTeX Warning: Reference `fig:quantif' on page 6 undefined on input line 273. @@ -1629,7 +1500,39 @@ []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_1.fa\T1/cmr/m/n/12 : al-ter- -[7] +[7/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Overfull \hbox (3.92465pt too wide) in paragraph at lines 342--343 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_2.fa\T1/cmr/m/n/12 : in-ex- @@ -1654,8 +1557,10 @@ []\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] -[9] +[8][ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o + +[9]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + Underfull \hbox (badness 10000) in paragraph at lines 408--409 @@ -1666,44 +1571,125 @@ (/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.a ux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 -[ 89%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_print_bcc -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 -[ 93%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSplice -[ 93%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSNPS -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_print_bcc -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -[ 94%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_error_removal -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 -[ 94%] Built target ks_print_bcc -/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_kissreadsSplice /usr/lib/x86_64-linux-gnu/libz.so -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_kissreadsSNPS /usr/lib/x86_64-linux-gnu/libz.so -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +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 ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/PrintBcc.cpp:50: +/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 = Printer]': +/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/PrintBcc.cpp: In member function 'void Printer::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp:64:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 64 | fgets(buffer, 100 * MAX, in_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 = Printer]': +/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 67%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 68%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 70%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 74%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 75%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 77%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 79%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 +[ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 ectt1095 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/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) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf[ 84%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o +[ 86%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o + (/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]/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_error_removal - [200]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' - [201] [202] [203] + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mfcd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + + Ok [192]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + [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][ 94%] Built target ks_error_removal - [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] +[216] [217] [218] [219] [220] [221] [222] [223]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf[ 87%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o + + Ok [224] [225]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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 -fcf-protection -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 + [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] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] +[140] [141] [142] [143] [144] [145] [146] [147] [148] [149]/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [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] @@ -1724,9 +1710,7 @@ (/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][ 94%] Built target ks_kissreadsSplice -[ 94%] Built target ks_kissreadsSNPS - [72] [73] [74] [75] [76] [77] [78] + 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] @@ -1757,6 +1741,11 @@ kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var /fonts/pk/ljfour/jknappen/ec/ectt1095.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 +[ 89%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_print_bcc +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_print_bcc +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 89%] Built target ks_print_bcc mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) @@ -1767,17 +1756,53 @@ 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][ 91%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSplice + [194] [195] [196]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 + [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] + Ok [224[ 93%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSNPS +]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 + [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] [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] [155]/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [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] @@ -1798,7 +1823,9 @@ 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]) +[79] [80] [81] [82] [83] [84] [85][ 94%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_error_removal + [86] [87]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 + [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] @@ -1810,11 +1837,20 @@ Font metrics written on ectt1440.tfm. Output written on ectt1440.600gf (256 characters, 61024 bytes). Transcript written on ectt1440.log. +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_kissreadsSNPS /usr/lib/x86_64-linux-gnu/libz.so -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_kissreadsSplice /usr/lib/x86_64-linux-gnu/libz.so -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 94%] Built target ks_kissreadsSNPS +[ 94%] Built target ks_kissreadsSplice +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_error_removal +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 94%] Built target ks_error_removal mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) @@ -2068,9 +2104,7 @@ 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[ 96%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_clean_duplicates -] [89]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 - [90]) +[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] @@ -2082,23 +2116,10 @@ Font metrics written on ectt1200.tfm. Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. -[ 98%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_run_modules -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 -[100%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_bubble_enumeration -cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_clean_duplicates -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -[100%] Built target ks_clean_duplicates -/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_run_modules -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_bubble_enumeration -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -[100%] Built target ks_bubble_enumeration -[100%] Built target ks_run_modules mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) @@ -2153,10 +2174,15 @@ Output written on ectt1728.600gf (256 characters, 72884 bytes). Transcript written on ectt1728.log. mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1728.600pk: successfully generated. +[ 96%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_run_modules +cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_run_modules +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[ 96%] 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/dev/Debian) (preloaded base=mf) @@ -2168,7 +2194,9 @@ 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] +[204] [205] [206] [207][ 98%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_clean_duplicates + [208] [209] [210] [211] [212] [213] [214]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 + [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] @@ -2211,11 +2239,14 @@ Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_clean_duplicates +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' mktexpk: /build/reproducible-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 +[ 98%] 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/dev/Debian) (preloaded base=mf) @@ -2235,7 +2266,9 @@ [248] [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] [144] [145] [146] [147] [148] [149] [150] [151] +[140] [141] [142] [143] [144] [145] [146] [147[100%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_bubble_enumeration +] [148] [149]cd /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 + [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] @@ -2275,6 +2308,9 @@ e-path/kissplice-2.6.7/debian/.debhelper/generated/_source/home/.texlive2024/te xmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1728.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1440 +/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 -fcf-protection -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/x86_64-linux-gnu/kissplice/ks_bubble_enumeration +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' +[100%] Built target ks_bubble_enumeration mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1440 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) @@ -2706,10 +2742,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu @@ -2770,11 +2806,14 @@ 6: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-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 +1/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.08 sec 8: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-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 -1/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.05 sec -2/8 Test #8: ksErrorRemovalTest ............... Passed 0.05 sec +2/8 Test #8: ksErrorRemovalTest ............... Passed 0.10 sec +7: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-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 1: usage: kissplice [-h] [-r READFILES] [-k KVAL] [-b BVAL] [-l LLMAX] 1: [-m LL_MIN] [-M UL_MAX] [-g GRAPH_PREFIX] [-o OUT_DIR] 1: [-d PATH_TO_TMP] [-t NBPROCS] [-s OUTPUT_SNPS] [-v] [-u] @@ -2900,33 +2939,30 @@ 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). -7: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-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 -3/8 Test #1: KisspliceBasicTest ............... Passed 0.08 sec -4/8 Test #7: ksRunModulesTest ................. Passed 0.08 sec +3/8 Test #7: ksRunModulesTest ................. Passed 0.14 sec +4/8 Test #1: KisspliceBasicTest ............... Passed 0.18 sec 5: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_492893\n\n\nElapsed time: 0.0 seconds\n\n[03:47:34 29/12/2025] --> Finding the BCCs...\n[03:47:34 29/12/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[03:47:34 29/12/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:47:35 29/12/2025] --> Done!\nElapsed time: 0.3 seconds\n\n[03:47:35 29/12/2025] --> Starting Bubble Output Module\n[03:47:35 29/12/2025] --> Sampling bubbles by type...\n[03:47:35 29/12/2025] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[03:47:35 29/12/2025] --> Removing low-complexity/redundant bubbles...\n[03:47:35 29/12/2025] --> Done!\nElapsed time: 0.1 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_492893**********\n' +5: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_560388\n\n\nElapsed time: 0.0 seconds\n\n[23:29:40 26/11/2024] --> Finding the BCCs...\n[23:29:40 26/11/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[23:29:40 26/11/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[23:29:41 26/11/2024] --> Done!\nElapsed time: 1.4 seconds\n\n[23:29:41 26/11/2024] --> Starting Bubble Output Module\n[23:29:41 26/11/2024] --> Sampling bubbles by type...\n[23:29:41 26/11/2024] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[23:29:41 26/11/2024] --> Removing low-complexity/redundant bubbles...\n[23:29:41 26/11/2024] --> 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_560388**********\n' 5: kisspliceGraphTest.py: test SUCCESSFUL -5/8 Test #5: KisspliceGraphTest ............... Passed 0.58 sec +5/8 Test #5: KisspliceGraphTest ............... Passed 1.66 sec 4: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_494704\n\n\nElapsed time: 0.0 seconds\n\n[03:47:34 29/12/2025] --> Finding the BCCs...\n[03:47:34 29/12/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[03:47:34 29/12/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:47:35 29/12/2025] --> Done!\nElapsed time: 0.3 seconds\n\n[03:47:35 29/12/2025] --> 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[03:47:35 29/12/2025] --> Sampling bubbles by type...\n[03:47:35 29/12/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[03:47:35 29/12/2025] --> Removing low-complexity/redundant bubbles...\n[03:47:35 29/12/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[03:47:35 29/12/2025] --> Computing read coherence and coverage...\n[03:47:35 29/12/2025] --> Done!\n[03:47:35 29/12/2025] --> Sorting all bubbles...\n[03:47:35 29/12/2025] --> 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_494704**********\n' +4: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_664900\n\n\nElapsed time: 0.0 seconds\n\n[23:29:40 26/11/2024] --> Finding the BCCs...\n[23:29:40 26/11/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[23:29:40 26/11/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[23:29:41 26/11/2024] --> Done!\nElapsed time: 1.3 seconds\n\n[23:29:41 26/11/2024] --> 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[23:29:41 26/11/2024] --> Sampling bubbles by type...\n[23:29:41 26/11/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[23:29:41 26/11/2024] --> Removing low-complexity/redundant bubbles...\n[23:29:41 26/11/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[23:29:41 26/11/2024] --> Computing read coherence and coverage...\n[23:29:42 26/11/2024] --> Done!\n[23:29:42 26/11/2024] --> Sorting all bubbles...\n[23:29:42 26/11/2024] --> Done!\nElapsed time: 0.7 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_664900**********\n' 4: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -6/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 0.93 sec -7/8 Test #2: KisspliceDBGTest ................. Passed 4.79 sec +6/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 2.35 sec +7/8 Test #2: KisspliceDBGTest ................. Passed 13.11 sec 3: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_629873\n\n\n[03:47:34 29/12/2025] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[03:47:37 29/12/2025] --> Done!\nElapsed time: 3.1 seconds\nElapsed time: 0.0 seconds\n\n[03:47:37 29/12/2025] --> Finding the BCCs...\n[03:47:37 29/12/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[03:47:37 29/12/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[03:47:39 29/12/2025] --> Done!\nElapsed time: 1.8 seconds\n\n[03:47:39 29/12/2025] --> 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[03:47:39 29/12/2025] --> Sampling bubbles by type...\n[03:47:39 29/12/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[03:47:39 29/12/2025] --> Removing low-complexity/redundant bubbles...\n[03:47:39 29/12/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[03:47:40 29/12/2025] --> Computing read coherence and coverage...\n[03:47:40 29/12/2025] --> Done!\n[03:47:40 29/12/2025] --> Sorting all bubbles...\n[03:47:40 29/12/2025] --> Done!\nElapsed time: 1.0 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-12-29_03-47-34_629873**********\n' +3: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_126156\n\n\n[23:29:40 26/11/2024] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[23:29:48 26/11/2024] --> Done!\nElapsed time: 8.0 seconds\nElapsed time: 0.0 seconds\n\n[23:29:48 26/11/2024] --> Finding the BCCs...\n[23:29:48 26/11/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[23:29:48 26/11/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[23:29:55 26/11/2024] --> Done!\nElapsed time: 7.0 seconds\n\n[23:29:55 26/11/2024] --> 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[23:29:55 26/11/2024] --> Sampling bubbles by type...\n[23:29:55 26/11/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[23:29:55 26/11/2024] --> Removing low-complexity/redundant bubbles...\n[23:29:55 26/11/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[23:29:56 26/11/2024] --> Computing read coherence and coverage...\n[23:29:56 26/11/2024] --> Done!\n[23:29:56 26/11/2024] --> Sorting all bubbles...\n[23:29:56 26/11/2024] --> Done!\nElapsed time: 1.4 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-11-26_23-29-40_126156**********\n' 3: kisspliceTwoSequencesTest.py: test SUCCESSFUL -8/8 Test #3: KisspliceTwoSequencesTest ........ Passed 6.11 sec +8/8 Test #3: KisspliceTwoSequencesTest ........ Passed 16.97 sec 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 6.12 sec +Total Test time (real) = 16.98 sec make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kissplice/ - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/kissplice-2.6.7/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/kissplice-2.6.7/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kissplice-2.6.7 -B/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2983,12 +3019,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2247549/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2247549/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/3218117 and its subdirectories -I: Current time: Mon Dec 29 03:47:53 -12 2025 -I: pbuilder-time-stamp: 1767023273 +I: removing directory /srv/workspace/pbuilder/2247549 and its subdirectories +I: Current time: Tue Nov 26 23:30:21 +14 2024 +I: pbuilder-time-stamp: 1732613421