Diff of the two buildlogs: -- --- b1/build.log 2025-08-24 13:45:59.001562937 +0000 +++ b2/build.log 2025-08-24 13:50:57.809920594 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 24 01:40:43 -12 2025 -I: pbuilder-time-stamp: 1756042843 +I: Current time: Sun Sep 27 10:09:00 +14 2026 +I: pbuilder-time-stamp: 1790453340 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying tests-2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14736/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1098099/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Sep 26 20:09 /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/1098099/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1098099/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=40 ' - DISTRIBUTION='forky' - 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='312b70d42eba4a92bc61742412f6c253' - 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='14736' - PS1='# ' - PS2='> ' + INVOCATION_ID=22ef5f01afbd4ddfac325267584e0525 + 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=1098099 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.8ZGUmhE9/pbuilderrc_uvJu --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8ZGUmhE9/b1 --logfile b1/build.log kissplice_2.6.7-2.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.8ZGUmhE9/pbuilderrc_YJ5L --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8ZGUmhE9/b2 --logfile b2/build.log kissplice_2.6.7-2.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14736/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1098099/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +289,7 @@ Get: 135 http://deb.debian.org/debian forky/main amd64 texlive-base all 2025.20250727-2 [23.1 MB] Get: 136 http://deb.debian.org/debian forky/main amd64 texlive-latex-base all 2025.20250727-2 [1318 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 texlive-latex-recommended all 2025.20250727-2 [8455 kB] -Fetched 114 MB in 2s (52.6 MB/s) +Fetched 114 MB in 5s (21.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19855 files and directories currently installed.) @@ -717,8 +749,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Aug 24 13:43:47 UTC 2025. -Universal Time is now: Sun Aug 24 13:43:47 UTC 2025. +Local time is now: Sat Sep 26 20:12:04 UTC 2026. +Universal Time is now: Sat Sep 26 20:12:04 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -849,7 +881,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kissplice-2.6.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kissplice_2.6.7-2_source.changes +I: user script /srv/workspace/pbuilder/1098099/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1098099/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kissplice-2.6.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kissplice_2.6.7-2_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.7-2 dpkg-buildpackage: info: source distribution unstable @@ -892,7 +928,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex --- Configuring done (2.8s) +-- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -905,7 +941,7 @@ -- 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 -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "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 @@ -937,109 +973,113 @@ 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=" 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]: 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[3]: Leaving 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 -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[3]: Entering 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 thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.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 -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' -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' 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' 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 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' -[ 3%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -[ 3%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -[ 8%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -[ 18%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -[ 20%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -[ 22%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -[ 29%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -[ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.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/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 -[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.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_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 +[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o +[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +[ 6%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o +[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o +[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o +[ 17%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +[ 17%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o +[ 17%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.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/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 +[ 20%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o +[ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o +[ 22%] 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/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 -[ 51%] 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/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 -[ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -[ 62%] 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_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 -[ 62%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -cd 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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 -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 -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 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-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/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/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 +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 +[ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.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 +[ 63%] 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/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/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 +[ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o +[ 67%] 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_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 +[ 68%] Generating user_guide.pdf 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 -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 -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 +[ 70%] 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/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/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/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 +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 +[ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o /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 +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 This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': @@ -1052,10 +1092,7 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1074:4: note: in expansion of macro 'LOAD_AND_RETURN' 1074 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ -entering extended mode - -(/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.t -ex/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: 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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1065,16 +1102,6 @@ /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* 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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/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* 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)); \ @@ -1095,10 +1122,7 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ - -LaTeX2e <2025-06-01> patch level 1 -L3 programming layer <2025-07-19> -(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': +/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ @@ -1135,16 +1159,6 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ -/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/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 'u_long SparseRead(FILE*, SparseBin**)': /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)); \ @@ -1158,9 +1172,39 @@ /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]); | ^~~~~~~ +[ 74%] 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 +entering extended mode + +(/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/doc/user_guide.t +ex +LaTeX2e <2025-06-01> patch level 1 +L3 programming layer <2025-07-19> +(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/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)); + | ^~~~~~~~~~~~~~~ Document Class: article 2025/01/22 v1.4n Standard LaTeX document class -(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': +(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo[ 75%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/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); + | ^~~~~~~~~~~~~~~ +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 +/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1170,7 +1214,8 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro 'LOAD_AND_RETURN' 1142 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ -)/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': +[ 77%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +/build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1180,6 +1225,7 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ +[ 79%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); @@ -1211,7 +1257,7 @@ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/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] +)/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.7/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' @@ -1230,6 +1276,8 @@ /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]); | ^~~~~~~ +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 +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 ) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty @@ -1237,22 +1285,22 @@ (/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[ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.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 -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 -))) - (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty[ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -[ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -[ 75%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -[ 77%] 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/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/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 +(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))[ 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_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 +[ 84%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o +[ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +[ 87%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.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 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 +(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.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_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/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 @@ -1260,14 +1308,8 @@ (/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 -(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))[ 79%] 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 - -(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty[ 81%] 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 -[ 82%] 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 - +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/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) @@ -1275,7 +1317,38 @@ (/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.ltxIn file included from /build/reproducible-path/kissplice-2.6.7/modules/PrintBcc.cpp:51: +(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) +(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) +(/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty) +(/usr/share/texlive/texmf-dist/tex/latex/tools/enumerate.sty) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty +(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) +(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) +(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty +(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) +(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty +(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))) +(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) +(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty +(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) +(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty +(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) +(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty) +(/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/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/hyperref/hpdftex.def +(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty +(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) +(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) +(/usr/share/texlive/texmf-dist/tex/latex/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))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 ); @@ -1314,7 +1387,47 @@ /build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -))/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': + +(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) +No file user_guide.aux. +*geometry* driver: auto-detecting +*geometry* detected driver: pdftex +*geometry* verbose mode - [ preamble ] result: +* driver: pdftex +* paper: letterpaper +* layout: +* layoutoffset:(h,v)=(0.0pt,0.0pt) +* modes: +* h-part:(L,W,R)=(71.13188pt, 472.03123pt, 71.13188pt) +* v-part:(T,H,B)=(56.9055pt, 652.70622pt, 85.35826pt) +* \paperwidth=614.295pt +* \paperheight=794.96999pt +* \textwidth=472.03123pt +* \textheight=652.70622pt +* \oddsidemargin=-1.1381pt +* \evensidemargin=-1.1381pt +* \topmargin=-52.36449pt +* \headheight=12.0pt +* \headsep=25.0pt +* \topskip=12.0pt +* \footskip=30.0pt +* \marginparwidth=35.0pt +* \marginparsep=10.0pt +* \columnsep=10.0pt +* \skip\footins=10.8pt plus 4.0pt minus 2.0pt +* \hoffset=0.0pt +* \voffset=0.0pt +* \mag=1000 +* \@twocolumnfalse +* \@twosidefalse +* \@mparswitchfalse +* \@reversemarginfalse +* (1in=72.27pt=25.4mm, 1cm=28.453pt) + +(/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)/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1346,9 +1459,90 @@ /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +)[ 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/share/texlive/texmf-dist/tex/latex/base/alltt.sty) -(/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty/build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) +(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) +No file user_guide.toc. + +[1 +Non-PDF special ignored! + papersize=614.295pt,794.96999pt +{/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] +Overfull \hbox (24.58913pt too wide) in paragraph at lines 151--160 +[]\T1/cmr/m/n/12 The \T1/cmtt/m/n/12 sample_example \T1/cmr/m/n/12 di-rec-tory +con-tains four files \T1/cmtt/m/n/12 mock1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 m +ock2.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 virus1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/ +12 virus2.fq + +LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 171 +. + + +Overfull \hbox (24.90025pt too wide) in paragraph at lines 189--189 +[]\T1/cmr/m/n/12 Figure 1: []Content of the file \T1/cmtt/m/n/12 results_mock1_ +mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , + +LaTeX Warning: Reference `fig:extype1_C0' on page 4 undefined on input line 199 +. + + +[4 <./MBTD1_C2.pngIn file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:61: +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 84 | fscanf(info_file, "%d \n",&bcc_size ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 85 | fscanf(info_file, "%d \n",&records_per_file ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:60: +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:198:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 198 | fgets(buffer, 100 * MAX, node_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:277:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 277 | fgets(buffer, 100 * MAX, edge_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 +/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1364,35 +1558,7 @@ /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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -[ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o 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-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 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/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1408,8 +1574,7 @@ /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty/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: 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1425,156 +1590,23 @@ /build/reproducible-path/kissplice-2.6.7/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)))In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:61: -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 84 | fscanf(info_file, "%d \n",&bcc_size ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 85 | fscanf(info_file, "%d \n",&records_per_file ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/kissplice-2.6.7/modules/BubbleEnumeration.cpp:60: -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); +/build/reproducible-path/kissplice-2.6.7/modules/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/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:198:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 198 | fgets(buffer, 100 * MAX, node_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.7/modules/CGraph.h:277:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 277 | fgets(buffer, 100 * MAX, edge_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -) -(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty -(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) -(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty -(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) -(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)[ 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/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) 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\T1/cmtt/m/n/12 results_mock1_ -mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , - -LaTeX Warning: Reference `fig:extype1_C0' on page 4 undefined on input line 199 -. - - -[4 <./MBTD1_C2.png>]/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' - +/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 (24.90025pt too wide) in paragraph at lines 203--203 []\T1/cmr/m/n/12 Figure 2: []Content of the file \T1/cmtt/m/n/12 results_mock1_ mock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , @@ -1583,20 +1615,12 @@ . -[5 <./MBTD1_C0.png[ 93%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSplice -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 -[ 94%] 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 ->] +[5 <./MBTD1_C0.png>] LaTeX Warning: Reference `fig:quantif' on page 6 undefined on input line 273. 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../../../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 - <./quantifModel.pngmake[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_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' ->] +[6 <./quantifModel.png>] Overfull \hbox (1.2115pt too wide) in paragraph at lines 327--328 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes \T1/cmr/m/n/12 for the nodes @@ -1613,7 +1637,8 @@ []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_1.fa\T1/cmr/m/n/12 : al-ter- -[7] +[7][ 91%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSNPS + 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- @@ -1638,7 +1663,8 @@ []\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] +[8cd /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 +] [9] Underfull \hbox (badness 10000) in paragraph at lines 408--409 @@ -1650,10 +1676,15 @@ (/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 +/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' +[ 93%] 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 +/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' +[ 93%] Built target ks_kissreadsSNPS mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 -[ 94%] Built target ks_error_removal This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) -[ 94%] Built target ks_kissreadsSplice (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) @@ -1662,8 +1693,11 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] + Ok [192] [193] [194] [195] [196] [197] [198] [199][ 93%] Built target ks_error_removal + [200] [201] [202] [203] +[204] [205] [206] [207][ 94%] Linking CXX executable ../../../lib/x86_64-linux-gnu/kissplice/ks_kissreadsSplice + [208]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 + [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] @@ -1672,11 +1706,13 @@ (/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][ 94%] Built target ks_kissreadsSNPS - [155] [156] [157]) +[152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] + Ok [158] [160] [161] [162]/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 + [163]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' + [164] [165] [166] [167] [168] [169] [170] +[171] [172] [173] [174][ 94%] Built target ks_kissreadsSplice + [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] @@ -1828,9 +1864,7 @@ 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][ 96%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_run_modules - [196]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 - [197] [198] [199] [200] [201] [202] [203] + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf @@ -1838,38 +1872,25 @@ [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][ 98%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_bubble_enumeration -[100%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_clean_duplicates - -[140]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 -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 - [141] [142] [143] [144]/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' - [145] [146] [147] [148] [149] [150] [151] + Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] +[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176][100%] Built target ks_run_modules - [177] [178] [179] [180] [181] [182] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf - Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46]/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 - [47] [58] -[59] [61] [96]/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 - [189]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' - [17] [45] [16] [21]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' - [22]) + Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] +[59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26][100%] Built target ks_clean_duplicates -[100%] Built target ks_bubble_enumeration - [28] [27] [29] [30] [31]) + Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf @@ -1950,6 +1971,8 @@ r/generated/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecb x1440.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 +[ 96%] 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 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -1961,15 +1984,20 @@ Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exileast.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] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180]/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 + [181]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' + [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] + Ok [224] [225] [226][ 96%] Built target ks_bubble_enumeration + [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf 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] [208] [209] [210] [211] [212] [213][ 98%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_run_modules + [214]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 + [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] @@ -1989,9 +2017,12 @@ Ok [25] [26] [27] [28] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf Ok [38] [63] [190]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf - Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] -[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf/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 + + Ok [65] [66]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' + [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] +[79] [80] [81] [82] [83][ 98%] Built target ks_run_modules + [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.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] @@ -2009,6 +2040,11 @@ ted/_source/home/.texlive2025/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.60 0pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 +[100%] Linking CXX executable ../lib/x86_64-linux-gnu/kissplice/ks_clean_duplicates +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 +/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 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/Debian) (preloaded base=mf) @@ -2817,14 +2853,14 @@ 1: --type1-only Only quantify Type 1 bubbles (alternative splicing 1: events, MAJOR SPEED UP with -b > 10 BUT all other 1: bubbles will not appear in the result file). -1/8 Test #1: KisspliceBasicTest ............... Passed 0.08 sec +1/8 Test #1: KisspliceBasicTest ............... Passed 0.07 sec test 2 Start 2: KisspliceDBGTest 2: Test command: /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceDBGTest.py "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin" 2: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests 2: Test timeout computed to be: 10000000 -2/8 Test #2: KisspliceDBGTest ................. Passed 4.88 sec +2/8 Test #2: KisspliceDBGTest ................. Passed 3.33 sec test 3 Start 3: KisspliceTwoSequencesTest @@ -2832,9 +2868,9 @@ 3: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests 3: Test timeout computed to be: 10000000 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_2025-08-24_01-45-37_613612\n\n\n[01:45:37 24/08/2025] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[01:45:41 24/08/2025] --> Done!\nElapsed time: 3.9 seconds\nElapsed time: 0.0 seconds\n\n[01:45:41 24/08/2025] --> Finding the BCCs...\n[01:45:41 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[01:45:41 24/08/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[01:45:44 24/08/2025] --> Done!\nElapsed time: 2.7 seconds\n\n[01:45:44 24/08/2025] --> 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[01:45:44 24/08/2025] --> Sampling bubbles by type...\n[01:45:44 24/08/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[01:45:44 24/08/2025] --> Removing low-complexity/redundant bubbles...\n[01:45:44 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[01:45:44 24/08/2025] --> Computing read coherence and coverage...\n[01:45:44 24/08/2025] --> Done!\n[01:45:44 24/08/2025] --> Sorting all bubbles...\n[01:45:44 24/08/2025] --> Done!\nElapsed time: 0.8 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 8 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-08-24_01-45-37_613612**********\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_2026-09-27_10-13-44_827678\n\n\n[10:13:44 27/09/2026] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[10:13:46 27/09/2026] --> Done!\nElapsed time: 2.5 seconds\nElapsed time: 0.0 seconds\n\n[10:13:46 27/09/2026] --> Finding the BCCs...\n[10:13:46 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[10:13:46 27/09/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[10:13:47 27/09/2026] --> Done!\nElapsed time: 0.3 seconds\n\n[10:13:47 27/09/2026] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[10:13:47 27/09/2026] --> Sampling bubbles by type...\n[10:13:47 27/09/2026] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[10:13:47 27/09/2026] --> Removing low-complexity/redundant bubbles...\n[10:13:47 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[10:13:47 27/09/2026] --> Computing read coherence and coverage...\n[10:13:48 27/09/2026] --> Done!\n[10:13:48 27/09/2026] --> Sorting all bubbles...\n[10:13:48 27/09/2026] --> Done!\nElapsed time: 0.8 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 8 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-09-27_10-13-44_827678**********\n' 3: kisspliceTwoSequencesTest.py: test SUCCESSFUL -3/8 Test #3: KisspliceTwoSequencesTest ........ Passed 7.61 sec +3/8 Test #3: KisspliceTwoSequencesTest ........ Passed 3.79 sec test 4 Start 4: KisspliceGraphAndSequenceTest @@ -2842,9 +2878,9 @@ 4: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests 4: Test timeout computed to be: 10000000 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_2025-08-24_01-45-45_710163\n\n\nElapsed time: 0.0 seconds\n\n[01:45:45 24/08/2025] --> Finding the BCCs...\n[01:45:45 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[01:45:45 24/08/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[01:45:46 24/08/2025] --> Done!\nElapsed time: 1.6 seconds\n\n[01:45:46 24/08/2025] --> 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[01:45:46 24/08/2025] --> Sampling bubbles by type...\n[01:45:46 24/08/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[01:45:46 24/08/2025] --> Removing low-complexity/redundant bubbles...\n[01:45:46 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[01:45:47 24/08/2025] --> Computing read coherence and coverage...\n[01:45:47 24/08/2025] --> Done!\n[01:45:47 24/08/2025] --> Sorting all bubbles...\n[01:45:47 24/08/2025] --> 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_2025-08-24_01-45-45_710163**********\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_2026-09-27_10-13-48_263663\n\n\nElapsed time: 0.0 seconds\n\n[10:13:48 27/09/2026] --> Finding the BCCs...\n[10:13:48 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[10:13:48 27/09/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[10:13:48 27/09/2026] --> Done!\nElapsed time: 0.5 seconds\n\n[10:13:48 27/09/2026] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[10:13:48 27/09/2026] --> Sampling bubbles by type...\n[10:13:48 27/09/2026] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[10:13:48 27/09/2026] --> Removing low-complexity/redundant bubbles...\n[10:13:48 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[10:13:48 27/09/2026] --> Computing read coherence and coverage...\n[10:13:49 27/09/2026] --> Done!\n[10:13:49 27/09/2026] --> Sorting all bubbles...\n[10:13:49 27/09/2026] --> Done!\nElapsed time: 0.4 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-09-27_10-13-48_263663**********\n' 4: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -4/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 2.32 sec +4/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 1.01 sec test 5 Start 5: KisspliceGraphTest @@ -2852,9 +2888,9 @@ 5: Working Directory: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests 5: Test timeout computed to be: 10000000 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_2025-08-24_01-45-47_34954\n\n\nElapsed time: 0.0 seconds\n\n[01:45:47 24/08/2025] --> Finding the BCCs...\n[01:45:47 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[01:45:47 24/08/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[01:45:47 24/08/2025] --> Done!\nElapsed time: 0.4 seconds\n\n[01:45:47 24/08/2025] --> Starting Bubble Output Module\n[01:45:47 24/08/2025] --> Sampling bubbles by type...\n[01:45:47 24/08/2025] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[01:45:47 24/08/2025] --> Removing low-complexity/redundant bubbles...\n[01:45:47 24/08/2025] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-08-24_01-45-47_34954**********\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_2026-09-27_10-13-49_707745\n\n\nElapsed time: 0.0 seconds\n\n[10:13:49 27/09/2026] --> Finding the BCCs...\n[10:13:49 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\n\n[10:13:49 27/09/2026] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[10:13:49 27/09/2026] --> Done!\nElapsed time: 0.3 seconds\n\n[10:13:49 27/09/2026] --> Starting Bubble Output Module\n[10:13:49 27/09/2026] --> Sampling bubbles by type...\n[10:13:49 27/09/2026] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[10:13:49 27/09/2026] --> Removing low-complexity/redundant bubbles...\n[10:13:49 27/09/2026] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2026-09-27_10-13-49_707745**********\n' 5: kisspliceGraphTest.py: test SUCCESSFUL -5/8 Test #5: KisspliceGraphTest ............... Passed 0.55 sec +5/8 Test #5: KisspliceGraphTest ............... Passed 0.45 sec test 6 Start 6: ksBubbleEnumerationTest @@ -2874,7 +2910,7 @@ 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 -7/8 Test #7: ksRunModulesTest ................. Passed 0.13 sec +7/8 Test #7: ksRunModulesTest ................. Passed 0.06 sec test 8 Start 8: ksErrorRemovalTest @@ -2888,13 +2924,13 @@ 100% tests passed, 0 tests failed out of 8 -Total Test time (real) = 15.76 sec +Total Test time (real) = 8.81 sec make[2]: Leaving directory '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.7' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kissplice/ - cd obj-x86_64-linux-gnu && make -j40 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 -j42 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 @@ -2951,12 +2987,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1098099/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1098099/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/14736 and its subdirectories -I: Current time: Sun Aug 24 01:45:58 -12 2025 -I: pbuilder-time-stamp: 1756043158 +I: removing directory /srv/workspace/pbuilder/1098099 and its subdirectories +I: Current time: Sun Sep 27 10:13:57 +14 2026 +I: pbuilder-time-stamp: 1790453637