Diff of the two buildlogs: -- --- b1/build.log 2024-05-10 02:14:47.987462250 +0000 +++ b2/build.log 2024-05-10 02:18:32.685890697 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 11 20:35:36 -12 2025 -I: pbuilder-time-stamp: 1749717336 +I: Current time: Fri May 10 16:14:51 +14 2024 +I: pbuilder-time-stamp: 1715307291 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying tests-2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1235563/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2560013/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 10 02:14 /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/2560013/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2560013/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='4fa54d42e4774dd2aef83d0418b4f344' - 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='1235563' - PS1='# ' - PS2='> ' + INVOCATION_ID=f062c0d1ce5b448f9e8aa50325d75a08 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2560013 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.ePLbVDsc/pbuilderrc_e26J --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ePLbVDsc/b1 --logfile b1/build.log kissplice_2.6.2-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ePLbVDsc/pbuilderrc_Tnal --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ePLbVDsc/b2 --logfile b2/build.log kissplice_2.6.2-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 9 17:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1235563/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 8 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2560013/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -256,7 +288,7 @@ Get: 131 http://deb.debian.org/debian trixie/main arm64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 132 http://deb.debian.org/debian trixie/main arm64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] -Fetched 106 MB in 1s (195 MB/s) +Fetched 106 MB in 1s (105 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) @@ -699,8 +731,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jun 12 08:36:06 UTC 2025. -Universal Time is now: Thu Jun 12 08:36:06 UTC 2025. +Local time is now: Fri May 10 02:15:47 UTC 2024. +Universal Time is now: Fri May 10 02:15:47 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -834,7 +866,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kissplice-2.6.2/ && 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_2.6.2-3_source.changes +I: user script /srv/workspace/pbuilder/2560013/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2560013/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kissplice-2.6.2/ && 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_2.6.2-3_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.2-3 dpkg-buildpackage: info: source distribution unstable @@ -876,8 +912,8 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex --- Configuring done (1.3s) --- Generating done (0.1s) +-- Configuring done (1.8s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -905,71 +941,62 @@ make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake "--color=" -[ 1%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake "--color=" -[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +[ 1%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/commons.cpp -[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp -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-2.6.2/obj-aarch64-linux-gnu' -[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/libchash.cpp +make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build +[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 10%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp +make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend +[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF 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CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CleanDuplicates.cpp +[ 10%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build -[ 15%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -cd 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/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -MF CMakeFiles/ks_run_modules.dir/run.cpp.o.d -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/run.cpp +[ 18%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/ErrorRemoval.cpp [ 20%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -MF CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp -/usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex -This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) - restricted \write18 enabled. /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:580:44: warning: comparison of integer expressions of different signedness: 'long int' and 'u_long' {aka 'long unsigned int'} [-Wsign-compare] 580 | for ( iter->posGroup++; iter->posGroup < SPARSE_GROUPS(iter->cBuckets); @@ -1064,10 +1091,334 @@ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp: In function 'float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp:439:44: warning: comparison of integer expressions of different signedness: 'int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] + 439 | for (ii=offset_seed; iiposGroup++; iter->posGroup < SPARSE_GROUPS(iter->cBuckets); + | ^ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' + 1154 | LOAD_AND_RETURN(ht, retval); + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': +/build/reproducible-path/kissplice-2.6.2/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' + 1272 | READ_UL(fp, ht->cchKey); + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' + 1273 | READ_UL(fp, ht->cItems); + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' + 1274 | READ_UL(fp, ht->cDeletedItems); + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' + 1277 | READ_UL(fp, cchKey); + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' + 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ + | ^~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' + 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); + | ^~~~~~~ +[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp +[ 29%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp +[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp +[ 32%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_index.cpp +[ 34%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/NGraph.cpp +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/kissReads.cpp +[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/list.cpp +In file included from /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp:51: +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/PrintBcc.cpp:50: +/build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/PrintBcc.cpp: In member function 'void Printer::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp:64:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 64 | fgets(buffer, 100 * MAX, in_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 96 | for(i=0;i='A' && in[i]<='Z') count++; + | ~^~~~~~~~~~~ +[ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; + | ~^~~~~~~~~~~ +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/tree.cpp +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] + 155 | int i,j,z,stop; + | ^ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] + 156 | char validSeed; + | ^~~~~~~~~ +[ 41%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp +[ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp +[ 44%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp +[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_info.cpp +[ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/Utils.cpp +In file included from /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp:61: +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/BubbleEnumeration.cpp:60: +/build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': +/build/reproducible-path/kissplice-2.6.2/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_index.cpp +[ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/kissReads.cpp +[ 55%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp +[ 56%] Linking CXX executable ../lib/kissplice/ks_print_bcc +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/kissplice/ks_print_bcc +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 56%] Built target ks_print_bcc +make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 96 | for(i=0;i='A' && in[i]<='Z') count++; + | ~^~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; + | ~^~~~~~~~~~~ +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake "--color=" +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] + 155 | int i,j,z,stop; + | ^ +/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] + 156 | char validSeed; + | ^~~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build +make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 58%] Generating user_guide.pdf +cd /build/reproducible-path/kissplice-2.6.2/doc && /build/reproducible-path/kissplice-2.6.2/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex +/usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex +This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) + restricted \write18 enabled. +[ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/list.cpp +[ 62%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp +[ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp entering extended mode (/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide. -tex +tex[ 65%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 + LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls @@ -1076,50 +1427,83 @@ (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) -(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp: In function 'float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp:439:44: warning: comparison of integer expressions of different signedness: 'int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] - 439 | for (ii=offset_seed; iiw)-kmer_size;j++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ->]/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - +[4 <./MBTD1_C2.png>] LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 275. -[5 <./MBTD1_C0.png[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp -[ 36%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp -In file included from /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp:61: -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/BubbleEnumeration.cpp:60: -/build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': -/build/reproducible-path/kissplice-2.6.2/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/tree.cpp ->] [6 <./quantifModel.png/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 96 | for(i=0;i='A' && in[i]<='Z') count++; - | ~^~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; - | ~^~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] - 155 | int i,j,z,stop; - | ^ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] - 156 | char validSeed; - | ^~~~~~~~~ -[ 39%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/NGraph.cpp +[5 <./MBTD1_C0.png[ 75%] Linking CXX executable ../lib/kissplice/ks_error_removal +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-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-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_error_removal +[ 77%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/SplitBcc.cpp +>] [6[ 79%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o + <./quantifModel.pngcd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/CycleCompression.cpp >] Overfull \hbox (1.2115pt too wide) in paragraph at lines 329--330 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes @@ -1398,131 +1651,69 @@ [8] Underfull \hbox (badness 10000) in paragraph at lines 410--411 -[9] +[9make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +] Underfull \hbox (badness 10000) in paragraph at lines 424--426 [10] (/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide. -aux) +aux)/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.2/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 -[ 41%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp -[ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_info.cpp -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:580:44: warning: comparison of integer expressions of different signedness: 'long int' and 'u_long' {aka 'long unsigned int'} [-Wsign-compare] - 580 | for ( iter->posGroup++; iter->posGroup < SPARSE_GROUPS(iter->cBuckets); - | ^ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' - 1154 | LOAD_AND_RETURN(ht, retval); - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': -/build/reproducible-path/kissplice-2.6.2/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' - 1272 | READ_UL(fp, ht->cchKey); - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' - 1273 | READ_UL(fp, ht->cItems); - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' - 1274 | READ_UL(fp, ht->cDeletedItems); - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' - 1277 | READ_UL(fp, cchKey); - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' - 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ - | ^~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' - 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); - | ^~~~~~~ -[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/Utils.cpp -[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp -[ 50%] Linking CXX executable ../lib/kissplice/ks_print_bcc -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/kissplice/ks_print_bcc -[ 51%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Built target ks_error_removal +[ 81%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp +[ 82%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/NGraph.cpp +[ 84%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp +[ 86%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/LabelledCEdge.cpp +[ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp +[ 89%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_kissreadsSNPS /usr/lib/aarch64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic +[ 91%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 91%] Built target ks_kissreadsSNPS +[ 93%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o +[ 94%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/LabelledCEdge.cpp +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf @@ -1538,15 +1729,13 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] -[96] [126] [127] [128] [129] [130] [131] [132] [133] [134]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' - [135] [136] [137] +[96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf - Ok [48] [49] [50] [51] [52] [53] [54][ 51%] Built target ks_print_bcc - [55] [56] [57]) + Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf @@ -1555,12 +1744,6 @@ Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. -[ 53%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp -[ 55%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -[ 56%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/LabelledCEdge.cpp -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp mktexpk: /build/reproducible-path/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. @@ -1574,10 +1757,6 @@ kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var /fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 -[ 58%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp -[ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/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); @@ -1610,49 +1789,6 @@ /build/reproducible-path/kissplice-2.6.2/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp -[ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp -[ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_index.cpp -[ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/kissReads.cpp -[ 68%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/list.cpp -[ 70%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_kissreadsSNPS /usr/lib/aarch64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 96 | for(i=0;i='A' && in[i]<='Z') count++; - | ~^~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; - | ~^~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] - 155 | int i,j,z,stop; - | ^ -/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] - 156 | char validSeed; - | ^~~~~~~~~ mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) @@ -1665,9 +1801,7 @@ Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216][ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o - [217] [218] [219] [220] [221]cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/tree.cpp - [222] [223]) +[216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] @@ -1676,8 +1810,7 @@ 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.mfmake[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' - +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) @@ -1692,15 +1825,12 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28][ 74%] Linking CXX executable ../lib/kissplice/ks_error_removal - [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 - Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74]cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 - [75] [76] [77] [78] -[79] [80][ 74%] Built target ks_kissreadsSNPS - [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] +[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] @@ -1712,64 +1842,11 @@ Font metrics written on ecbx1200.tfm. Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_error_removal -[ 75%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/fragment_info.cpp -[ 77%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp -[ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/thirdparty/kissreads/src/Utils.cpp mktexpk: /build/reproducible-path/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 -[ 81%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/NGraph.cpp -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 81%] Built target ks_error_removal -[ 82%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp -[ 84%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/CGraph.cpp -[ 86%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/LabelledCEdge.cpp -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1094 | fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/SplitBcc.cpp -[ 89%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/Utils.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) @@ -1777,12 +1854,10 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf - Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf[ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o - + 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 [192cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -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-2.6.2/modules/LabelledCEdge.cpp -] [193] [194] [195] [196] [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 @@ -1816,9 +1891,7 @@ [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] -[109] [110][ 93%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o - [111]cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp - [112] [113] [114] [115] [116] [117] [118] [119] [120] +[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) @@ -1832,44 +1905,17 @@ debian/.debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour /jknappen/ec/ectt1440.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 -[ 94%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_kissreadsSplice /usr/lib/aarch64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/reproducible-path/kissplice-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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-2.6.2/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-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-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_clean_duplicates +[ 98%] Linking CXX executable ../lib/kissplice/ks_run_modules +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_run_modules +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 98%] Built target ks_clean_duplicates make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 94%] Built target ks_kissreadsSplice mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 +[ 98%] Built target ks_run_modules This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf @@ -1927,6 +1973,11 @@ debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappe n/ec/ectt1095.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 +[100%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration +cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_bubble_enumeration +make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' +[100%] Built target ks_bubble_enumeration mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) @@ -2045,13 +2096,7 @@ ted/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.60 0pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 -[ 96%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_bubble_enumeration -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 96%] Built target ks_bubble_enumeration mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 -[ 98%] Linking CXX executable ../lib/kissplice/ks_run_modules This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1200.mf @@ -2060,10 +2105,8 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf - Ok)cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 - (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_run_modules - [198] [199] [200] [201] [202] [203] + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf @@ -2075,10 +2118,8 @@ [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]make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' - [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181][ 98%] Built target ks_run_modules - [182] + Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] @@ -2109,14 +2150,9 @@ Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. mktexpk: /build/reproducible-path/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2023/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. -[100%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates -cd /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/kissplice/ks_clean_duplicates -make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' -[100%] Built target ks_clean_duplicates mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) @@ -2816,7 +2852,6 @@ 1: -redo-links (0 arg) : same, but redo links 1: -skip-links (0 arg) : same, but skip links 1: -nb-glue-partitions (1 arg) : number of glue partitions (automatically calculated by default) [default '0'] -1/9 Test #1: IsBcalmStartable ................. Passed 0.15 sec 2: usage: kissplice [-h] [-r READFILES] [-k KVAL] [-b BVAL] [-l LLMAX] 2: [-m LL_MIN] [-M UL_MAX] [-g GRAPH_PREFIX] [-o OUT_DIR] 2: [-d PATH_TO_TMP] [-t NBPROCS] [-s OUTPUT_SNPS] [-v] [-u] @@ -2942,36 +2977,37 @@ 2: --type1-only Only quantify Type 1 bubbles (alternative splicing 2: events, MAJOR SPEED UP with -b > 10 BUT all other 2: bubbles will not appear in the result file). +1/9 Test #1: IsBcalmStartable ................. Passed 0.13 sec +2/9 Test #2: KisspliceBasicTest ............... Passed 0.12 sec 7: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_bubble_enumeration /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_info_bcc /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_contents_edges_bcc /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_contents_nodes_bcc /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_all_edges_bcc /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_all_nodes_bcc 2 25 /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/test_ks_bubble_enumeration_output 3 bcc_test 0 -u 1000 -L 49 -l 42 -M 10000 -b 5 7: b'\t Enumerating bubbles with at most 5 branching nodes in each path!\n============================================================================\nSummary of results\n============================================================================\nNo of bubbles: 4\n============================================================================\n' 7: Ks_Bubble_Enumeration_Test: test SUCCESSFUL -2/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.09 sec -3/9 Test #2: KisspliceBasicTest ............... Passed 0.17 sec +3/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.13 sec 9: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_error_removal /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance 0.02/build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/test_ks_error_removal_output 9: b'252 out of 5336 edges removed\n' 9: ks_error_removal: test SUCCESSFUL 8: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_run_modules /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes 25 /build/reproducible-path/kissplice-2.6.2/tests/functional_tests/data/test_ks_run_modules_output_graph 8: 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' 8: ks_run_modules: test SUCCESSFUL -4/9 Test #8: ksRunModulesTest ................. Passed 0.14 sec -5/9 Test #9: ksErrorRemovalTest ............... Passed 0.13 sec +4/9 Test #9: ksErrorRemovalTest ............... Passed 0.12 sec +5/9 Test #8: ksRunModulesTest ................. Passed 0.15 sec 6: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -C 0 -6: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/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-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_511979\n\n\nElapsed time: 0.0 seconds\n\n[20:37:27 11/06/2025] --> Finding the BCCs...\n[20:37:27 11/06/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[20:37:27 11/06/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[20:37:30 11/06/2025] --> Done!\nElapsed time: 2.9 seconds\n\n[20:37:30 11/06/2025] --> Starting Bubble Output Module\n[20:37:30 11/06/2025] --> Sampling bubbles by type...\n[20:37:30 11/06/2025] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[20:37:30 11/06/2025] --> Removing low-complexity/redundant bubbles...\n[20:37:30 11/06/2025] --> Done!\nElapsed time: 0.1 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_511979**********\n' +6: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/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-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_948815\n\n\nElapsed time: 0.0 seconds\n\n[16:18:03 10/05/2024] --> Finding the BCCs...\n[16:18:03 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[16:18:03 10/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[16:18:07 10/05/2024] --> Done!\nElapsed time: 4.0 seconds\n\n[16:18:07 10/05/2024] --> Starting Bubble Output Module\n[16:18:07 10/05/2024] --> Sampling bubbles by type...\n[16:18:07 10/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[16:18:07 10/05/2024] --> Removing low-complexity/redundant bubbles...\n[16:18:07 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_948815**********\n' 6: kisspliceGraphTest.py: test SUCCESSFUL -6/9 Test #6: KisspliceGraphTest ............... Passed 3.21 sec +6/9 Test #6: KisspliceGraphTest ............... Passed 4.43 sec 5: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -C 0 -5: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.2/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-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_815598\n\n\nElapsed time: 0.0 seconds\n\n[20:37:27 11/06/2025] --> Finding the BCCs...\n[20:37:27 11/06/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[20:37:27 11/06/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[20:37:30 11/06/2025] --> Done!\nElapsed time: 2.6 seconds\n\n[20:37:30 11/06/2025] --> 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[20:37:30 11/06/2025] --> Sampling bubbles by type...\n[20:37:30 11/06/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[20:37:30 11/06/2025] --> Removing low-complexity/redundant bubbles...\n[20:37:30 11/06/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[20:37:30 11/06/2025] --> Computing read coherence and coverage...\n[20:37:30 11/06/2025] --> Done!\n[20:37:30 11/06/2025] --> Sorting all bubbles...\n[20:37:30 11/06/2025] --> Done!\nElapsed time: 0.7 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_815598**********\n' +5: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/reproducible-path/kissplice-2.6.2/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-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_999609\n\n\nElapsed time: 0.0 seconds\n\n[16:18:03 10/05/2024] --> Finding the BCCs...\n[16:18:03 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[16:18:03 10/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[16:18:07 10/05/2024] --> Done!\nElapsed time: 4.1 seconds\n\n[16:18:07 10/05/2024] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[16:18:07 10/05/2024] --> Sampling bubbles by type...\n[16:18:07 10/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[16:18:07 10/05/2024] --> Removing low-complexity/redundant bubbles...\n[16:18:07 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[16:18:07 10/05/2024] --> Computing read coherence and coverage...\n[16:18:07 10/05/2024] --> Done!\n[16:18:07 10/05/2024] --> Sorting all bubbles...\n[16:18:07 10/05/2024] --> Done!\nElapsed time: 0.5 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-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_999609**********\n' 5: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 3.57 sec -8/9 Test #3: KisspliceDBGTest ................. Passed 8.76 sec +7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 4.99 sec +8/9 Test #3: KisspliceDBGTest ................. Passed 11.51 sec 4: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta -C 0 -4: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_704594\n\n\n[20:37:27 11/06/2025] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[20:37:33 11/06/2025] --> Done!\nElapsed time: 5.6 seconds\nElapsed time: 0.0 seconds\n\n[20:37:33 11/06/2025] --> Finding the BCCs...\n[20:37:33 11/06/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[20:37:33 11/06/2025] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[20:37:35 11/06/2025] --> Done!\nElapsed time: 2.8 seconds\n\n[20:37:35 11/06/2025] --> 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[20:37:35 11/06/2025] --> Sampling bubbles by type...\n[20:37:35 11/06/2025] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[20:37:35 11/06/2025] --> Removing low-complexity/redundant bubbles...\n[20:37:36 11/06/2025] --> Done!\nElapsed time: 0.0 seconds\n\n[20:37:36 11/06/2025] --> Computing read coherence and coverage...\n[20:37:36 11/06/2025] --> Done!\n[20:37:36 11/06/2025] --> Sorting all bubbles...\n[20:37:36 11/06/2025] --> 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-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-06-11_20-37-27_704594**********\n' +4: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta /build/reproducible-path/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_428844\n\n\n[16:18:03 10/05/2024] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[16:18:11 10/05/2024] --> Done!\nElapsed time: 8.4 seconds\nElapsed time: 0.0 seconds\n\n[16:18:11 10/05/2024] --> Finding the BCCs...\n[16:18:11 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[16:18:11 10/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[16:18:15 10/05/2024] --> Done!\nElapsed time: 4.4 seconds\n\n[16:18:15 10/05/2024] --> Starting Bubble Output Module\nBefore checking for read coherency, all bubbles will be written to folder results/results_without_read_coherency\nThis enables you to access them even before the read coherency module finishes, which can take a long time\n[16:18:15 10/05/2024] --> Sampling bubbles by type...\n[16:18:15 10/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[16:18:15 10/05/2024] --> Removing low-complexity/redundant bubbles...\n[16:18:16 10/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[16:18:16 10/05/2024] --> Computing read coherence and coverage...\n[16:18:17 10/05/2024] --> Done!\n[16:18:17 10/05/2024] --> Sorting all bubbles...\n[16:18:17 10/05/2024] --> Done!\nElapsed time: 1.2 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-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-10_16-18-03_428844**********\n' 4: kisspliceTwoSequencesTest.py: test SUCCESSFUL -9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 9.52 sec +9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 14.50 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 9.58 sec +Total Test time (real) = 14.54 sec make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -3037,12 +3073,14 @@ 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/2560013/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2560013/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/1235563 and its subdirectories -I: Current time: Wed Jun 11 20:37:46 -12 2025 -I: pbuilder-time-stamp: 1749717466 +I: removing directory /srv/workspace/pbuilder/2560013 and its subdirectories +I: Current time: Fri May 10 16:18:31 +14 2024 +I: pbuilder-time-stamp: 1715307511