Diff of the two buildlogs: -- --- b1/build.log 2023-04-11 18:15:09.447967534 +0000 +++ b2/build.log 2023-04-11 18:20:42.120834085 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 13 12:33:54 -12 2024 -I: pbuilder-time-stamp: 1715646834 +I: Current time: Wed Apr 12 08:15:14 +14 2023 +I: pbuilder-time-stamp: 1681236914 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./kissplice_2.6.2.orig.tar.gz] I: copying [./kissplice_2.6.2-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Jan 20 07:11:29 2023 -12 +gpgv: Signature made Sat Jan 21 09:11:29 2023 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kissplice_2.6.2-2.dsc: no acceptable signature found @@ -27,11 +27,20 @@ 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/3569/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8864/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/8864/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8864/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -41,38 +50,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='3569' + PPID='8864' PS1='# ' PS2='> ' 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.CnRzFl8S/pbuilderrc_ydR0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CnRzFl8S/b1 --logfile b1/build.log kissplice_2.6.2-2.dsc' + 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.CnRzFl8S/pbuilderrc_uRXd --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CnRzFl8S/b2 --logfile b2/build.log --extrapackages usrmerge kissplice_2.6.2-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink15-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3569/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 11 00:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/8864/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -243,7 +252,7 @@ Get: 119 http://deb.debian.org/debian bookworm/main arm64 texlive-base all 2022.20230122-2 [21.9 MB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-base all 2022.20230122-2 [1181 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-recommended all 2022.20230122-2 [8880 kB] -Fetched 101 MB in 3s (30.5 MB/s) +Fetched 101 MB in 2s (46.7 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 ... 19616 files and directories currently installed.) @@ -762,8 +771,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_2.6.2-2_source.changes +I: user script /srv/workspace/pbuilder/8864/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/8864/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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_2.6.2-2_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.2-2 dpkg-buildpackage: info: source distribution unstable @@ -817,18 +835,18 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake --color= +make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/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]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend @@ -838,48 +856,48 @@ make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake --color= make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-2.6.2 /build/kissplice-2.6.2/doc /build/kissplice-2.6.2/obj-aarch64-linux-gnu /build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake --color= -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build +make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build make[3]: Entering directory '/build/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 make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/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 -[ 1%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 1%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o make[3]: Leaving directory '/build/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]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp -make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build -make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -[ 5%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/kissplice-2.6.2/modules/CleanDuplicates.cpp -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp -[ 6%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 3%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/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 make[3]: Entering directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/ErrorRemoval.cpp +[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp +[ 6%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +[ 8%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/run.cpp -[ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/PrintBcc.cpp +[ 10%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/BubbleEnumeration.cpp -[ 10%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -[ 12%] Generating user_guide.pdf -[ 13%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp +[ 13%] Generating user_guide.pdf cd /build/kissplice-2.6.2/doc && /build/kissplice-2.6.2/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/ErrorRemoval.cpp -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/PrintBcc.cpp /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. @@ -1022,11 +1040,7 @@ LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 275. -[5 <./MBTD1_C0.png>] [6 <./quantifModel.png[ 15%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp -[ 17%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp ->] +[5 <./MBTD1_C0.png>] [6 <./quantifModel.png>] Overfull \hbox (1.2115pt too wide) in paragraph at lines 329--330 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes \T1/cmr/m/n/12 for the nodes @@ -1074,6 +1088,10 @@ [10] (/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 +[ 15%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp +[ 17%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1096,11 +1114,7 @@ [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]/build/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/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; ii + +kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 +[ 18%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp -mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 +[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp +mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1200.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf @@ -1183,7 +1259,9 @@ [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] + Ok [224][ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp + [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf @@ -1191,15 +1269,16 @@ [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161]In file included from /build/kissplice-2.6.2/modules/BubbleEnumeration.cpp:61: + Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] +[171]In file included from /build/kissplice-2.6.2/modules/BubbleEnumeration.cpp:61: /build/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/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 ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [162] [163] [164]/build/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] +/build/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/kissplice-2.6.2/modules/BubbleEnumeration.cpp:60: + [172] [173]In file included from /build/kissplice-2.6.2/modules/BubbleEnumeration.cpp:60: /build/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': /build/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); @@ -1217,7 +1296,7 @@ /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [165] [166] [167]/build/kissplice-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': + [174] [175] [176] [177]/build/kissplice-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1230,15 +1309,12 @@ /build/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/kissplice-2.6.2/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': + [178] [179] [180]/build/kissplice-2.6.2/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [168] [169] [170] -[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] -[183] [184][ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp - [185] [186] [187] [188]) + [181] [182] +[183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) @@ -1262,25 +1338,41 @@ [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) -Font metrics written on ecbx1200.tfm. -Output written on ecbx1200.600gf (256 characters, 59220 bytes). -Transcript written on ecbx1200.log. -mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. - - -kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 +Font metrics written on ectt1440.tfm. +Output written on ectt1440.600gf (256 characters, 61024 bytes). +Transcript written on ectt1440.log. +mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. + +kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 [ 24%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp -[ 25%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o +[ 25%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp +[ 27%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CycleCompression.cpp -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': +mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 +This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) + +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf + Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf + Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] +[204] [205] [206] [207] [208] [209] [210]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': /build/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/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': + [211] [212] [213] [214] [215] +[216] [217] [218] [219] [220] [221] [222] [223]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf + Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] +[236] [237] [238] [239]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1290,7 +1382,7 @@ /build/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/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': + [240] [241] [242] [243] [244] [245] [246] [247]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1300,8 +1392,8 @@ /build/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); | ^~~~~~~~~~~~~~~ -[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': + +[248] [249]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1321,8 +1413,7 @@ /build/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); | ^~~~~~~~~~~~~~~ -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': + [250] [251] [252/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ @@ -1372,34 +1463,17 @@ /build/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]); | ^~~~~~~ -mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 -This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) - -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf - Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217] [218] [219] [220] [221] [222] [223]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] -[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] -[248] [249] [250] [251] [252] [253]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': +] [253] [254] [255]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf + Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] +[140] [141]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': /build/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); | ^ - [254] [255]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf - Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] + [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf - Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': + Ok [158] [160] [161] [162] [163] [164]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1409,7 +1483,7 @@ /build/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)); | ^~~~~~~~~~~~~~~ - [175] [176] [177] [178] [179] [180] [181] [182]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': + [165] [166] [167]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1419,9 +1493,7 @@ /build/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); | ^~~~~~~~~~~~~~~ - -[183] [184] [185] [186] [187] [188]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': + [168] [169]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1431,8 +1503,7 @@ /build/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); | ^~~~~~~~~~~~~~~ - - Ok [94] [126] [23] [40] [41] [60] [124] [62]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1442,10 +1513,8 @@ /build/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); | ^~~~~~~~~~~~~~~ - [91] [93] [92] [123] [125] -[95] [127] [32]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf - Ok [14]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': + [170] +[171] [172]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ @@ -1482,7 +1551,7 @@ /build/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 */ | ^~~~~~~ - [15]/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': /build/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1495,69 +1564,7 @@ /build/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]); | ^~~~~~~ - [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] -[59] [61] [96] [189] [17] [45] [16] [21] [22]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf - Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf - Ok [24] [34] [35] [36] [37] [64] [191] [159]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28] [27] [29] [30] [31]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf - Ok [38] [63] [190]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf - Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] -[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf - Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] -[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] -[121] [122]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf - Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf - Ok) ) ) ) -Font metrics written on ectt1440.tfm. -Output written on ectt1440.600gf (256 characters, 61024 bytes). -Transcript written on ectt1440.log. -[ 29%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp -mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. - -kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 -[ 31%] Linking CXX executable ../lib/kissplice/ks_print_bcc -cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 31%] Built target ks_print_bcc -[ 32%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp -[ 34%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp -This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) - -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf - Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf - Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217] [218] [219] [220] [221] [222] [223]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf - Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] -[236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] -[248] [249] [250] [251] [252] [253] [254] [255]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf - Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] -[152] [153] [154] [155] [156] [157]) -(/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] + [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] @@ -1587,15 +1594,16 @@ Font metrics written on ectt1095.tfm. Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. -[ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1095.600pk: successfully generated. -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 -[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp +[ 29%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp +[ 31%] Linking CXX executable ../lib/kissplice/ks_print_bcc +cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1606,17 +1614,19 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' + [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217] [218] [219] [220] [221] [222] [223]) +[216] [217][ 31%] Built target ks_print_bcc + [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] + Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235][ 32%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o + +[236]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp + [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf - Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138][ 39%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o - [139]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp - + Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf @@ -1627,18 +1637,10 @@ Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf - Ok [14] [15]/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': -/build/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] + Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf - Ok [0] [1] [2] [3] [4]/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': -/build/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [5] [6] [7] [8] [9] [10] [11] [12]) + Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf @@ -1650,7 +1652,9 @@ [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] +[109] [110] [111] [112] [113] [114] [115] [116] [117][ 34%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o + [118] [119] [120]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp + [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) @@ -1665,21 +1669,6 @@ /_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1440.600pk > kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 -[ 41%] Linking CXX executable ../lib/kissplice/ks_error_removal -cd /build/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 -/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': -/build/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': -/build/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 41%] Built target ks_error_removal -[ 43%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1704,7 +1693,9 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] -[152] [153] [154] [155] [156] [157]) +[152][ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o + [153] [154]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp + [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) @@ -1721,39 +1712,7 @@ Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] -[79] [80] [81]/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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/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/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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [82]/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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 ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [83/build/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/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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [84] [85] [86] [87] [88] [89] [90]) +[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] @@ -1766,16 +1725,12 @@ Font metrics written on ecti1200.tfm. Output written on ecti1200.600gf (256 characters, 63048 bytes). Transcript written on ecti1200.log. -[ 44%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CycleCompression.cpp mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 -[ 46%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/SplitBcc.cpp -[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp +[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1795,15 +1750,11 @@ [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149][ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o - [150] [151]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp - +[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174][ 51%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o - [175]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp - [176] [177] [178] [179] [180] [181] [182] +[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] @@ -1823,9 +1774,7 @@ 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][ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp - + Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf @@ -1835,17 +1784,36 @@ Font metrics written on ectt1200.tfm. Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. +[ 39%] Linking CXX executable ../lib/kissplice/ks_error_removal +cd /build/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 +[ 41%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 -[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp -[ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp -[ 58%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': +/build/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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': +/build/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++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 41%] Built target ks_error_removal +[ 43%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp +/build/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': +/build/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/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': +/build/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++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1856,38 +1824,8 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199]/build/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': -/build/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++; - | ~^~~~~~~~~~~ - [200]/build/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': -/build/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/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/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/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] - 156 | char validSeed; - | ^~~~~~~~~ - [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] +[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] @@ -1934,46 +1872,12 @@ d/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1728.600p k> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 -[ 60%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CycleCompression.cpp -/build/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': -/build/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/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': -/build/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/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/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; - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp -/build/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] - 156 | char validSeed; - | ^~~~~~~~~ -[ 63%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp +[ 44%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/SplitBcc.cpp +[ 46%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CycleCompression.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) -[ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) @@ -2026,18 +1930,48 @@ Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. -[ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 -[ 68%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp -[ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp +/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) +[ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) @@ -2095,8 +2029,16 @@ /debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfou r/jknappen/ec/ecbx1728.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1440 -[ 72%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp +[ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o +[ 51%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp +[ 55%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp +[ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp +[ 58%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -2108,41 +2050,7 @@ Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] -[204][ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o - [205] [206] [207]/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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/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 ); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_info.cpp -/build/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/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/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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/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/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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [208] [209] [210] [211] [212] [213] [214] [215] +[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] @@ -2167,32 +2075,15 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28] [27] [29]/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp: In function 'int main(int, char**)': -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:702:9: warning: 'strandTheLeftReadsMapsTo' may be used uninitialized [-Wmaybe-uninitialized] - 702 | if (strandTheLeftReadsMapsTo=='-') { - | ^~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:695:14: note: 'strandTheLeftReadsMapsTo' was declared here - 695 | char strandTheLeftReadsMapsTo; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:526:50: warning: 'strandRelativeThreshold' may be used uninitialized [-Wmaybe-uninitialized] - 526 | (((double)(largestValue)/total) >= strandRelativeThreshold); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:182:9: note: 'strandRelativeThreshold' was declared here - 182 | float strandRelativeThreshold; - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: 'strandAbsoluteThreshold' may be used uninitialized [-Wmaybe-uninitialized] - 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) - | ^~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:181:7: note: 'strandAbsoluteThreshold' was declared here - 181 | int strandAbsoluteThreshold; - | ^~~~~~~~~~~~~~~~~~~~~~~ - [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] [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 +[79] [80] [81] [82] [83] [84] [85] [86] [87][ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o + [88] [89] [90]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mfcd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp + Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) @@ -2209,25 +2100,68 @@ ed/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1440.600 pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm2074 -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp: In function 'int main(int, char**)': -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:702:9: warning: 'strandTheLeftReadsMapsTo' may be used uninitialized [-Wmaybe-uninitialized] - 702 | if (strandTheLeftReadsMapsTo=='-') { - | ^~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:695:14: note: 'strandTheLeftReadsMapsTo' was declared here - 695 | char strandTheLeftReadsMapsTo; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:526:50: warning: 'strandRelativeThreshold' may be used uninitialized [-Wmaybe-uninitialized] - 526 | (((double)(largestValue)/total) >= strandRelativeThreshold); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:182:9: note: 'strandRelativeThreshold' was declared here - 182 | float strandRelativeThreshold; - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: 'strandAbsoluteThreshold' may be used uninitialized [-Wmaybe-uninitialized] - 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) - | ^~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:181:7: note: 'strandAbsoluteThreshold' was declared here - 181 | int strandAbsoluteThreshold; - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 62%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp +/build/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': +/build/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/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': +/build/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/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/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/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] + 156 | char validSeed; + | ^~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': +/build/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/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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': +/build/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/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/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/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/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 ecrm2074 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -2258,48 +2192,12 @@ [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] -[59] [61] [96] [189] [17] [45] [16] [21][ 75%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o - [22]) +[59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf - Ok [0] [1] [2] [3] [4]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/Utils.cpp - [5] [6] [7] [8] [9] [10] [11] [12]) + Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf - Ok [24] [34]/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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/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/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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [35]/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': -/build/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/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/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/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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - [36] [37][ 77%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o - [64] [191] [159]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mfcd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp - + Ok [24] [34] [35] [36] [37] [64] [191] [159]) +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) @@ -2322,10 +2220,8 @@ kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt2074 -[ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp -[ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_info.cpp +[ 63%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt2074 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -2339,10 +2235,8 @@ 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[ 82%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o - - Ok [224]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp - [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf + Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf @@ -2351,7 +2245,9 @@ [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] +[171] [172] [173][ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o + [174]cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp + [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] @@ -2371,7 +2267,9 @@ 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] + Ok [97] [98] [99] [100][ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp + [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf @@ -2396,29 +2294,24 @@ /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc /build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. -[ 84%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice -cd /build/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 entering extended mode (/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.tex LaTeX2e <2022-11-01> patch level 1 -L3 programming layer <2023-01-16>[ 86%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp - +L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) -(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -) +(/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/base/latin1.def))[ 68%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o + (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty -(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) +(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp + (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty -(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)[ 87%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/Utils.cpp - +(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) @@ -2430,7 +2323,9 @@ (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) -(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty +(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty[ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp + (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) @@ -2446,10 +2341,8 @@ (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) -(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' - -(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)[ 87%] Built target ks_kissreadsSplice - +(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) +(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (/build/kissplice-2.6.2/obj-aarch64-linux-gnu/doc/user_guide.aux) *geometry* driver: auto-detecting *geometry* detected driver: pdftex @@ -2488,9 +2381,7 @@ (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty -(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)[ 89%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -)cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp - +(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) @@ -2528,9 +2419,9 @@ LaTeX Warning: `!h' float specifier changed to `!ht'. -[4 <./MBTD1_C2.png[ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp ->] [5 <./MBTD1_C0.png>] [6 <./quantifModel.png>] +[4 <./MBTD1_C2.png>] [5 <./MBTD1_C0.png>] [6 <./quantifModel.png>][ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/fragment_info.cpp + Overfull \hbox (1.2115pt too wide) in paragraph at lines 329--330 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes \T1/cmr/m/n/12 for the nodes @@ -2596,10 +2487,8 @@ /debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfou r/jknappen/ec/ecbx1728.600pk> = strandRelativeThreshold); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:182:9: note: 'strandRelativeThreshold' was declared here + 182 | float strandRelativeThreshold; + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: 'strandAbsoluteThreshold' may be used uninitialized [-Wmaybe-uninitialized] + 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) + | ^~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:181:7: note: 'strandAbsoluteThreshold' was declared here + 181 | int strandAbsoluteThreshold; + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CycleCompression.cpp +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp: In function 'int main(int, char**)': +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:702:9: warning: 'strandTheLeftReadsMapsTo' may be used uninitialized [-Wmaybe-uninitialized] + 702 | if (strandTheLeftReadsMapsTo=='-') { + | ^~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:695:14: note: 'strandTheLeftReadsMapsTo' was declared here + 695 | char strandTheLeftReadsMapsTo; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:526:50: warning: 'strandRelativeThreshold' may be used uninitialized [-Wmaybe-uninitialized] + 526 | (((double)(largestValue)/total) >= strandRelativeThreshold); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:182:9: note: 'strandRelativeThreshold' was declared here + 182 | float strandRelativeThreshold; + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: 'strandAbsoluteThreshold' may be used uninitialized [-Wmaybe-uninitialized] + 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) + | ^~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:181:7: note: 'strandAbsoluteThreshold' was declared here + 181 | int strandAbsoluteThreshold; + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/NGraph.cpp +[ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -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/kissplice-2.6.2/thirdparty/kissreads/src/Utils.cpp +[ 82%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice +cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' +[ 82%] Built target ks_kissreadsSplice +[ 84%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp +[ 86%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp +[ 87%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp +[ 89%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/CGraph.cpp +[ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/LabelledCEdge.cpp +[ 93%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[3]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 96%] Built target ks_run_modules +[ 93%] Built target ks_kissreadsSNPS +[ 94%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-aarch64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -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/kissplice-2.6.2/modules/Utils.cpp +/build/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': +/build/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/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/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/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/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_run_modules +cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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/kissplice-2.6.2/obj-aarch64-linux-gnu' -[ 96%] Built target ks_kissreadsSNPS +[ 96%] Built target ks_run_modules [ 98%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates cd /build/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/kissplice-2.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -2753,7 +2771,7 @@ 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 0.10 sec +1/9 Test #1: IsBcalmStartable ................. Passed 0.16 sec test 9 Start 9: ksErrorRemovalTest @@ -2763,6 +2781,14 @@ 7: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_bubble_enumeration /build/kissplice-2.6.2/tests/functional_tests/data/graph_info_bcc /build/kissplice-2.6.2/tests/functional_tests/data/graph_contents_edges_bcc /build/kissplice-2.6.2/tests/functional_tests/data/graph_contents_nodes_bcc /build/kissplice-2.6.2/tests/functional_tests/data/graph_all_edges_bcc /build/kissplice-2.6.2/tests/functional_tests/data/graph_all_nodes_bcc 2 25 /build/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 +8: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_run_modules /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes 25 /build/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 +2/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.63 sec +9: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_error_removal /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance 0.02/build/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 +3/9 Test #8: ksRunModulesTest ................. Passed 0.69 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] @@ -2888,33 +2914,25 @@ 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). -9: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_error_removal /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance 0.02/build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/lib/kissplice/ks_run_modules /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges /build/kissplice-2.6.2/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes 25 /build/kissplice-2.6.2/tests/functional_tests/data/test_ks_run_modules_output_graph -2/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.35 sec -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 -3/9 Test #9: ksErrorRemovalTest ............... Passed 0.37 sec -4/9 Test #2: KisspliceBasicTest ............... Passed 0.50 sec -5/9 Test #8: ksRunModulesTest ................. Passed 0.43 sec +4/9 Test #9: ksErrorRemovalTest ............... Passed 0.69 sec +5/9 Test #2: KisspliceBasicTest ............... Passed 0.88 sec 6: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-29_806223\n\n\nElapsed time: 0.0 seconds\n\n[12:37:29 13/05/2024] --> Finding the BCCs...\n[12:37:30 13/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[12:37:30 13/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[12:37:33 13/05/2024] --> Done!\nElapsed time: 3.6 seconds\n\n[12:37:33 13/05/2024] --> Starting Bubble Output Module\n[12:37:33 13/05/2024] --> Sampling bubbles by type...\n[12:37:33 13/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[12:37:33 13/05/2024] --> Removing low-complexity/redundant bubbles...\n[12:37:33 13/05/2024] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-29_806223**********\n' +6: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_790845\n\n\nElapsed time: 0.0 seconds\n\n[08:19:55 12/04/2023] --> Finding the BCCs...\n[08:19:56 12/04/2023] --> Done!\nElapsed time: 0.3 seconds\n\n[08:19:56 12/04/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[08:19:59 12/04/2023] --> Done!\nElapsed time: 3.7 seconds\n\n[08:19:59 12/04/2023] --> Starting Bubble Output Module\n[08:19:59 12/04/2023] --> Sampling bubbles by type...\n[08:19:59 12/04/2023] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[08:19:59 12/04/2023] --> Removing low-complexity/redundant bubbles...\n[08:19:59 12/04/2023] --> Done!\nElapsed time: 0.0 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_790845**********\n' 6: kisspliceGraphTest.py: test SUCCESSFUL -6/9 Test #6: KisspliceGraphTest ............... Passed 4.45 sec +6/9 Test #6: KisspliceGraphTest ............... Passed 5.08 sec 5: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/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/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-29_513804\n\n\nElapsed time: 0.0 seconds\n\n[12:37:29 13/05/2024] --> Finding the BCCs...\n[12:37:30 13/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[12:37:30 13/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[12:37:33 13/05/2024] --> Done!\nElapsed time: 3.5 seconds\n\n[12:37:33 13/05/2024] --> 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[12:37:33 13/05/2024] --> Sampling bubbles by type...\n[12:37:33 13/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[12:37:33 13/05/2024] --> Removing low-complexity/redundant bubbles...\n[12:37:33 13/05/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[12:37:34 13/05/2024] --> Computing read coherence and coverage...\n[12:37:34 13/05/2024] --> Done!\n[12:37:34 13/05/2024] --> Sorting all bubbles...\n[12:37:34 13/05/2024] --> Done!\nElapsed time: 1.0 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-29_513804**********\n' +5: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g /build/kissplice-2.6.2/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 -r /build/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/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta\nResults will be stored in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_846938\n\n\nElapsed time: 0.0 seconds\n\n[08:19:55 12/04/2023] --> Finding the BCCs...\n[08:19:56 12/04/2023] --> Done!\nElapsed time: 0.2 seconds\n\n[08:19:56 12/04/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[08:20:00 12/04/2023] --> Done!\nElapsed time: 3.9 seconds\n\n[08:20:00 12/04/2023] --> 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[08:20:00 12/04/2023] --> Sampling bubbles by type...\n[08:20:00 12/04/2023] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[08:20:00 12/04/2023] --> Removing low-complexity/redundant bubbles...\n[08:20:00 12/04/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[08:20:00 12/04/2023] --> Computing read coherence and coverage...\n[08:20:01 12/04/2023] --> Done!\n[08:20:01 12/04/2023] --> Sorting all bubbles...\n[08:20:01 12/04/2023] --> Done!\nElapsed time: 1.7 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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_846938**********\n' 5: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 5.33 sec -8/9 Test #3: KisspliceDBGTest ................. Passed 15.27 sec +7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 6.98 sec +8/9 Test #3: KisspliceDBGTest ................. Passed 21.42 sec 4: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/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/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta /build/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-30_596057\n\n\n[12:37:30 13/05/2024] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[12:37:41 13/05/2024] --> Done!\nElapsed time: 11.6 seconds\nElapsed time: 0.0 seconds\n\n[12:37:41 13/05/2024] --> Finding the BCCs...\n[12:37:41 13/05/2024] --> Done!\nElapsed time: 0.1 seconds\n\n[12:37:41 13/05/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[12:37:44 13/05/2024] --> Done!\nElapsed time: 2.5 seconds\n\n[12:37:44 13/05/2024] --> 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[12:37:44 13/05/2024] --> Sampling bubbles by type...\n[12:37:44 13/05/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[12:37:44 13/05/2024] --> Removing low-complexity/redundant bubbles...\n[12:37:44 13/05/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[12:37:45 13/05/2024] --> Computing read coherence and coverage...\n[12:37:46 13/05/2024] --> Done!\n[12:37:46 13/05/2024] --> Sorting all bubbles...\n[12:37:46 13/05/2024] --> Done!\nElapsed time: 2.1 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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-05-13_12-37-30_596057**********\n' +4: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r /build/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta -r /build/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta -C 0\nUsing the read files: /build/kissplice-2.6.2/tests/integration_tests/data/HBM75brain_100000.fasta /build/kissplice-2.6.2/tests/integration_tests/data/HBM75liver_100000.fasta\nResults will be stored in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_181465\n\n\n[08:19:55 12/04/2023] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[08:20:12 12/04/2023] --> Done!\nElapsed time: 16.8 seconds\nElapsed time: 0.0 seconds\n\n[08:20:12 12/04/2023] --> Finding the BCCs...\n[08:20:12 12/04/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[08:20:12 12/04/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[08:20:15 12/04/2023] --> Done!\nElapsed time: 2.6 seconds\n\n[08:20:15 12/04/2023] --> 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[08:20:15 12/04/2023] --> Sampling bubbles by type...\n[08:20:15 12/04/2023] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[08:20:15 12/04/2023] --> Removing low-complexity/redundant bubbles...\n[08:20:15 12/04/2023] --> Done!\nElapsed time: 0.0 seconds\n\n[08:20:16 12/04/2023] --> Computing read coherence and coverage...\n[08:20:17 12/04/2023] --> Done!\n[08:20:17 12/04/2023] --> Sorting all bubbles...\n[08:20:17 12/04/2023] --> Done!\nElapsed time: 2.2 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/kissplice-2.6.2/obj-aarch64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-04-12_08-19-55_181465**********\n' 4: kisspliceTwoSequencesTest.py: test SUCCESSFUL -9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 16.86 sec +9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 22.75 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 16.89 sec +Total Test time (real) = 22.77 sec make[1]: Leaving directory '/build/kissplice-2.6.2/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -2971,8 +2989,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'kissplice' in '../kissplice_2.6.2-2_arm64.deb'. dpkg-deb: building package 'kissplice-dbgsym' in '../kissplice-dbgsym_2.6.2-2_arm64.deb'. +dpkg-deb: building package 'kissplice' in '../kissplice_2.6.2-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kissplice_2.6.2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../kissplice_2.6.2-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2980,12 +2998,14 @@ 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/8864/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8864/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/3569 and its subdirectories -I: Current time: Mon May 13 12:38:07 -12 2024 -I: pbuilder-time-stamp: 1715647087 +I: removing directory /srv/workspace/pbuilder/8864 and its subdirectories +I: Current time: Wed Apr 12 08:20:40 +14 2023 +I: pbuilder-time-stamp: 1681237240