Diff of the two buildlogs: -- --- b1/build.log 2023-05-13 02:06:18.242445496 +0000 +++ b2/build.log 2023-05-13 02:08:19.609127375 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 12 13:59:41 -12 2023 -I: pbuilder-time-stamp: 1683943181 +I: Current time: Fri Jun 14 22:29:23 +14 2024 +I: pbuilder-time-stamp: 1718353763 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 @@ -27,135 +27,167 @@ 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/1580822/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1918556/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 14 22:29 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1918556/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1918556/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' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='303d9f0790c042f48279894baae53442' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1580822' - PS1='# ' - PS2='> ' + INVOCATION_ID=a1d43b6ff35342f7bd056dde7f05e3cf + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1918556 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.nRkxX7f2/pbuilderrc_OhE5 --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.nRkxX7f2/b1 --logfile b1/build.log kissplice_2.6.2-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nRkxX7f2/pbuilderrc_fxWs --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.nRkxX7f2/b2 --logfile b2/build.log --extrapackages usrmerge kissplice_2.6.2-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1580822/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 14 22:29 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1918556/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -327,7 +359,7 @@ Get: 120 http://deb.debian.org/debian bookworm/main amd64 texlive-base all 2022.20230122-3 [21.9 MB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] -Fetched 108 MB in 3s (33.4 MB/s) +Fetched 108 MB in 1s (97.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -850,8 +882,19 @@ 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/1918556/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1918556/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 @@ -898,108 +941,100 @@ -- Build files have been written to: /build/kissplice-2.6.2/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/kissplice-2.6.2' dh_auto_build - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-2.6.2 -B/build/kissplice-2.6.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.6.2/obj-x86_64-linux-gnu/CMakeFiles /build/kissplice-2.6.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend -make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend +make -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 -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend +make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend +make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= +make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/kissplice-2.6.2/obj-x86_64-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 make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake --color= -make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake --color= -make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build -make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu /build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc /build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build +make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build +make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' +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-x86_64-linux-gnu' -[ 1%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -[ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o +make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +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-x86_64-linux-gnu' -cd /build/kissplice-2.6.2/obj-x86_64-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 make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build -cd /build/kissplice-2.6.2/obj-x86_64-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 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'/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 1%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o +[ 5%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o +[ 5%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o +[ 6%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o +[ 10%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o +[ 10%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o +[ 12%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o +[ 13%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o +[ 15%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o +[ 17%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 18%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o cd /build/kissplice-2.6.2/obj-x86_64-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 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thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 12%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -[ 13%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -[ 15%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -[ 17%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 20%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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=. 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CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/kissplice-2.6.2/modules/CycleCompression.cpp -[ 18%] Generating user_guide.pdf +cd /build/kissplice-2.6.2/obj-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o +[ 22%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 24%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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 +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 25%] 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-x86_64-linux-gnu/doc /build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex -[ 24%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -[ 25%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o +[ 27%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc /build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex -cd /build/kissplice-2.6.2/obj-x86_64-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 -cd /build/kissplice-2.6.2/obj-x86_64-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 This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. /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); | ^ -entering extended mode -(/build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex -LaTeX2e <2022-11-01> patch level 1 -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/share/texlive/texmf-dist/tex/latex/base/inputenc.sty -(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) -(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty/build/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: 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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1009,10 +1044,7 @@ /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)); | ^~~~~~~~~~~~~~~ - -(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) -(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty -(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))/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: 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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1032,7 +1064,7 @@ /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); | ^~~~~~~~~~~~~~~ -)/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1073,8 +1105,7 @@ /build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - -(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty/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] +/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)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' @@ -1093,7 +1124,21 @@ /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]); | ^~~~~~~ - +entering extended mode +(/build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex +LaTeX2e <2022-11-01> patch level 1 +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/share/texlive/texmf-dist/tex/latex/base/inputenc.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) +(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty +(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) +(/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty +(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) +(/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) @@ -1162,9 +1207,7 @@ (/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 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-1216,116 +1259,30 @@ LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 212 . -[4 <./MBTD1_C2.png[ 29%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -/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; iiw)-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++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 275. + +[5 <./MBTD1_C0.png[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 32%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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/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] - -LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 275. - -[5 <./MBTD1_C0.png/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)': -/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/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*)': -/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro 'LOAD_AND_RETURN' - 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); - | ^~~~~~~~~~~~~~~ -/build/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro 'LOAD_AND_RETURN' - 1142 | LOAD_AND_RETURN(ht, retval); - | ^~~~~~~~~~~~~~~ -/build/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' - 220 | READ_UL((ht)->fpData, cchData); \ - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' - 1154 | LOAD_AND_RETURN(ht, retval); - | ^~~~~~~~~~~~~~~ -/build/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' - 1272 | READ_UL(fp, ht->cchKey); - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' - 1273 | READ_UL(fp, ht->cItems); - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' - 1274 | READ_UL(fp, ht->cDeletedItems); - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' - 1277 | READ_UL(fp, cchKey); - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1279 | fread(rgchKeys, 1, cchKey, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' - 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ - | ^~~~~~~ -/build/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)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' - 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ - | ^~~~~~~ -/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/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]); - | ^~~~~~~ ->] [6 <./quantifModel.png[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 +>] [6 <./quantifModel.png[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 >] Overfull \hbox (1.2115pt too wide) in paragraph at lines 329--330 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes @@ -1350,7 +1307,7 @@ Overfull \hbox (4.96884pt too wide) in paragraph at lines 345--346 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_3.fa\T1/cmr/m/n/12 : short -[7][ 32%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +[7][ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o Overfull \hbox (1.06976pt too wide) in paragraph at lines 346--347 []\T1/cmtt/m/n/12 results_NameReadFile1_..._NameReadFileN_kXX_type_4 .fa\T1/cmr @@ -1367,7 +1324,7 @@ Underfull \hbox (badness 4752) in paragraph at lines 353--354 []\T1/cmtt/m/n/12 KisSplice \T1/cmr/m/n/12 also cre-ates a sum-mary log file in the re-sults di-rec-tory named -[8]cd /build/kissplice-2.6.2/obj-x86_64-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 +[8]cd /build/kissplice-2.6.2/obj-x86_64-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 Underfull \hbox (badness 10000) in paragraph at lines 410--411 @@ -1376,26 +1333,78 @@ [10] (/build/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 -[ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 36%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -[ 41%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +/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='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; + | ^~~~~~~~~ +[ 41%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kissplice-2.6.2/modules/PrintBcc.cpp:51: /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 = Printer; TNodeFunctor = Printer]': /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] @@ -1435,18 +1444,6 @@ /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/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -/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++){ - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 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) @@ -1465,10 +1462,10 @@ [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] -[150] [151] [152] [153] [154][ 48%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o +[150] [151] [152] [153][ 43%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o + [154]cd /build/kissplice-2.6.2/obj-x86_64-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 [155] [156] [157] [158] [159] [160] [161] -[162] [163] [164] [165] [166] [167] [168] [169] [171] [172]cd /build/kissplice-2.6.2/obj-x86_64-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 - [173] [174] +[162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) @@ -1480,36 +1477,14 @@ Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. -/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; - | ^~~~~~~~~ +[ 44%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. @@ -1523,76 +1498,12 @@ bian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/j knappen/ec/tcrm1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 -[ 50%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o +[ 51%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 53%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 55%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o cd /build/kissplice-2.6.2/obj-x86_64-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 -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -/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; - | ^~~~~~~~~ -[ 55%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 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] @@ -1636,6 +1547,108 @@ /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 56%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 58%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 60%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 62%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +/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)': +/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/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*)': +/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro 'LOAD_AND_RETURN' + 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); + | ^~~~~~~~~~~~~~~ +/build/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro 'LOAD_AND_RETURN' + 1142 | LOAD_AND_RETURN(ht, retval); + | ^~~~~~~~~~~~~~~ +/build/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' + 220 | READ_UL((ht)->fpData, cchData); \ + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' + 1154 | LOAD_AND_RETURN(ht, retval); + | ^~~~~~~~~~~~~~~ +/build/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' + 1272 | READ_UL(fp, ht->cchKey); + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' + 1273 | READ_UL(fp, ht->cItems); + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' + 1274 | READ_UL(fp, ht->cDeletedItems); + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' + 1277 | READ_UL(fp, cchKey); + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1279 | fread(rgchKeys, 1, cchKey, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' + 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ + | ^~~~~~~ +/build/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)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' + 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ + | ^~~~~~~ +/build/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/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 ecbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1646,11 +1659,11 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192] [193] [194] [195] [196] [197] [198] [199] [200][ 56%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o - [201] [202]cd /build/kissplice-2.6.2/obj-x86_64-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 - [203] -[204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] -[216] [217] [218] [219] [220] [221] [222] [223]) + 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][ 63%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o + +[216]cd /build/kissplice-2.6.2/obj-x86_64-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 + [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] @@ -1678,9 +1691,7 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf - Ok [65] [66] [67][ 58%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o - [68] [69] [70] [71]cd /build/kissplice-2.6.2/obj-x86_64-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 - [72] [73] [74] [75] [76] [77] [78] + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] @@ -1693,25 +1704,18 @@ Font metrics written on ecbx1200.tfm. Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. -[ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 65%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 67%] Linking CXX executable ../lib/kissplice/ks_print_bcc +cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/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: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. +[ 68%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 -[ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -[ 63%] Linking CXX executable ../lib/kissplice/ks_print_bcc -cd /build/kissplice-2.6.2/obj-x86_64-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 -cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/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 -[ 65%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -[ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 68%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 /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=='-') { @@ -1731,11 +1735,18 @@ /build/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp:181:7: note: 'strandAbsoluteThreshold' was declared here 181 | int strandAbsoluteThreshold; | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 68%] Built target ks_print_bcc -[ 70%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 72%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 70%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 72%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 72%] Built target ks_print_bcc +[ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 75%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 77%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 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) @@ -1749,9 +1760,13 @@ 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] +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf[ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o + + Ok [224] [225]cd /build/kissplice-2.6.2/obj-x86_64-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 + [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] +[236] [237] [238] [239] [240] [241][ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o + [242]cd /build/kissplice-2.6.2/obj-x86_64-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 + [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] @@ -1759,78 +1774,163 @@ [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] -[171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] -[183] [184] [185] [186] [187] [188]) +[171] [172] [173] [174][ 82%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice + [175] [176]cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 + [177] [178] [179] [180] [181]/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++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [182] +[183] [184] [185] [186]/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++){ + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf - Ok [14] [15] [19] [20] [13] [18][ 74%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o - [33] [39] [42] [43] [44] [46] [47] [58] -[59cd /build/kissplice-2.6.2/obj-x86_64-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 -] [61] [96] [189] [17] [45] [16] [21] [22]) + Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] +[59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf - Ok [25] [26] [28] [27] [29] [30] [31]) + Ok [25] [26] [28]/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); } + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [27/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +] [29] [30][ 84%] Linking CXX executable ../lib/kissplice/ks_error_removal + [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] + Ok [65] [66] [67]cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 + [68] [69] [70] [71] [72] [73]/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/x86_64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic + [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[ 75%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -] [116] [117] [118] [119] [120] +[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120]/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 + [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf - Ok [48] [49] [50] [51] [52]cd /build/kissplice-2.6.2/obj-x86_64-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 + Ok [48] [49][ 86%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o + [50] [51] [52]cd /build/kissplice-2.6.2/obj-x86_64-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 [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. -[ 77%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 87%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. +cd /build/kissplice-2.6.2/obj-x86_64-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 kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 -[ 79%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS -cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 -/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; - | ^~~~~~~~~~~~~~~~~~~~~~~ -/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/x86_64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic -[ 81%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 82%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 84%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -[ 86%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -cd /build/kissplice-2.6.2/obj-x86_64-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 -mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 +/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 87%] Built target ks_error_removal +[ 89%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 89%] Built target ks_kissreadsSplice +/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; + | ^~~~~~~~~ +[ 91%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +[ 93%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o +cd /build/kissplice-2.6.2/obj-x86_64-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 +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 @@ -1840,23 +1940,13 @@ 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][ 86%] Built target ks_kissreadsSNPS - [197] [198] [199] [200][ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o - [201] [202] [203] -[204]cd /build/kissplice-2.6.2/obj-x86_64-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 - [205] [206] [207] [208] [209] [210] [211] [212] [213] [214][ 89%] Linking CXX executable ../lib/kissplice/ks_error_removal - [215] -[216] [217]cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_error_removal.dir/link.txt --verbose=1 - [218] [219][ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o - [220]cd /build/kissplice-2.6.2/obj-x86_64-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 - [221] [222] [223]) + 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]/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 - [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] -[248][ 93%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o - [249] [250]cd /build/kissplice-2.6.2/obj-x86_64-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 - [251] [252] [253] [254] [255]) +[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] @@ -1881,15 +1971,13 @@ 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]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' - [89] [90]) +[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf - Ok [48] [49] [50] [51] [52] [53] [54] [55][ 93%] Built target ks_error_removal - [56] [57]) + 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 ectt1095.tfm. @@ -1900,43 +1988,6 @@ ebian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/ jknappen/ec/ectt1095.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 -[ 94%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice -cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/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/x86_64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' -[ 94%] Built target ks_kissreadsSplice mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -1991,43 +2042,30 @@ Font metrics written on ecbx1440.tfm. Output written on ecbx1440.600gf (256 characters, 70764 bytes). Transcript written on ecbx1440.log. +/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; + | ^~~~~~~~~~~~~~~~~~~~~~~ mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 -/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) @@ -2069,13 +2107,16 @@ Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] -[79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) +[79] [80] [81] [82] [83] [84] [85] [86][ 94%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS + [87] [88]cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSNPS.dir/link.txt --verbose=1 + [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] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exidigit.mf - Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) + Ok [48] [49] [50] [51] [52] [53] [54] [55] [56]/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/x86_64-linux-gnu/libz.so -lm -lgomp -Wl,-Bstatic -lpthread -Wl,-Bdynamic + [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exiligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) @@ -2086,6 +2127,8 @@ kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 94%] Built target ks_kissreadsSNPS 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) @@ -2105,9 +2148,12 @@ [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] +[140] [141] [142] [143] [144] [145][ 96%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates + [146] [147]cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 + [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) -(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf +(/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf/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 + Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) @@ -2144,6 +2190,8 @@ debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour /jknappen/ec/ectt1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 +make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' +[ 96%] Built target ks_clean_duplicates mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -2202,9 +2250,6 @@ 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 -[ 96%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration -cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/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_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/kissplice/ks_bubble_enumeration 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) @@ -2235,8 +2280,7 @@ [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]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' - [16] [21] [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] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf @@ -2246,8 +2290,7 @@ (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf - Ok [65][ 96%] Built target ks_bubble_enumeration - [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] @@ -2334,10 +2377,7 @@ Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf - Ok [192[ 98%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates -cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 -] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202]/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 - [203] + Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf @@ -2361,20 +2401,20 @@ (/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]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' - [34] [35] [36] [37] [64] [191] [159]) + 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][ 98%] Built target ks_clean_duplicates - [74] [75] [76] [77] [78] + Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] -[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] -[121] [122]) +[109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120][ 98%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration + +[121] [122])cd /build/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 + (/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 @@ -2383,11 +2423,17 @@ Font metrics written on ecrm1440.tfm. Output written on ecrm1440.600gf (256 characters, 71064 bytes). Transcript written on ecrm1440.log. +/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_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/kissplice/ks_bubble_enumeration mktexpk: /build/kissplice-2.6.2/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm2074 +[100%] Linking CXX executable ../lib/kissplice/ks_run_modules +cd /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu' +[100%] Built target ks_bubble_enumeration 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) @@ -2404,10 +2450,12 @@ (/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]) +[248] [249] [250] [251] [252] [253]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' + [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] -[140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] +[140][100%] Built target ks_run_modules + [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] @@ -2446,9 +2494,6 @@ kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt2074 -[100%] Linking CXX executable ../lib/kissplice/ks_run_modules -cd /build/kissplice-2.6.2/obj-x86_64-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 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) @@ -2459,10 +2504,8 @@ 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]make[3]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' - [198] [199] [200] [201] [202] [203] -[204] [205] [206] [207] [208] [209] [210][100%] Built target ks_run_modules - [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] @@ -2724,10 +2767,10 @@ /usr/bin/cmake -E cmake_progress_start /build/kissplice-2.6.2/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[1]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j15 +/usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/kissplice-2.6.2/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/kissplice-2.6.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/kissplice-2.6.2/obj-x86_64-linux-gnu @@ -2847,7 +2890,18 @@ 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 0.17 sec +1/9 Test #1: IsBcalmStartable ................. Passed 0.03 sec +7: /build/kissplice-2.6.2/obj-x86_64-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 +2/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.06 sec +9: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-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 +3/9 Test #9: ksErrorRemovalTest ............... Passed 0.07 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] @@ -2973,41 +3027,30 @@ 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). -7: /build/kissplice-2.6.2/obj-x86_64-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 -2/9 Test #2: KisspliceBasicTest ............... Passed 0.29 sec -3/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.22 sec -9: /build/kissplice-2.6.2/obj-x86_64-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 -4/9 Test #9: ksErrorRemovalTest ............... Passed 0.28 sec -8: /build/kissplice-2.6.2/obj-x86_64-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 -5/9 Test #8: ksRunModulesTest ................. Passed 0.39 sec +4/9 Test #8: ksRunModulesTest ................. Passed 0.09 sec +5/9 Test #2: KisspliceBasicTest ............... Passed 0.11 sec 6: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_688836\n\n\nElapsed time: 0.0 seconds\n\n[14:05:16 12/05/2023] --> Finding the BCCs...\n[14:05:16 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[14:05:16 12/05/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[14:05:21 12/05/2023] --> Done!\nElapsed time: 5.4 seconds\n\n[14:05:21 12/05/2023] --> Starting Bubble Output Module\n[14:05:21 12/05/2023] --> Sampling bubbles by type...\n[14:05:21 12/05/2023] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[14:05:21 12/05/2023] --> Removing low-complexity/redundant bubbles...\n[14:05:21 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final results are in files results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_688836**********\n' +6: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_677392\n\n\nElapsed time: 0.0 seconds\n\n[22:31:05 14/06/2024] --> Finding the BCCs...\n[22:31:05 14/06/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[22:31:05 14/06/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:31:05 14/06/2024] --> Done!\nElapsed time: 0.5 seconds\n\n[22:31:05 14/06/2024] --> Starting Bubble Output Module\n[22:31:05 14/06/2024] --> Sampling bubbles by type...\n[22:31:05 14/06/2024] --> Done!\nYou can now access all bubbles without read coherency in: results\n\n[22:31:05 14/06/2024] --> Removing low-complexity/redundant bubbles...\n[22:31:05 14/06/2024] --> 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_677392**********\n' 6: kisspliceGraphTest.py: test SUCCESSFUL -6/9 Test #6: KisspliceGraphTest ............... Passed 6.22 sec +6/9 Test #6: KisspliceGraphTest ............... Passed 0.71 sec 5: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_147818\n\n\nElapsed time: 0.0 seconds\n\n[14:05:16 12/05/2023] --> Finding the BCCs...\n[14:05:16 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[14:05:16 12/05/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[14:05:21 12/05/2023] --> Done!\nElapsed time: 5.2 seconds\n\n[14:05:21 12/05/2023] --> 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[14:05:21 12/05/2023] --> Sampling bubbles by type...\n[14:05:21 12/05/2023] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[14:05:21 12/05/2023] --> Removing low-complexity/redundant bubbles...\n[14:05:21 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[14:05:23 12/05/2023] --> Computing read coherence and coverage...\n[14:05:24 12/05/2023] --> Done!\n[14:05:24 12/05/2023] --> Sorting all bubbles...\n[14:05:24 12/05/2023] --> Done!\nElapsed time: 2.6 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_147818**********\n' +5: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_256636\n\n\nElapsed time: 0.0 seconds\n\n[22:31:05 14/06/2024] --> Finding the BCCs...\n[22:31:05 14/06/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[22:31:05 14/06/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:31:05 14/06/2024] --> Done!\nElapsed time: 0.5 seconds\n\n[22:31:05 14/06/2024] --> 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[22:31:05 14/06/2024] --> Sampling bubbles by type...\n[22:31:05 14/06/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[22:31:05 14/06/2024] --> Removing low-complexity/redundant bubbles...\n[22:31:05 14/06/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[22:31:06 14/06/2024] --> Computing read coherence and coverage...\n[22:31:06 14/06/2024] --> Done!\n[22:31:06 14/06/2024] --> Sorting all bubbles...\n[22:31:06 14/06/2024] --> Done!\nElapsed time: 0.7 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_256636**********\n' 5: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL -7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 8.57 sec -8/9 Test #3: KisspliceDBGTest ................. Passed 28.15 sec +7/9 Test #5: KisspliceGraphAndSequenceTest .... Passed 1.39 sec +8/9 Test #3: KisspliceDBGTest ................. Passed 5.89 sec 4: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_89144\n\n\n[14:05:16 12/05/2023] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[14:05:38 12/05/2023] --> Done!\nElapsed time: 22.1 seconds\nElapsed time: 0.0 seconds\n\n[14:05:38 12/05/2023] --> Finding the BCCs...\n[14:05:38 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[14:05:38 12/05/2023] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[14:05:43 12/05/2023] --> Done!\nElapsed time: 4.9 seconds\n\n[14:05:43 12/05/2023] --> 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[14:05:43 12/05/2023] --> Sampling bubbles by type...\n[14:05:43 12/05/2023] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[14:05:43 12/05/2023] --> Removing low-complexity/redundant bubbles...\n[14:05:43 12/05/2023] --> Done!\nElapsed time: 0.1 seconds\n\n[14:05:45 12/05/2023] --> Computing read coherence and coverage...\n[14:05:46 12/05/2023] --> Done!\n[14:05:46 12/05/2023] --> Sorting all bubbles...\n[14:05:46 12/05/2023] --> Done!\nElapsed time: 3.3 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-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2023-05-12_14-05-16_89144**********\n' +4: b'\nThis is KisSplice, version 2.6.2\n\nThe command line was: /build/kissplice-2.6.2/obj-x86_64-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-x86_64-linux-gnu/tests/integration_tests/results\nSummary log file will be saved in: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_397792\n\n\n[22:31:05 14/06/2024] --> Building de Bruijn graph...\nGraph will be written in results/graph_HBM75brain_100000_HBM75liver_100000_k25.[edges/nodes]\n[22:31:10 14/06/2024] --> Done!\nElapsed time: 5.2 seconds\nElapsed time: 0.0 seconds\n\n[22:31:10 14/06/2024] --> Finding the BCCs...\n[22:31:10 14/06/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[22:31:10 14/06/2024] --> Enumerating all bubbles...\nTotal number of bubbles found: 57.0\n[22:31:10 14/06/2024] --> Done!\nElapsed time: 0.5 seconds\n\n[22:31:10 14/06/2024] --> 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[22:31:10 14/06/2024] --> Sampling bubbles by type...\n[22:31:10 14/06/2024] --> Done!\nYou can now access all bubbles without read coherency in: results/results_without_read_coherency\n\n[22:31:10 14/06/2024] --> Removing low-complexity/redundant bubbles...\n[22:31:10 14/06/2024] --> Done!\nElapsed time: 0.0 seconds\n\n[22:31:11 14/06/2024] --> Computing read coherence and coverage...\n[22:31:12 14/06/2024] --> Done!\n[22:31:12 14/06/2024] --> Sorting all bubbles...\n[22:31:12 14/06/2024] --> Done!\nElapsed time: 1.4 seconds\n\n\n\n \t\t ******** We are done, final coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_coherents_type_*.fa ********** \n \t\t ******** All non read coherent results are in files results/results_HBM75brain_100000_HBM75liver_100000_k25_uncoherent.fa ****** \n\n\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution errors, 69 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing substitution errors, 8 found\n\t\t\t 1: Alternative Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution can be found in the log file: /build/kissplice-2.6.2/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2024-06-14_22-31-05_397792**********\n' 4: kisspliceTwoSequencesTest.py: test SUCCESSFUL -9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 31.02 sec +9/9 Test #4: KisspliceTwoSequencesTest ........ Passed 7.19 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 31.07 sec +Total Test time (real) = 7.20 sec make[1]: Leaving directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kissplice/ - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/kissplice-2.6.2/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/kissplice-2.6.2/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kissplice-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-2.6.2 -B/build/kissplice-2.6.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -3059,8 +3102,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'kissplice-dbgsym' in '../kissplice-dbgsym_2.6.2-2_amd64.deb'. dpkg-deb: building package 'kissplice' in '../kissplice_2.6.2-2_amd64.deb'. +dpkg-deb: building package 'kissplice-dbgsym' in '../kissplice-dbgsym_2.6.2-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kissplice_2.6.2-2_amd64.buildinfo dpkg-genchanges --build=binary -O../kissplice_2.6.2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3068,12 +3111,14 @@ 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/1918556/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1918556/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/1580822 and its subdirectories -I: Current time: Fri May 12 14:06:17 -12 2023 -I: pbuilder-time-stamp: 1683943577 +I: removing directory /srv/workspace/pbuilder/1918556 and its subdirectories +I: Current time: Fri Jun 14 22:31:21 +14 2024 +I: pbuilder-time-stamp: 1718353881