Sat Jun 8 06:22:27 UTC 2024 I: starting to build kissplice/unstable/amd64 on jenkins on '2024-06-08 06:22' Sat Jun 8 06:22:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/15662/console.log Sat Jun 8 06:22:27 UTC 2024 I: Downloading source for unstable/kissplice=2.6.2-3 --2024-06-08 06:22:27-- http://deb.debian.org/debian/pool/main/k/kissplice/kissplice_2.6.2-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2329 (2.3K) [text/prs.lines.tag] Saving to: ‘kissplice_2.6.2-3.dsc’ 0K .. 100% 267M=0s 2024-06-08 06:22:27 (267 MB/s) - ‘kissplice_2.6.2-3.dsc’ saved [2329/2329] Sat Jun 8 06:22:27 UTC 2024 I: kissplice_2.6.2-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kissplice Binary: kissplice Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64 any-ppc64el any-sparc64 loong64 riscv64 Version: 2.6.2-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Francois Gindraud Homepage: https://kissplice.prabi.fr/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kissplice Vcs-Git: https://salsa.debian.org/med-team/kissplice.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cmake, python3-dev, libpython3-stdlib, zlib1g-dev, texlive-latex-recommended, bcalm Package-List: kissplice deb science optional arch=any-amd64,any-arm64,any-mips64,any-mips64el,any-ia64,any-ppc64,any-ppc64el,any-sparc64,loong64,riscv64 Checksums-Sha1: 228561b311f56d551361422000d3ed176c0f77fb 5247282 kissplice_2.6.2.orig.tar.gz 9f470b599e1a72d7839b703c3afcd72054d55d76 6532 kissplice_2.6.2-3.debian.tar.xz Checksums-Sha256: e2a4f8108c7668a8e50263d105889004f9f18b24f7a20f13ddb7dc903389f3e6 5247282 kissplice_2.6.2.orig.tar.gz 81dadd42581b9736f95abd9615d1b94ca3f5f94aa9872823b18ecec12a44e6dd 6532 kissplice_2.6.2-3.debian.tar.xz Files: abbc5f1e2c7f3ca5c59753eb91fe1f68 5247282 kissplice_2.6.2.orig.tar.gz d3e8e97da31522474283ae26907f6503 6532 kissplice_2.6.2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWdo2IRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHwmg/8CuwkSeOx3hsIekvRBerN+z7NiCWJaY44 zNZuU5YSpx9sm0aXA03B08WGN0uLtjhFaT6dqvUEHjXQqoio/ghRhvybjveB8qeJ 1RvJckRJp/Yjt7J3epO4tDpk2PXWHhg41UooKt9LuRsmy014k9OLDm/HLaDKiIx3 3whOA+f/jxFXTkhS1Tgg5bfClR6yWKWUPVUD30PQOOlKj1MBIAf6xTsVOMBHr6Sw 5EQn4uC+eZ43ypgHnuLBn67IGwMiOSf9qx/0mSPDkXRBbF8l0EbUUemsnj56jXFO 0DhYZh1BtX4D8ZGX31RlQugILJOpJel9WGomsjChUwie3zipYVMZhcI7UKpQP+JS UXi30qfSUwm4YV9ziNCge4zM1LhexINLroyGl358Uzv4zjMru2rLiXAcz2By0b1B uiCHqfHC5KIKVXiatCPKLbbHjVQP80Z1q0CE1esClxNKNkhpfLFsj1GFn2nMsw/Z Ibd4a0RIL/Z25J1yToLkwUJrQqmTDxHGD1wa7za0txscsgTVAuvL0EVvqmzg82sQ UrwXokUemBRbMfyoRD3zJna7TaNoDmWvwwVaF0e9qCx2pytE4/X511gDuilMPWAy rrfoeGZV+gVUoBAtBSvaLyeFhkuLLpktDsyjVDZmrv2X2ztNMyRrUoOT15Q380uH uu8RT7FiPvE= =K+dz -----END PGP SIGNATURE----- Sat Jun 8 06:22:27 UTC 2024 I: Checking whether the package is not for us Sat Jun 8 06:22:27 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Sat Jun 8 06:22:27 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Sat Jun 8 06:25:20 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 11 00:45:29 -12 2025 I: pbuilder-time-stamp: 1752237929 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [kissplice_2.6.2-3.dsc] I: copying [./kissplice_2.6.2.orig.tar.gz] I: copying [./kissplice_2.6.2-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 9 19:49:54 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kissplice_2.6.2-3.dsc: no acceptable signature found dpkg-source: info: extracting kissplice in kissplice-2.6.2 dpkg-source: info: unpacking kissplice_2.6.2.orig.tar.gz dpkg-source: info: unpacking kissplice_2.6.2-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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/2021135/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bb1aff7a48274230aa2a70a176321e5b' 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='2021135' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Y2mnOKPs/pbuilderrc_MfBw --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Y2mnOKPs/b1 --logfile b1/build.log kissplice_2.6.2-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jul 9 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2021135/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cmake, python3-dev, libpython3-stdlib, zlib1g-dev, texlive-latex-recommended, bcalm dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19716 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on libpython3-stdlib; however: Package libpython3-stdlib is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on bcalm; however: Package bcalm is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcalm{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgatbcore3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libice6{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libnghttp2-14{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1t64{a} libsynctex2{a} libsz2{a} libteckit0{a} libtexlua53-5{a} libtool{a} libuchardet0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dvisvgm javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lmodern lynx psmisc publicsuffix shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After unpacking 377 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-8.1 [96.2 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgatbcore3 amd64 1.4.2+dfsg-13+b1 [1802 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 50 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 bcalm amd64 2.2.3-5+b1 [35.4 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2.1 [346 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.4-1 [2167 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.4-1 [10.7 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-8 [150 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-2 [156 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-2 [48.5 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-2 [62.2 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-2 [113 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-2 [8438 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20240401-2 [22.7 MB] Get: 132 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20240401-2 [1258 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20240401-2 [8847 kB] Fetched 111 MB in 1s (106 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 ... 19716 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20032 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21024 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.1-8.1_amd64.deb ... Unpacking bsdextrautils (2.40.1-8.1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-2_amd64.deb ... Unpacking man-db (2.12.1-2) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libgatbcore3:amd64. Preparing to unpack .../019-libgatbcore3_1.4.2+dfsg-13+b1_amd64.deb ... Unpacking libgatbcore3:amd64 (1.4.2+dfsg-13+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../020-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../021-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../022-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../023-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../024-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../025-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../026-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../027-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../028-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../029-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../030-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../031-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../032-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../033-libssh2-1t64_1.11.0-5_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-5) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../034-libcurl4t64_8.8.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.8.0-1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../035-libaec0_1.1.3-1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../036-libsz2_1.1.3-1_amd64.deb ... Unpacking libsz2:amd64 (1.1.3-1) ... Selecting previously unselected package libhdf5-103-1t64:amd64. Preparing to unpack .../037-libhdf5-103-1t64_1.10.10+repack-3.3_amd64.deb ... Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Selecting previously unselected package bcalm. Preparing to unpack .../038-bcalm_2.2.3-5+b1_amd64.deb ... Unpacking bcalm (2.2.3-5+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../039-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../040-libxml2_2.12.7+dfsg-3_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-3) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../041-libarchive13t64_3.7.2-2.1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.2-2.1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../042-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../043-librhash0_1.4.3-3+b1_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../044-libuv1t64_1.48.0-4_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../045-cmake-data_3.29.4-1_all.deb ... Unpacking cmake-data (3.29.4-1) ... Selecting previously unselected package cmake. Preparing to unpack .../046-cmake_3.29.4-1_amd64.deb ... Unpacking cmake (3.29.4-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../052-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../053-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../054-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../055-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../056-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../057-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../058-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../059-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../060-python3-lib2to3_3.12.3-3.1_all.deb ... Unpacking python3-lib2to3 (3.12.3-3.1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../061-python3-distutils_3.12.3-3.1_all.deb ... Unpacking python3-distutils (3.12.3-3.1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../062-python3-setuptools_68.1.2-2_all.deb ... Unpacking python3-setuptools (68.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../063-dh-python_6.20240422_all.deb ... Unpacking dh-python (6.20240422) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../064-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../065-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../066-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../067-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../068-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../069-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../070-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../071-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../072-libpixman-1-0_0.42.2-1+b1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../073-libxau6_1%3a1.0.9-1+b1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../074-libxdmcp6_1%3a1.1.2-3+b1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../075-libxcb1_1.17.0-2_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../076-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../077-libx11-6_2%3a1.8.7-1+b1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../078-libxcb-render0_1.17.0-2_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../079-libxcb-shm0_1.17.0-2_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../080-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../081-libxrender1_1%3a0.9.10-1.1+b1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../082-libcairo2_1.18.0-3+b1_amd64.deb ... Unpacking libcairo2:amd64 (1.18.0-3+b1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../083-libexpat1-dev_2.6.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.2-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../084-libglib2.0-0t64_2.80.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.80.2-2) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../085-libgraphite2-3_1.3.14-2_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../086-libharfbuzz0b_8.3.0-2+b1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (8.3.0-2+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../087-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../088-libice6_2%3a1.0.10-1+b1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../089-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../090-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../091-libjs-sphinxdoc_7.2.6-8_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-8) ... Selecting previously unselected package libkpathsea6:amd64. Preparing to unpack .../092-libkpathsea6_2024.20240313.70630+ds-2_amd64.deb ... Unpacking libkpathsea6:amd64 (2024.20240313.70630+ds-2) ... Selecting previously unselected package libmpfi0:amd64. Preparing to unpack .../093-libmpfi0_1.5.4+ds-3_amd64.deb ... Unpacking libmpfi0:amd64 (1.5.4+ds-3) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../094-libpaper1_1.1.29+b1_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../095-libpaper-utils_1.1.29+b1_amd64.deb ... Unpacking libpaper-utils (1.1.29+b1) ... Selecting previously unselected package libpotrace0:amd64. Preparing to unpack .../096-libpotrace0_1.16-2+b1_amd64.deb ... Unpacking libpotrace0:amd64 (1.16-2+b1) ... Selecting previously unselected package libptexenc1:amd64. Preparing to unpack .../097-libptexenc1_2024.20240313.70630+ds-2_amd64.deb ... Unpacking libptexenc1:amd64 (2024.20240313.70630+ds-2) ... Selecting previously unselected package libpython3.11t64:amd64. Preparing to unpack .../098-libpython3.11t64_3.11.9-1_amd64.deb ... Unpacking libpython3.11t64:amd64 (3.11.9-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../099-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../100-libpython3.11-dev_3.11.9-1_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.9-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../101-libpython3-dev_3.11.8-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.8-1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../102-libsm6_2%3a1.2.3-1+b1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1+b1) ... Selecting previously unselected package libsynctex2:amd64. Preparing to unpack .../103-libsynctex2_2024.20240313.70630+ds-2_amd64.deb ... Unpacking libsynctex2:amd64 (2024.20240313.70630+ds-2) ... Selecting previously unselected package libteckit0:amd64. Preparing to unpack .../104-libteckit0_2.5.12+ds1-1_amd64.deb ... Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... Selecting previously unselected package libtexlua53-5:amd64. Preparing to unpack .../105-libtexlua53-5_2024.20240313.70630+ds-2_amd64.deb ... Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-2) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../106-libxt6t64_1%3a1.2.1-1.2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ... Selecting previously unselected package libxmu6:amd64. Preparing to unpack .../107-libxmu6_2%3a1.1.3-3+b2_amd64.deb ... Unpacking libxmu6:amd64 (2:1.1.3-3+b2) ... Selecting previously unselected package libxpm4:amd64. Preparing to unpack .../108-libxpm4_1%3a3.5.17-1+b1_amd64.deb ... Unpacking libxpm4:amd64 (1:3.5.17-1+b1) ... Selecting previously unselected package libxaw7:amd64. Preparing to unpack .../109-libxaw7_2%3a1.0.14-1+b2_amd64.deb ... Unpacking libxaw7:amd64 (2:1.0.14-1+b2) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../110-libxi6_2%3a1.8.1-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.8.1-1) ... Selecting previously unselected package libzzip-0-13t64:amd64. Preparing to unpack .../111-libzzip-0-13t64_0.13.72+dfsg.1-1.2+b1_amd64.deb ... Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../112-python3.11-dev_3.11.9-1_amd64.deb ... Unpacking python3.11-dev (3.11.9-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../113-python3-dev_3.11.8-1_amd64.deb ... Unpacking python3-dev (3.11.8-1) ... Selecting previously unselected package t1utils. Preparing to unpack .../114-t1utils_1.41-4_amd64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package tex-common. Preparing to unpack .../115-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../116-texlive-binaries_2024.20240313.70630+ds-2_amd64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-2) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../117-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../118-texlive-base_2024.20240401-2_all.deb ... Unpacking texlive-base (2024.20240401-2) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../119-texlive-latex-base_2024.20240401-2_all.deb ... Unpacking texlive-latex-base (2024.20240401-2) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../120-texlive-latex-recommended_2024.20240401-2_all.deb ... Unpacking texlive-latex-recommended (2024.20240401-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-8.1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libuv1t64:amd64 (1.48.0-4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jul 11 12:47:20 UTC 2025. Universal Time is now: Fri Jul 11 12:47:20 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-2) ... No schema files found: doing nothing. Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-2) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgatbcore3:amd64 (1.4.2+dfsg-13+b1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up fonts-lmodern (2.005-1) ... Setting up netbase (6.4) ... Setting up cmake-data (3.29.4-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsz2:amd64 (1.1.3-1) ... Setting up libsynctex2:amd64 (2024.20240313.70630+ds-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.2.6-8) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2.1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up cmake (3.29.4-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up bcalm (2.2.3-5+b1) ... Setting up texlive-binaries (2024.20240313.70630+ds-2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up texlive-base (2024.20240401-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-3.1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up texlive-latex-base (2024.20240401-2) ... Setting up python3-dev (3.11.8-1) ... Setting up texlive-latex-recommended (2024.20240401-2) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.38-12.1) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/kissplice-2.6.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kissplice_2.6.2-3_source.changes dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.2' dh_auto_clean find . -name __pycache__/ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.2' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.2' dh_auto_configure -- -DCMAKE_INSTALL_LIBEXECDIR=lib/ cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_INSTALL_LIBEXECDIR=lib/ .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found bcalm tool: /usr/bin/bcalm -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex -- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.2' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kissplice-2.6.2 -B/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/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 -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[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.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/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake "--color=" make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake "--color=" make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_run_modules.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kissplice-2.6.2 /build/reproducible-path/kissplice-2.6.2/doc /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build make[3]: Leaving directory '/build/reproducible-path/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_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build make[3]: Entering directory '/build/reproducible-path/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 make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/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]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/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/build make[3]: Entering directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [ 3%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o [ 3%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o [ 5%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp [ 6%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -MF CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp [ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o [ 10%] Generating user_guide.pdf [ 12%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp cd /build/reproducible-path/kissplice-2.6.2/doc && /build/reproducible-path/kissplice-2.6.2/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex [ 13%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -MF CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o.d -o CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/ErrorRemoval.cpp [ 15%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp [ 17%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.tex cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CleanDuplicates.cpp cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -MF CMakeFiles/ks_run_modules.dir/run.cpp.o.d -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/run.cpp [ 18%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/commons.cpp This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. [ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp entering extended mode (/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.t ex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-03-14> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def)) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifvtex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty))) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def) (/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf)) (/usr/share/texlive/texmf-dist/tex/generic/babel/locale/en/babel-english.tex) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/dvips.def))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/amscls/amsthm.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/enumerate.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/listings/lstpatch.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file user_guide.aux. *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: letterpaper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(71.13188pt, 472.03123pt, 71.13188pt) * v-part:(T,H,B)=(56.9055pt, 652.70622pt, 85.35826pt) * \paperwidth=614.295pt * \paperheight=794.96999pt * \textwidth=472.03123pt * \textheight=652.70622pt * \oddsidemargin=-1.1381pt * \evensidemargin=-1.1381pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=12.0pt * \footskip=30.0pt * \marginparwidth=35.0pt * \marginparsep=10.0pt * \columnsep=10.0pt * \skip\footins=10.8pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp: In function 'float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp:439:44: warning: comparison of integer expressions of different signedness: 'int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] 439 | for (ii=offset_seed; ii papersize=614.295pt,794.96999pt {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Underfull \hbox (badness 10000) in paragraph at lines 58--60 Underfull \hbox (badness 10000) in paragraph at lines 61--63 Overfull \hbox (19.60004pt too wide) in paragraph at lines 68--69 \T1/cmr/m/n/12 If you have ques-tions, please use pri-mar-ily the biostars fo-r um: $\T1/cmtt/m/n/12 www . biostars . org / t / kissplice/$ Overfull \hbox (13.7669pt too wide) in paragraph at lines 71--76 \T1/cmr/m/n/12 To do so, please sub-scribe at : $\T1/cmtt/m/n/12 http : / / lis ts . gforge . inria . fr / cgi-[]bin / mailman / listinfo / [2] Overfull \hbox (24.58913pt too wide) in paragraph at lines 153--162 []\T1/cmr/m/n/12 The \T1/cmtt/m/n/12 sample_example \T1/cmr/m/n/12 di-rec-tory con-tains four files \T1/cmtt/m/n/12 mock1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 m ock2.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 virus1.fq\T1/cmr/m/n/12 , \T1/cmtt/m/n/ 12 virus2.fq [3][ 24%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 173 . Overfull \hbox (24.90025pt too wide) in paragraph at lines 191--191 []\T1/cmr/m/n/12 Figure 1: Con-tent of the file \T1/cmtt/m/n/12 results_mock1_m ock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , LaTeX Warning: Reference `fig:extype1_C0' on page 4 undefined on input line 201 . Overfull \hbox (24.90025pt too wide) in paragraph at lines 205--205 []\T1/cmr/m/n/12 Figure 2: Con-tent of the file \T1/cmtt/m/n/12 results_mock1_m ock2_virus1_virus2_k41_coherents_type_1.fa\T1/cmr/m/n/12 , LaTeX Warning: `!h' float specifier changed to `!ht'. LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 212 . [4cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp <./MBTD1_C2.pngIn file included from /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp:51: /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = Printer; TNodeFunctor = Printer]': /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(info_file, "%d \n",&bcc_size ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(info_file, "%d \n",&records_per_file ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp:50: /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp: In member function 'void Printer::operator()(FILE*, int)': /build/reproducible-path/kissplice-2.6.2/modules/PrintBcc.cpp:64:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 64 | fgets(buffer, 100 * MAX, in_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:580:44: warning: comparison of integer expressions of different signedness: 'long int' and 'u_long' {aka 'long unsigned int'} [-Wsign-compare] 580 | for ( iter->posGroup++; iter->posGroup < SPARSE_GROUPS(iter->cBuckets); | ^ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1074:4: note: in expansion of macro 'LOAD_AND_RETURN' 1074 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro 'LOAD_AND_RETURN' 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro 'LOAD_AND_RETURN' 1142 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' 1272 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' 1273 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' 1274 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' 1277 | READ_UL(fp, cchKey); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [ 25%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp: In function 'float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/extension_algorithm.cpp:439:44: warning: comparison of integer expressions of different signedness: 'int' and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] 439 | for (ii=offset_seed; ii] LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 275. [5 <./MBTD1_C0.png[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp [ 29%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -MF CMakeFiles/ks_print_bcc.dir/Utils.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp >] [6 <./quantifModel.png[ 31%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/interface_libchash.cpp [ 32%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp [ 34%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp [ 36%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* SparseNextBucket(SparseIterator*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:580:44: warning: comparison of integer expressions of different signedness: 'long int' and 'u_long' {aka 'long unsigned int'} [-Wsign-compare] 580 | for ( iter->posGroup++; iter->posGroup < SPARSE_GROUPS(iter->cBuckets); | ^ >]cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/CGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp Overfull \hbox (1.2115pt too wide) in paragraph at lines 329--330 []\T1/cmtt/m/n/12 graph_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX.nodes \T1/cmr/m/n/12 for the nodes Overfull \hbox (5.2035pt too wide) in paragraph at lines 341--342 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_0a.fa\T1/cmr/m/n/12 : Sin- Overfull \hbox (9.44136pt too wide) in paragraph at lines 342--343 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_0b.fa\T1/cmr/m/n/12 : Mul- Overfull \hbox (6.20883pt too wide) in paragraph at lines 343--344 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_1.fa\T1/cmr/m/n/12 : al-ter- Overfull \hbox (3.92465pt too wide) in paragraph at lines 344--345 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_2.fa\T1/cmr/m/n/12 : in-ex- 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]/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1074:4: note: in expansion of macro 'LOAD_AND_RETURN' 1074 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ 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 /m/n/12 : all oth-ers, com-posed Underfull \hbox (badness 1655) in paragraph at lines 351--352 []\T1/cmr/m/n/12 Since the read co-herency step may take a long time, \T1/cmtt/ m/n/12 KisSplice \T1/cmr/m/n/12 pre-emp-tively Underfull \hbox (badness 2393) in paragraph at lines 351--352 \T1/cmr/m/n/12 out-puts these six fasta files be-fore check-ing for read co-her ency in the di-rec-tory 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]/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro 'LOAD_AND_RETURN' 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ Underfull \hbox (badness 10000) in paragraph at lines 410--411 [9/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro 'LOAD_AND_RETURN' 1142 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro 'READ_UL' 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro 'LOAD_AND_RETURN' 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ ]/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro 'READ_UL' 1272 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro 'READ_UL' 1273 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro 'READ_UL' 1274 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro 'READ_UL' 1277 | READ_UL(fp, cchKey); | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro 'READ_UL' 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro 'READ_UL' 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro 'READ_UL' 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ Underfull \hbox (badness 10000) in paragraph at lines 424--426 [10] (/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/user_guide.a ux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 [ 37%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o In file included from /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp:61: /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h: In function 'bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]': /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h:84:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | fscanf(info_file, "%d \n",&bcc_size ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(info_file, "%d \n",&records_per_file ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CycleCompression.cpp In file included from /build/reproducible-path/kissplice-2.6.2/modules/BubbleEnumeration.cpp:60: /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:235:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:236:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fscanf(contents_file_node, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:237:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 237 | fscanf(contents_file_node, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:248:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 248 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In member function 'void NodeLoader::operator()(FILE*, int)': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:198:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 198 | fgets(buffer, 100 * MAX, node_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In function 'void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:313:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:314:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 314 | fscanf(contents_file_edge, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:315:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 315 | fscanf(contents_file_edge, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:322:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h: In member function 'void EdgeLoader::operator()(FILE*, int)': /build/reproducible-path/kissplice-2.6.2/modules/CGraph.h:277:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp [ 41%] Linking CXX executable ../lib/kissplice/ks_print_bcc cd /build/reproducible-path/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 [ 43%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp: In function 'void print_sequence_i(FILE*, fragment_info* const*, int, int, int)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [ 44%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mfcd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp [ 46%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o ) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mfcd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179[ 46%] Built target ks_print_bcc ] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on /build/reproducible-path/kissplice-2.6.2/obj-x86_64-lin ux-gnu/doc/tcrm1200.tfm. Output written on /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu /doc/tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux -gnu/doc/tcrm1200.log. mktexpk: `mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200' failed to make tcrm1200.600pk. kpathsea: Appending font creation commands to /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/doc/missfont.log. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) !pdfTeX error: /usr/bin/pdflatex (file tcrm1200): Font tcrm1200 at 600 not foun d ==> Fatal error occurred, no output PDF file produced! make[3]: *** [doc/CMakeFiles/doc.dir/build.make:78: doc/user_guide.pdf] Error 1 make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:428: doc/CMakeFiles/doc.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... [ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o [ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/coherent_algorithm.cpp cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp [ 53%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp [ 55%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp [ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o [ 58%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/couple.cpp /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 96 | for(i=0;i='A' && in[i]<='Z') count++; | ~^~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; | ~^~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] 155 | int i,j,z,stop; | ^ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] 156 | char validSeed; | ^~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp [ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp [ 63%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp [ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp [ 67%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/kissReads.cpp [ 68%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_info.cpp /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_upper_case(char*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 96 | for(i=0;i='A' && in[i]<='Z') count++; | ~^~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; | ~^~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp: In function 'char* strdup_first_lower(char*)': /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable 'j' [-Wunused-variable] 155 | int i,j,z,stop; | ^ /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable 'validSeed' [-Wunused-variable] 156 | char validSeed; | ^~~~~~~~~ [ 70%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp [ 72%] Linking CXX executable ../lib/kissplice/ks_error_removal cd /build/reproducible-path/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1032:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1033:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1034:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1043:56: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1047:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp: In function 'void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)': /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1079:68: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1080:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1081:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1090:58: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kissplice-2.6.2/modules/NGraph.cpp:1094:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1094 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 72%] Built target ks_error_removal [ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/list.cpp [ 75%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/CGraph.cpp [ 77%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/Utils.cpp [ 79%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/LabelledCEdge.cpp [ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/tree.cpp [ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/fragment_info.cpp [ 84%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -MF CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o.d -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/SplitBcc.cpp [ 86%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp [ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp [ 89%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -fopenmp -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/thirdparty/kissreads/src/Utils.cpp [ 91%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice cd /build/reproducible-path/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/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [ 93%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o cd /build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -MD -MT modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -MF CMakeFiles/ks_run_modules.dir/Utils.cpp.o.d -o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -c /build/reproducible-path/kissplice-2.6.2/modules/Utils.cpp [ 94%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS cd /build/reproducible-path/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [ 94%] Built target ks_kissreadsSplice [ 94%] Built target ks_kissreadsSNPS [ 96%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration cd /build/reproducible-path/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/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [ 98%] Linking CXX executable ../lib/kissplice/ks_run_modules cd /build/reproducible-path/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/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/kissplice/ks_run_modules make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [ 98%] Built target ks_bubble_enumeration [ 98%] Built target ks_run_modules [100%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates cd /build/reproducible-path/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kissplice-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/kissplice/ks_clean_duplicates make[3]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' [100%] Built target ks_clean_duplicates make[2]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' make[1]: *** [Makefile:149: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/kissplice-2.6.2/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:19: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/2021135 and its subdirectories Sat Jun 8 06:25:22 UTC 2024 W: No second build log, what happened?