Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/k/kissplice/kissplice_2.6.1-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/kissplice-2.6.1-1k1wz4jzk/kissplice_2.6.1-1_amd64.buildinfo Get source package info: kissplice=2.6.1-1 Source URL: http://snapshot.notset.fr/mr/package/kissplice/2.6.1-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 bcalm=2.2.3-2 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 cmake=3.23.0-1 cmake-data=3.23.0-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-19 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-3 findutils=4.9.0-2 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 fonts-lmodern=2.005-1 g++=4:11.2.0-2 g++-11=11.2.0-19 gcc=4:11.2.0-2 gcc-11=11.2.0-19 gcc-11-base=11.2.0-19 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libarchive13=3.6.0-1 libasan6=11.2.0-19 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblkid1=2.37.3-1+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl4=7.82.0-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.7 libelf1=0.186-1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-1 libgatbcore3=1.4.2+dfsg-8 libgcc-11-dev=11.2.0-19 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libglib2.0-0=2.72.0-1+b1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1 libhdf5-103-1=1.10.7+repack-4 libhogweed6=3.7.3-1 libice6=2:1.0.10-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220319-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-sphinxdoc=4.5.0-1 libjs-underscore=1.13.2~dfsg-2 libjsoncpp25=1.9.5-4 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkpathsea6=2021.20210626.59705-1 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 libldap-2.5-0=2.5.11+dfsg-1 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmd0=1.0.4-1 libmount1=2.37.3-1+b1 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-2 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.39-3 libpcre3=2:8.39-14 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-7+b1 libpsl5=0.21.0-1.2 libptexenc1=2021.20210626.59705-1 libpython3-dev=3.10.4-1 libpython3-stdlib=3.10.4-1 libpython3.10=3.10.4-3 libpython3.10-dev=3.10.4-3 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libquadmath0=12-20220319-1 libreadline8=8.1.2-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-2+b1 libsasl2-modules-db=2.1.28+dfsg-2+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsm6=2:1.2.3-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-19 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsynctex2=2021.20210626.59705-1 libsystemd0=250.4-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libteckit0=2.5.11+ds1-1 libtexlua53=2021.20210626.59705-1 libtexluajit2=2021.20210626.59705-1 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.2.0-19 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libuv1=1.44.1-2 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.14-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxi6=2:1.8-1 libxml2=2.9.13+dfsg-1 libxmu6=2:1.1.3-3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.1-1 libzstd1=1.4.10+dfsg-1 libzzip-0-13=0.13.72+dfsg.1-1.1 linux-libc-dev=5.16.18-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 po-debconf=1.0.21+nmu1 procps=2:3.3.17-7+b1 python3=3.10.4-1 python3-dev=3.10.4-1 python3-distutils=3.9.12-1 python3-lib2to3=3.9.12-1 python3-minimal=3.10.4-1 python3.10=3.10.4-3 python3.10-dev=3.10.4-3 python3.10-minimal=3.10.4-3 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 texlive-base=2021.20220204-1 texlive-binaries=2021.20210626.59705-1 texlive-latex-base=2021.20220204-1 texlive-latex-recommended=2021.20220204-1 ucf=3.0043 util-linux=2.37.3-1+b1 x11-common=1:7.7+23 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220408T211210Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d kissplice=2.6.1-1 && mkdir -p /build/kissplice-dmhtiV && dpkg-source --no-check -x /*.dsc /build/kissplice-dmhtiV/kissplice-2.6.1 && chown -R builduser:builduser /build/kissplice-dmhtiV" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/kissplice-dmhtiV/kissplice-2.6.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649254789" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/kissplice-dmhtiV /tmp/kissplice-2.6.1-1k1wz4jzk bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220408T211210Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.Jx_AmBPVma as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.Jx_AmBPVma Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220408T211210Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220408T211210Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (923 kB/s) Selecting previously unselected package libfakeroot: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 ... 4701 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220409T024953Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220408T211210Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Jx_AmBPVma Get:1 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220408T211210Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main Sources [12.0 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main amd64 Packages [11.4 MB] Fetched 23.5 MB in 19s (1209 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.Jx_AmBPVma I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d kissplice=2.6.1-1 && mkdir -p /build/kissplice-dmhtiV && dpkg-source --no-check -x /*.dsc /build/kissplice-dmhtiV/kissplice-2.6.1 && chown -R builduser:builduser /build/kissplice-dmhtiV"' exec /tmp/mmdebstrap.Jx_AmBPVma Reading package lists... NOTICE: 'kissplice' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kissplice.git Please use: git clone https://salsa.debian.org/med-team/kissplice.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5248 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main kissplice 2.6.1-1 (dsc) [2306 B] Get:2 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main kissplice 2.6.1-1 (tar) [5239 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220409T024953Z bookworm/main kissplice 2.6.1-1 (diff) [6556 B] Fetched 5248 kB in 4s (1273 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'kissplice_2.6.1-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting kissplice in /build/kissplice-dmhtiV/kissplice-2.6.1 dpkg-source: info: unpacking kissplice_2.6.1.orig.tar.gz dpkg-source: info: unpacking kissplice_2.6.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/kissplice-dmhtiV/kissplice-2.6.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649254789" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.Jx_AmBPVma dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.6.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Francois Gindraud dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_auto_clean find . -name __pycache__/ -type d | xargs rm -rf make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_auto_configure -- -DCMAKE_INSTALL_LIBEXECDIR=lib/ cd obj-x86_64-linux-gnu && 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 -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/ .. -- The CXX compiler identification is GNU 11.2.0 -- 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 "1.2.11") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found LATEX: /usr/bin/latex -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-dmhtiV/kissplice-2.6.1 -B/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/CMakeFiles /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/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[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/depend make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake --color= make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/depend make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_run_modules.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/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_error_removal.dir/DependInfo.cmake --color= make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/depend make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_print_bcc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/kissplice-dmhtiV/kissplice-2.6.1 /build/kissplice-dmhtiV/kissplice-2.6.1/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/CMakeFiles/doc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/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[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 1%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/commons.cpp make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 3%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 5%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o [ 6%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CycleCompression.cpp cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CleanDuplicates.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build [ 8%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o make[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/commons.cpp [ 10%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o [ 12%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/run.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -MF CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/PrintBcc.cpp cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/run.cpp.o -MF CMakeFiles/ks_run_modules.dir/run.cpp.o.d -o CMakeFiles/ks_run_modules.dir/run.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/run.cpp [ 13%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -MF CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o.d -o CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/ErrorRemoval.cpp [ 15%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/extension_algorithm.cpp [ 17%] Generating user_guide.pdf cd /build/kissplice-dmhtiV/kissplice-2.6.1/doc && /build/kissplice-dmhtiV/kissplice-2.6.1/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.tex /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.tex This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.te x LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-01-21> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 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/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/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/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/extension_algorithm.cpp: In function ‘float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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 * 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))[ 18%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -MF CMakeFiles/ks_print_bcc.dir/Utils.cpp.o.d -o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/Utils.cpp (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) No file user_guide.toc. [1 Non-PDF special ignored! papersize=614.295pt,794.96999pt {/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Underfull \hbox (badness 10000) in paragraph at lines 57--59 Underfull \hbox (badness 10000) in paragraph at lines 60--62 Overfull \hbox (19.60004pt too wide) in paragraph at lines 67--68 \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 70--75 \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 152--161 []\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] LaTeX Warning: Reference `fig:extype1_C2' on page 4 undefined on input line 172 . Overfull \hbox (24.90025pt too wide) in paragraph at lines 190--190 []\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 200 . Overfull \hbox (24.90025pt too wide) in paragraph at lines 204--204 []\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 211 . [4 <./MBTD1_C2.png[ 20%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/extension_algorithm.cpp In file included from /build/kissplice-dmhtiV/kissplice-2.6.1/modules/PrintBcc.cpp:51: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.h: In function ‘bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = Printer; TNodeFunctor = Printer]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(info_file, "%d \n",&records_per_file ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kissplice-dmhtiV/kissplice-2.6.1/modules/PrintBcc.cpp:50: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In function ‘bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/PrintBcc.cpp: In member function ‘void Printer::operator()(FILE*, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kissplice-dmhtiV/kissplice-2.6.1/modules/PrintBcc.cpp:50: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In function ‘void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = Printer]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/interface_libchash.cpp >] LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 274. [5 <./MBTD1_C0.png[ 24%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/LabelledCEdge.cpp [ 25%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp >] [6 <./quantifModel.png[ 27%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp >] Overfull \hbox (1.2115pt too wide) in paragraph at lines 328--329 []\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 340--341 []\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 341--342 []\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 342--343 []\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 343--344 []\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 344--345 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_3.fa\T1/cmr/m/n/12 : short [7] Overfull \hbox (1.06976pt too wide) in paragraph at lines 345--346 []\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 350--351 []\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 350--351 \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 352--353 []\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] Underfull \hbox (badness 10000) in paragraph at lines 409--410 [9] Underfull \hbox (badness 10000) in paragraph at lines 423--425 [10] (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.au x) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 [ 29%] Linking CXX executable ../lib/kissplice/ks_print_bcc cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_print_bcc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_print_bcc.dir/PrintBcc.cpp.o CMakeFiles/ks_print_bcc.dir/Utils.cpp.o -o ../lib/kissplice/ks_print_bcc /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* SparseNextBucket(SparseIterator*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ^ [ 31%] Building CXX object modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_error_removal.dir/Utils.cpp.o -MF CMakeFiles/ks_error_removal.dir/Utils.cpp.o.d -o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/Utils.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/extension_algorithm.cpp: In function ‘float read_coherence(gzFile, char*, int, int, fragment_info**, int, int, int, int, int, FILE*, int, char, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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; iifpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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)); | ^~~~~~~~~~~~~~~ [ 31%] Built target ks_print_bcc /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashFindLast(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro ‘LOAD_AND_RETURN’ 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashFirstBucket(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro ‘LOAD_AND_RETURN’ 1142 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashNextBucket(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro ‘LOAD_AND_RETURN’ 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro ‘READ_UL’ 1272 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro ‘READ_UL’ 1273 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro ‘READ_UL’ 1274 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro ‘READ_UL’ 1277 | READ_UL(fp, cchKey); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro ‘READ_UL’ 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘u_long SparseRead(FILE*, SparseBin**)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro ‘READ_UL’ 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro ‘READ_UL’ 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [ 32%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.cpp In file included from /build/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.cpp:61: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.h: In function ‘bool read_edges_and_nodes_withoptimIO(char*, char*, char*, char*, char*, int*, TEdgeFunctor, TNodeFunctor&) [with TEdgeFunctor = EdgeLoader; TNodeFunctor = NodeLoader]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.h:85:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(info_file, "%d \n",&records_per_file ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kissplice-dmhtiV/kissplice-2.6.1/modules/BubbleEnumeration.cpp:60: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In function ‘bool read_node_noncontigous_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = NodeLoader]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In member function ‘void NodeLoader::operator()(FILE*, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In function ‘void read_edge_file_withoptimIO(FILE*, FILE*, int*, int*, TFunctor&) [with TFunctor = EdgeLoader]’: /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h:322:56: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 322 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.h: In member function ‘void EdgeLoader::operator()(FILE*, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_sequence_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:860:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 860 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Linking CXX executable ../lib/kissplice/ks_error_removal cd /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_error_removal.dir/ErrorRemoval.cpp.o CMakeFiles/ks_error_removal.dir/LabelledCEdge.cpp.o CMakeFiles/ks_error_removal.dir/Utils.cpp.o -o ../lib/kissplice/ks_error_removal [ 37%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/interface_libchash.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 37%] Built target ks_error_removal [ 39%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/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.mf) (/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.mf 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/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* SparseNextBucket(SparseIterator*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ^ ] [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][ 41%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/LabelledCEdge.cpp [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashFind(HashTable*, u_long)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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)); | ^~~~~~~~~~~~~~~ [154] [155] [156] [157] [158] [159]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashFindLast(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1079:4: note: in expansion of macro ‘LOAD_AND_RETURN’ 1079 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashFirstBucket(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1142:15: note: in expansion of macro ‘LOAD_AND_RETURN’ 1142 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HTItem* HashNextBucket(HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:220:7: note: in expansion of macro ‘READ_UL’ 220 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1154:15: note: in expansion of macro ‘LOAD_AND_RETURN’ 1154 | LOAD_AND_RETURN(ht, retval); | ^~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1263:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1263 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1272:4: note: in expansion of macro ‘READ_UL’ 1272 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1273:4: note: in expansion of macro ‘READ_UL’ 1273 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1274:4: note: in expansion of macro ‘READ_UL’ 1274 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1277:4: note: in expansion of macro ‘READ_UL’ 1277 | READ_UL(fp, cchKey); | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1279:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1279 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:1284:7: note: in expansion of macro ‘READ_UL’ 1284 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp: In function ‘u_long SparseRead(FILE*, SparseBin**)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:620:4: note: in expansion of macro ‘READ_UL’ 620 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:193:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 193 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/libchash.cpp:625:10: note: in expansion of macro ‘READ_UL’ 625 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [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] [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 tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. In function ‘float rank_phi_N(const int*, const int*, int)’, inlined from ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’ at /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:639:28: cc1plus: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:169:7: note: by argument 1 of type ‘const int*’ to ‘float _Z10rank_phi_NPKiS0_i.part.0(const int*, const int*, int)’ declared here 169 | float rank_phi_N (const int *sum_up, const int *sum_lo, const int number_of_read_sets) { | ^~~~~~~~~~ In function ‘float rank_phi_N(const int*, const int*, int)’, inlined from ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’ at /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:639:28: cc1plus: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:169:7: note: by argument 2 of type ‘const int*’ to ‘float _Z10rank_phi_NPKiS0_i.part.0(const int*, const int*, int)’ declared here 169 | float rank_phi_N (const int *sum_up, const int *sum_lo, const int number_of_read_sets) { | ^~~~~~~~~~ [ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. 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) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 [ 44%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -MF CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o.d -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/Utils.cpp /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1032:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1033:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1034:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1043:56: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1047:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1079:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1080:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1081:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1090:58: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/coherent_algorithm.cpp [ 48%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/couple.cpp [ 50%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/coherent_algorithm.cpp [ 51%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CycleCompression.cpp [ 53%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) [ 55%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mfcd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/couple.cpp Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217][ 56%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o [218]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242][ 58%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o [243]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp [244] [245] [246] [247] [248] [249] [250] [251]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:595:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 595 | for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_sequence_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4]In function ‘float rank_phi_N(const int*, const int*, int)’, inlined from ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’ at /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:639:28: cc1plus: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:169:7: note: by argument 1 of type ‘const int*’ to ‘float _Z10rank_phi_NPKiS0_i.part.0(const int*, const int*, int)’ declared here 169 | float rank_phi_N (const int *sum_up, const int *sum_lo, const int number_of_read_sets) { | ^~~~~~~~~~ In function ‘float rank_phi_N(const int*, const int*, int)’, inlined from ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’ at /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:639:28: cc1plus: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp: In function ‘void print_quadruplet_i(FILE*, fragment_info* const*, int, int, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/outputs.cpp:169:7: note: by argument 2 of type ‘const int*’ to ‘float _Z10rank_phi_NPKiS0_i.part.0(const int*, const int*, int)’ declared here 169 | float rank_phi_N (const int *sum_up, const int *sum_lo, const int number_of_read_sets) { | ^~~~~~~~~~ [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp: In function ‘char* strdup_upper_case(char*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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++; | ~^~~~~~~~~~~ [79]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; | ~^~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp: In function ‘char* strdup_first_lower(char*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:109:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 109 | for(i=0;iw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [86] [87]/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable ‘j’ [-Wunused-variable] 155 | int i,j,z,stop; | ^ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable ‘validSeed’ [-Wunused-variable] 156 | char validSeed; | ^~~~~~~~~ [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) Font metrics written on ecbx1200.tfm. Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp: In function ‘char* strdup_upper_case(char*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:96:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for(i=0;i='A' && in[i]<='Z') count++; | ~^~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:99:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 99 | for(i=0;i='A' && in[i]<='Z') temp[j++]=in[i]; | ~^~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp: In function ‘char* strdup_first_lower(char*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/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;i kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp: In function ‘fragment_info** index_starters_from_input_file(int, int, int, char, int)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:228:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 228 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:229:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 229 | for(z=0;zw); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:230:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 230 | for(z=0;zw); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:155:15: warning: unused variable ‘j’ [-Wunused-variable] 155 | int i,j,z,stop; | ^ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_index.cpp:156:14: warning: unused variable ‘validSeed’ [-Wunused-variable] 156 | char validSeed; | ^~~~~~~~~ [ 63%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/tree.cpp [ 65%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_info.cpp [ 67%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/NGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp: In function ‘int main(int, char**)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp:526:50: warning: ‘strandRelativeThreshold’ may be used uninitialized in this function [-Wmaybe-uninitialized] 526 | (((double)(largestValue)/total) >= strandRelativeThreshold); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: ‘strandAbsoluteThreshold’ may be used uninitialized in this function [-Wmaybe-uninitialized] 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) | ^~ mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131][ 68%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/Utils.cpp [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15][ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o [19] [20] [13] [18]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/list.cpp [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1440.tfm. Output written on ectt1440.600gf (256 characters, 61024 bytes). Transcript written on ectt1440.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp: In function ‘int main(int, char**)’: /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp:526:50: warning: ‘strandRelativeThreshold’ may be used uninitialized in this function [-Wmaybe-uninitialized] 526 | (((double)(largestValue)/total) >= strandRelativeThreshold); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp:529:11: warning: ‘strandAbsoluteThreshold’ may be used uninitialized in this function [-Wmaybe-uninitialized] 529 | if (!respectsAbsoluteThreshold || !respectsRelativeThreshold) | ^~ [ 72%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o [ 74%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/tree.cpp cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -MF CMakeFiles/ks_run_modules.dir/CGraph.cpp.o.d -o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.cpp [ 75%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/LabelledCEdge.cpp [ 77%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CycleCompression.cpp [ 79%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSNPS cd /build/kissplice-dmhtiV/kissplice-2.6.1/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/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/couple.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/tree.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSNPS.dir/Utils.cpp.o -o ../../../lib/kissplice/ks_kissreadsSNPS /usr/lib/x86_64-linux-gnu/libz.so -lm -lgomp -lpthread /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1032:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1033:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1034:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1043:56: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1047:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1079:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1080:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1081:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1090:58: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/fragment_info.cpp [ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/c++ -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -I/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/include -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fopenmp -std=gnu++11 -MD -MT thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/Utils.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 84%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -MF CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o.d -o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/SplitBcc.cpp [ 84%] Built target ks_kissreadsSNPS [ 86%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o -MF CMakeFiles/ks_run_modules.dir/Utils.cpp.o.d -o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/Utils.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210[ 87%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o ]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) 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Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. [ 89%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/CGraph.cpp mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 [ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/LabelledCEdge.cpp [ 93%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++11 -MD -MT modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -MF CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o.d -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/modules/Utils.cpp mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194][ 94%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice [195]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_kissreadsSplice.dir/link.txt --verbose=1 [196] [197] [198] [199] [200] [201] [202] [203] [204]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_kissreadsSplice.dir/commons.cpp.o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/libchash.cpp.o CMakeFiles/ks_kissreadsSplice.dir/outputs.cpp.o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o CMakeFiles/ks_kissreadsSplice.dir/couple.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.cpp.o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o CMakeFiles/ks_kissreadsSplice.dir/list.cpp.o CMakeFiles/ks_kissreadsSplice.dir/tree.cpp.o CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o -o ../../../lib/kissplice/ks_kissreadsSplice /usr/lib/x86_64-linux-gnu/libz.so -lm -lgomp -lpthread [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.10997pt) Font metrics written on ecbx1440.tfm. Output written on ecbx1440.600gf (256 characters, 70764 bytes). Transcript written on ecbx1440.log. make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/extextit.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exileast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.mf/build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_edges_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1032:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1032 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1033:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1033 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1034:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1034 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1043:56: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1043 | for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1047:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1047 | fgets(buffer, 100 * MAX, data_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp: In function ‘void read_graph_nodes_new(NGraph&, FILE*, FILE*, FILE*, int*, int*)’: /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1079:68: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1079 | for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1080:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1080 | fscanf(contents_file, "%d \n",&written_lines_before ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1081:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1081 | fscanf(contents_file, "%d \n",&written_lines_for_record ); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/modules/NGraph.cpp:1090:58: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1090 | for (int i = 0; i < written_lines_before ; i++) { fgets(buffer, 100 * MAX, data_file); } | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kissplice-dmhtiV/kissplice-2.6.1/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilig.mf Ok [25] [26] [27] [28] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exidigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exiligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) Font metrics written on ecti1200.tfm. Output written on ecti1200.600gf (256 characters, 63048 bytes). Transcript written on ecti1200.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 [ 96%] Linking CXX executable ../lib/kissplice/ks_bubble_enumeration cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/kissplice/ks_bubble_enumeration mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1200.tfm. Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. [ 96%] Built target ks_bubble_enumeration < /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/hom e/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk> kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 [ 98%] Linking CXX executable ../lib/kissplice/ks_run_modules cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_run_modules.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_run_modules.dir/run.cpp.o CMakeFiles/ks_run_modules.dir/CycleCompression.cpp.o CMakeFiles/ks_run_modules.dir/NGraph.cpp.o CMakeFiles/ks_run_modules.dir/CGraph.cpp.o CMakeFiles/ks_run_modules.dir/LabelledCEdge.cpp.o CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o CMakeFiles/ks_run_modules.dir/Utils.cpp.o -o ../lib/kissplice/ks_run_modules make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf[ 98%] Built target ks_run_modules Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1728.tfm. Output written on ectt1728.600gf (256 characters, 72884 bytes). Transcript written on ectt1728.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.13197pt) Font metrics written on ecbx1728.tfm. Output written on ecbx1728.600gf (256 characters, 84848 bytes). Transcript written on ecbx1728.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242][100%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates [243]cd /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/kissplice-dmhtiV/kissplice-2.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/kissplice/ks_clean_duplicates [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63]make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86][100%] Built target ks_clean_duplicates [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.08084pt) Font metrics written on ecrm1440.tfm. Output written on ecrm1440.600gf (256 characters, 71064 bytes). Transcript written on ecrm1440.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm2074 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm2074 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm2074.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.1171pt) Font metrics written on ecrm2074.tfm. 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Transcript written on ecrm2074.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm2074.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt2074 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt2074 This is METAFONT, Version 2.71828182 (TeX Live 2022/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt2074.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt2074.tfm. Output written on ectt2074.600gf (256 characters, 87072 bytes). Transcript written on ectt2074.log. mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt2074.600pk: successfully generated. Output written on /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/ doc/user_guide.pdf (10 pages, 358361 bytes). Transcript written on /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux- gnu/doc/user_guide.log. cd /build/kissplice-dmhtiV/kissplice-2.6.1/doc && /build/kissplice-dmhtiV/kissplice-2.6.1/doc/quiet.sh /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.tex /usr/bin/pdflatex -halt-on-error -interaction=nonstopmode -output-directory=/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.tex This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.te x LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-01-21> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 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/latex/tools/multicol.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[4 <./MBTD1_C2.png>] [5 <./MBTD1_C0.png>] [6 <./quantifModel.png>] Overfull \hbox (1.2115pt too wide) in paragraph at lines 328--329 []\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 340--341 []\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 341--342 []\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 342--343 []\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 343--344 []\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 344--345 []\T1/cmtt/m/n/12 results_NameReadFile1_NameReadFile2_..._NameReadFileN_kXX_typ e_3.fa\T1/cmr/m/n/12 : short [7] Overfull \hbox (1.06976pt too wide) in paragraph at lines 345--346 []\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 350--351 []\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 350--351 \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 352--353 []\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] Underfull \hbox (badness 10000) in paragraph at lines 409--410 [9] Underfull \hbox (badness 10000) in paragraph at lines 423--425 [10] (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.au x) ) (see the transcript file for additional information) < /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/hom e/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk> Output written on /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/ doc/user_guide.pdf (10 pages, 369276 bytes). Transcript written on /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux- gnu/doc/user_guide.log. make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [100%] Built target doc make[2]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/kissplice/ -a cd obj-x86_64-linux-gnu && make -j10 install DESTDIR=/build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/kissplice-dmhtiV/kissplice-2.6.1 -B/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/bin/kissplice -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/bcalm -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_kissreadsSNPS -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_kissreadsSplice -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_clean_duplicates -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_bubble_enumeration -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_run_modules -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_error_removal -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/lib/kissplice/ks_print_bcc -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/share/man/man1/kissplice.1 -- Installing: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/kissplice/usr/share/doc/kissplice/user_guide.pdf make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1' rm -rf debian/kissplice/usr/README.md debian/kissplice/build debian/kissplice/builds rm -f debian/kissplice/usr/lib/kissplice/bcalm mkdir -p debian/kissplice/usr/share/kissplice mv debian/kissplice/usr/bin/kissplice debian/kissplice/usr/share/kissplice/kissplice.py make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_python3 -a I: dh_python3 tools:114: replacing shebang in debian/kissplice/usr/share/kissplice/kissplice.py dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kissplice' in '../kissplice_2.6.1-1_amd64.deb'. dpkg-deb: building package 'kissplice-dbgsym' in '../kissplice-dbgsym_2.6.1-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../kissplice_2.6.1-1_amd64.buildinfo dpkg-genchanges --build=any -O../kissplice_2.6.1-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/kissplice-dmhtiV /tmp/kissplice-2.6.1-1k1wz4jzk I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.Jx_AmBPVma... I: success in 409.1104 seconds md5: kissplice-dbgsym_2.6.1-1_amd64.deb: OK md5: kissplice_2.6.1-1_amd64.deb: OK sha1: kissplice-dbgsym_2.6.1-1_amd64.deb: OK sha1: kissplice_2.6.1-1_amd64.deb: OK sha256: kissplice-dbgsym_2.6.1-1_amd64.deb: OK sha256: kissplice_2.6.1-1_amd64.deb: OK Checksums: OK