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-2.6.1-1jcl9s2vy/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-2.6.1-1jcl9s2vy 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.SMAbgyfskq 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.SMAbgyfskq 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 (1065 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.SMAbgyfskq 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 20s (1202 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.SMAbgyfskq 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.SMAbgyfskq 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 (1264 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.SMAbgyfskq 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 -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/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_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_clean_duplicates.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_bubble_enumeration.dir/DependInfo.cmake --color= 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]: 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 -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' make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_run_modules.dir/build.make modules/CMakeFiles/ks_run_modules.dir/build make[3]: Leaving directory '/build/kissplice-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' 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' [ 1%] 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 [ 3%] 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_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 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 -f modules/CMakeFiles/ks_error_removal.dir/build.make modules/CMakeFiles/ks_error_removal.dir/build [ 5%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/CycleCompression.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_run_modules.dir/CycleCompression.cpp.o -MF 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/build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/commons.cpp make -f modules/CMakeFiles/ks_print_bcc.dir/build.make modules/CMakeFiles/ks_print_bcc.dir/build make -f doc/CMakeFiles/doc.dir/build.make doc/CMakeFiles/doc.dir/build make[3]: Entering 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_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.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[3]: Entering directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 8%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.cpp.o [ 10%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/PrintBcc.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 [ 12%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o [ 13%] Generating user_guide.pdf 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 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 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 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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 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)/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)) (/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>] LaTeX Warning: Reference `fig:quantif' on page 5 undefined on input line 274. [5 <./MBTD1_C0.png[ 18%] 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 >] [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- 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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 [ 20%] 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 [ 22%] 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 [ 24%] 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 /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); | ^ /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)); | ^~~~~~~~~~~~~~~ /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]); | ^~~~~~~ [ 25%] 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: 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] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [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. 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 /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; iiw)-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++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) (/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.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[ 29%] 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 [144] [145] [146] [147] [148] [149] [150] [151] [152][ 31%] Building CXX object modules/CMakeFiles/ks_print_bcc.dir/Utils.cpp.o [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162cd /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 ] [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[ 32%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.cpp.o Ok [0] [1] [2] [3] [4] [5cd /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 ] [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][ 34%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.cpp.o [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. 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 [ 36%] Building CXX object modules/CMakeFiles/ks_run_modules.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_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 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) { | ^~~~~~~~~~ mktexpk: /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/home/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. /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); | ^ kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 /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)); | ^~~~~~~~~~~~~~~ /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]); | ^~~~~~~ [ 37%] 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 [ 39%] 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 [ 41%] 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 [ 43%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.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/kissReads.cpp.o -MF CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o.d -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/kissReads.cpp make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 44%] 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 /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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Built target ks_print_bcc /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;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; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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; | ^~~~~~~~~ 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][ 48%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/SplitBcc.cpp.o [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219]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 [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 ectt1440.tfm. 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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 [ 50%] 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 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] [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][ 51%] Building CXX object modules/CMakeFiles/ks_run_modules.dir/Utils.cpp.o [182] [183] [184]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 [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 ectt1095.tfm. Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. [ 53%] 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 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 [ 55%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.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/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 [ 56%] 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 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] [195] [196] [197] [198] [199]/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++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [200] [201] [202] [203] [204]/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++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [205] [206] [207] [208][ 58%] 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 [209] [210] [211] [212] [213] [214] [215]/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 [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] [133make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' ] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153[ 58%] Built target ks_error_removal ] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164][ 60%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o [165cd /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 ] [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][ 62%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_info.cpp.o [27] [29] [30]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 [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/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); | ^~~~~~~~~~~~~~~~~~~~~~~ ] [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. /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: /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 [ 63%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.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_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 [ 65%] 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 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) { | ^~~~~~~~~~ [ 67%] 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 [ 68%] 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 [ 70%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.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 -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 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][ 72%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.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 -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 [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.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/exruwest.mf Ok [192][ 74%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o [193]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 [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%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/Utils.cpp.o [75] [76] [77] [78] [79] [80] [81]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 [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. [ 77%] 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/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;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; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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; | ^~~~~~~~~ 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 [ 79%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.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/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 /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_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 [ 82%] Building CXX object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.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/list.cpp.o -MF CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o.d -o CMakeFiles/ks_kissreadsSNPS.dir/list.cpp.o -c /build/kissplice-dmhtiV/kissplice-2.6.1/thirdparty/kissreads/src/list.cpp [ 84%] Linking CXX executable ../../../lib/kissplice/ks_kissreadsSplice 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 /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 [ 86%] 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 make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 86%] Built target ks_kissreadsSplice [ 87%] 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 [ 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: 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][ 91%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o [134]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 [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147]/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [148]/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [149] [150] [151] [152] [153] [154] [155] [156] [157]) 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(/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][ 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 [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. 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. < /build/kissplice-dmhtiV/kissplice-2.6.1/debian/.debhelper/generated/_source/hom e/.texlive2021/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk/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) | ^~ > kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 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 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. [ 94%] 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 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 make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [ 94%] Built target ks_kissreadsSNPS 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 [ 96%] 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 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[ 96%] Built target ks_run_modules 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[ 98%] 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 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]make[3]: Leaving directory '/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu' [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[ 98%] Built target ks_bubble_enumeration 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 0.08084pt) 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. Output written on ecrm2074.600gf (256 characters, 101464 bytes). 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 [100%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates 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 /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 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 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][100%] Built target ks_clean_duplicates [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. (/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)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.au x) *geometry* driver: auto-detecting *geometry* detected driver: pdftex *geometry* verbose mode - [ preamble ] result: * driver: pdftex * paper: letterpaper * layout: * layoutoffset:(h,v)=(0.0pt,0.0pt) * modes: * h-part:(L,W,R)=(71.13188pt, 472.03123pt, 71.13188pt) * v-part:(T,H,B)=(56.9055pt, 652.70622pt, 85.35826pt) * \paperwidth=614.295pt * \paperheight=794.96999pt * \textwidth=472.03123pt * \textheight=652.70622pt * \oddsidemargin=-1.1381pt * \evensidemargin=-1.1381pt * \topmargin=-52.36449pt * \headheight=12.0pt * \headsep=25.0pt * \topskip=12.0pt * \footskip=30.0pt * \marginparwidth=35.0pt * \marginparsep=10.0pt * \columnsep=10.0pt * \skip\footins=10.8pt plus 4.0pt minus 2.0pt * \hoffset=0.0pt * \voffset=0.0pt * \mag=1000 * \@twocolumnfalse * \@twosidefalse * \@mparswitchfalse * \@reversemarginfalse * (1in=72.27pt=25.4mm, 1cm=28.453pt) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/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) (/build/kissplice-dmhtiV/kissplice-2.6.1/obj-x86_64-linux-gnu/doc/user_guide.to c) [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] 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 , 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'. [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-2.6.1-1jcl9s2vy I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.SMAbgyfskq... I: success in 432.3490 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