Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/macsyfinder/macsyfinder_2.0~rc1-3+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/macsyfinder-2.0~rc1-3+b1rx_ir3m_/macsyfinder_2.0~rc1-3+b1_amd64.buildinfo Get source package info: macsyfinder=2.0~rc1-3 Source URL: http://snapshot.notset.fr/mr/package/macsyfinder/2.0~rc1-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.50 bash=5.1-3 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-7 bsdutils=1:2.36.1-7 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.76 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-python=4.20201102+nmu1 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-4 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-lato=2.0-2.1 fonts-lmodern=2.004.5-6.1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 graphviz=2.42.2-5 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hmmer=3.3.2+dfsg-1 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 latexmk=1:4.70b-0.2 libacl1=2.2.53-10 libann0=1.1.2+doc-7 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.2-2 libblkid1=2.36.1-7 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-12 libc-dev-bin=2.31-12 libc6=2.31-12 libc6-dev=2.31-12 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcdt5=2.42.2-5 libcgraph6=2.42.2-5 libcom-err2=1.46.2-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.18-4 libcrypt1=1:4.4.18-4 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.259 libdebhelper-perl=13.3.4 libdeflate0=1.7-1 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.9 libelf1=0.183-3 libexpat1=2.2.10-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgd3=2.3.0-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libglib2.0-0=2.66.8-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-5 libgts-0.7-5=0.7.6+darcs121130-4+b1 libgvc6=2.42.2-5 libgvpr2=2.42.2-5 libharfbuzz0b=2.7.4-1 libice6=2:1.0.10-1 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-4 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-sphinxdoc=3.4.3-2 libjs-underscore=1.9.1~dfsg-3 libk5crypto3=1.18.3-5 libkeyutils1=1.6.1-2 libkpathsea6=2020.20200327.54578-7 libkrb5-3=1.18.3-5 libkrb5support0=1.18.3-5 liblab-gamut1=2.42.2-5 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.36.1-7 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-7 libpam-modules-bin=1.4.0-7 libpam-runtime=1.4.0-7 libpam0g=1.4.0-7 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpathplan4=2.42.2-5 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpdfbox-java=1:1.8.16-2 libperl5.32=5.32.1-4 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libptexenc1=2020.20200327.54578-7 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.2-1 libpython3.9-stdlib=3.9.2-1 libquadmath0=10.2.1-6 libreadline8=8.1-2 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-7 libsqlite3-0=3.34.1-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsynctex2=2020.20200327.54578-7 libsystemd0=247.3-5 libteckit0=2.5.10+ds1-3 libtexlua53=2020.20200327.54578-7 libtexluajit2=2020.20200327.54578-7 libthai-data=0.1.28-4 libthai0=0.1.28-4 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-5 libunistring2=0.9.10-4 libuuid1=2.36.1-7 libwebp6=0.6.1-2+b1 libx11-6=2:1.7.1-1 libx11-data=2:1.7.1-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.13-1.1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-6.7 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.0-1 libyaml-0-2=0.2.2-1 libzstd1=1.4.8+dfsg-2.1 libzzip-0-13=0.13.62-3.3 linux-libc-dev=5.10.40-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1k-1 patch=2.7.6-7 perl=5.32.1-4 perl-base=5.32.1-4 perl-modules-5.32=5.32.1-4 po-debconf=1.0.21+nmu1 preview-latex-style=12.2-1 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.9.2-3 python3-alabaster=0.7.8-1.1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-colorlog=4.7.2-1 python3-decorator=4.4.2-2 python3-distutils=3.9.2-1 python3-docutils=0.16+dfsg-4 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.3-1 python3-lib2to3=3.9.2-1 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.2-3 python3-networkx=2.5+ds-2 python3-packaging=20.9-2 python3-pkg-resources=52.0.0-3 python3-pygments=2.7.1+dfsg-2 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-setuptools=52.0.0-3 python3-six=1.16.0-1 python3-snowballstemmer=2.1.0-1 python3-sphinx=3.4.3-2 python3-sphinx-rtd-theme=0.5.1+dfsg-1 python3-tz=2021.1-1 python3-urllib3=1.26.4-1 python3-yaml=5.3.1-4 python3.9=3.9.2-1 python3.9-minimal=3.9.2-1 readline-common=8.1-2 sed=4.7-1 sensible-utils=0.0.14 sgml-base=1.30 sphinx-common=3.4.3-2 sphinx-rtd-theme-common=0.5.1+dfsg-1 sysvinit-utils=2.96-7 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.16 texlive-base=2020.20210202-3 texlive-binaries=2020.20200327.54578-7 texlive-fonts-recommended=2020.20210202-3 texlive-latex-base=2020.20210202-3 texlive-latex-extra=2020.20210202-3 texlive-latex-recommended=2020.20210202-3 texlive-pictures=2020.20210202-3 texlive-plain-generic=2020.20210202-3 tzdata=2021a-1 ucf=3.0043 util-linux=2.36.1-7 x11-common=1:7.7+22 xdg-utils=1.1.3-4.1 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 --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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210606T144214Z/ 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 macsyfinder=2.0~rc1-3 && mkdir -p /build/macsyfinder-lPXnIJ && dpkg-source --no-check -x /*.dsc /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && cd /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && { printf '%s' 'macsyfinder (2.0~rc1-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 03 Jun 2021 01:28:47 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/macsyfinder-lPXnIJ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1622683727" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/macsyfinder-lPXnIJ /tmp/macsyfinder-2.0~rc1-3+b1rx_ir3m_ bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210606T144214Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.6P27rTaDWX 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.6P27rTaDWX Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210606T144214Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210606T144214Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (711 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 ... 4667 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-12) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210606T144214Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.6P27rTaDWX Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210606T144214Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1150 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.6P27rTaDWX I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d macsyfinder=2.0~rc1-3 && mkdir -p /build/macsyfinder-lPXnIJ && dpkg-source --no-check -x /*.dsc /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && cd /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && { printf '%s' 'macsyfinder (2.0~rc1-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- all / amd64 / i386 Build Daemon (x86-conova-01) Thu, 03 Jun 2021 01:28:47 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/macsyfinder-lPXnIJ"' exec /tmp/mmdebstrap.6P27rTaDWX Reading package lists... NOTICE: 'macsyfinder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/macsyfinder.git Please use: git clone https://salsa.debian.org/med-team/macsyfinder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 29.6 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main macsyfinder 2.0~rc1-3 (dsc) [2348 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main macsyfinder 2.0~rc1-3 (tar) [29.6 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main macsyfinder 2.0~rc1-3 (diff) [8284 B] Fetched 29.6 MB in 25s (1208 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'macsyfinder_2.0~rc1-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting macsyfinder in /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 dpkg-source: info: unpacking macsyfinder_2.0~rc1.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.0~rc1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying allow_setuptools dpkg-source: info: applying debian_path dpkg-source: info: applying privacy I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1622683727" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.6P27rTaDWX dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0~rc1-3+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/system.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/database.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/__init__.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/package.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/definition_parser.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/search_genes.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/profile.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/cluster.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/report.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/hit.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/gene.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/registries.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/solution.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/serialization.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/utils.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/config.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/error.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy copying macsypy/model.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/__init__.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsydata.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py test running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating macsyfinder.egg-info writing macsyfinder.egg-info/PKG-INFO writing dependency_links to macsyfinder.egg-info/dependency_links.txt writing entry points to macsyfinder.egg-info/entry_points.txt writing requirements to macsyfinder.egg-info/requires.txt writing top-level names to macsyfinder.egg-info/top_level.txt writing manifest file 'macsyfinder.egg-info/SOURCES.txt' reading manifest file 'macsyfinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' writing manifest file 'macsyfinder.egg-info/SOURCES.txt' running build_ext test_Config (test_Config.TestConfig) ... ok test_Config_args (test_Config.TestConfig) ... ok test_Config_default_conf_file (test_Config.TestConfig) ... ok test_Config_file (test_Config.TestConfig) ... ok test_Config_file_bad_values (test_Config.TestConfig) ... ok test_Config_file_n_args (test_Config.TestConfig) ... ok test_bad_db_type (test_Config.TestConfig) ... ok test_bad_models_dir (test_Config.TestConfig) ... ok test_bad_sequence_db (test_Config.TestConfig) ... ok test_bad_topology (test_Config.TestConfig) ... ok test_bad_topology_file (test_Config.TestConfig) ... ok test_bad_values (test_Config.TestConfig) ... ok test_config_file_2_dict (test_Config.TestConfig) ... ok test_e_value_search (test_Config.TestConfig) ... ok test_hit_weights (test_Config.TestConfig) ... ok test_no_cut_ga (test_Config.TestConfig) ... ok test_out_dir (test_Config.TestConfig) ... ok test_previous_n_sequence_db (test_Config.TestConfig) ... ok test_previous_wo_cfg (test_Config.TestConfig) ... ok test_save (test_Config.TestConfig) ... ok test_str_2_tuple (test_Config.TestConfig) ... ok test_working_dir (test_Config.TestConfig) ... ok test_bad_gene_inter_gene_max_space_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_bad_max_nb_genes (test_DefinitionParser.TestModelParser) ... ok test_bad_min_genes_required (test_DefinitionParser.TestModelParser) ... ok test_bad_min_genes_required_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required_2 (test_DefinitionParser.TestModelParser) ... ok test_bad_min_mandatory_genes_required_4 (test_DefinitionParser.TestModelParser) ... ok test_gene_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_gene_no_name (test_DefinitionParser.TestModelParser) ... ok test_inter_gene_max_space_cfg (test_DefinitionParser.TestModelParser) ... ok test_invalid_homolog (test_DefinitionParser.TestModelParser) ... ok test_invalid_homolog_2 (test_DefinitionParser.TestModelParser) ... ok test_invalid_presence (test_DefinitionParser.TestModelParser) ... ok test_loner (test_DefinitionParser.TestModelParser) ... ok test_max_nb_genes_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_genes_required_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_mandatory_genes_required_cfg (test_DefinitionParser.TestModelParser) ... ok test_min_mandatory_genes_required_lesser_than_mandatory_genes (test_DefinitionParser.TestModelParser) ... ok test_multi_loci_cfg (test_DefinitionParser.TestModelParser) ... ok test_multi_system (test_DefinitionParser.TestModelParser) ... ok test_no_inter_gene_max_space (test_DefinitionParser.TestModelParser) ... ok test_parse_model_old_syntax (test_DefinitionParser.TestModelParser) ... ok test_parse_with_exchangeable (test_DefinitionParser.TestModelParser) ... ok test_wo_presence (test_DefinitionParser.TestModelParser) ... ok test_add_exchangeable (test_Exchangeable.TestExchangeable) ... ok test_alternate_of (test_Exchangeable.TestExchangeable) ... ok test_is_exchangeable (test_Exchangeable.TestExchangeable) ... ok test_loner (test_Exchangeable.TestExchangeable) ... ok test_model (test_Exchangeable.TestExchangeable) ... ok test_multi_system (test_Exchangeable.TestExchangeable) ... ok test_core_gene (test_Gene.TestCoreGene) ... ok test_str (test_Gene.TestGeneStatus) ... ok test_add_exchangeable (test_Gene.TestModelGene) ... ok test_alternate_of (test_Gene.TestModelGene) ... ok test_exhangeables (test_Gene.TestModelGene) ... ok test_hash (test_Gene.TestModelGene) ... ok test_init (test_Gene.TestModelGene) ... ok test_inter_gene_max_space (test_Gene.TestModelGene) test getter for inter_gene_max_space property ... ok test_is_Forbidden (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_is_accessory (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_is_exchangeable (test_Gene.TestModelGene) ... ok test_is_mandatory (test_Gene.TestModelGene) test if gene belong to model mandatory genes ... ok test_loner (test_Gene.TestModelGene) test getter for loner property ... ok test_model (test_Gene.TestModelGene) test getter/setter for model property ... ok test_multi_system (test_Gene.TestModelGene) test getter for multi_system property ... ok test_str (test_Gene.TestModelGene) ... ok test_unknown_attribute (test_Gene.TestModelGene) ... ok test_add_get_gene (test_GeneBank.Test) ... ok test_contains (test_GeneBank.Test) ... ok test_get_uniq_object (test_GeneBank.Test) ... ok test_iter (test_GeneBank.Test) ... ok test_build_force (test_Indexes.Test) ... ok test_build_my_indexes (test_Indexes.Test) ... ok test_build_no_idx (test_Indexes.Test) ... ok test_build_not_writable (test_Indexes.Test) ... ok test_build_with_idx (test_Indexes.Test) ... ok test_find_my_indexes (test_Indexes.Test) ... ok test_allowed_hits (test_LikelySystem.LikelySystemTest) ... ok test_forbidden_hits (test_LikelySystem.LikelySystemTest) ... ok test_hits (test_LikelySystem.LikelySystemTest) ... ok test_init (test_LikelySystem.LikelySystemTest) ... ok test_str (test_LikelySystem.LikelySystemTest) ... ok test_hits (test_LikelySystem.UnlikelySystemTest) ... ok test_init (test_LikelySystem.UnlikelySystemTest) ... ok test_reason (test_LikelySystem.UnlikelySystemTest) ... ok test_str (test_LikelySystem.UnlikelySystemTest) ... ok test_MacsyDefaults (test_MacsyDefaults.TestMacsyDefaults) ... ok test_MacsyDefaults_with_MACSY_DATA (test_MacsyDefaults.TestMacsyDefaults) ... ok test_ordered_match (test_MatchMaker.MatchMakerTest) ... ok test_sort_hits_by_status (test_MatchMaker.MatchMakerTest) ... ok test_unordered_match (test_MatchMaker.MatchMakerTest) ... ok test_accessor_mutator (test_Model.TestModel) ... ok test_eq (test_Model.TestModel) ... ok test_filter (test_Model.TestModel) ... ok test_fqn (test_Model.TestModel) ... ok test_get_gene (test_Model.TestModel) ... ok test_gt (test_Model.TestModel) ... ok test_hash (test_Model.TestModel) ... ok test_inter_gene_max_space (test_Model.TestModel) ... ok test_lt (test_Model.TestModel) ... ok test_max_nb_genes (test_Model.TestModel) ... ok test_min_genes_required (test_Model.TestModel) ... ok test_min_mandatory_genes_required (test_Model.TestModel) ... ok test_multi_loci (test_Model.TestModel) ... ok test_str (test_Model.TestModel) ... ok test_add_get_model (test_ModelBank.Test) ... ok test_contains (test_ModelBank.Test) ... ok test_get_uniq_object (test_ModelBank.Test) ... ok test_iter (test_ModelBank.Test) ... ok test_execute (test_Profile.TestProfile) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmmer_failed (test_Profile.TestProfile) ... ok test_execute_unknown_binary (test_Profile.TestProfile) ... ok test_ga_threshold (test_Profile.TestProfile) ... ok test_len (test_Profile.TestProfile) ... ok test_str (test_Profile.TestProfile) ... ok test_get_profile (test_ProfileFactory.TestProfileFactory) ... ok test_get_uniq_object (test_ProfileFactory.TestProfileFactory) ... ok test_unknow_profile (test_ProfileFactory.TestProfileFactory) ... ok test_hits (test_RejectedClusters.TestRejectedCluster) ... ok test_init (test_RejectedClusters.TestRejectedCluster) ... ok test_str (test_RejectedClusters.TestRejectedCluster) ... ok test_fill_gembase_min_max_default_topology (test_RepliconDB.Test) ... ok test_fill_gembase_min_max_with_topology (test_RepliconDB.Test) ... ok test_fill_ordered_replicon_min_max (test_RepliconDB.Test) ... ok test_fill_topology (test_RepliconDB.Test) ... ok test_get (test_RepliconDB.Test) ... ok test_getitem (test_RepliconDB.Test) ... ok test_in (test_RepliconDB.Test) ... ok test_items (test_RepliconDB.Test) ... ok test_iteritems (test_RepliconDB.Test) ... ok test_replicon_infos (test_RepliconDB.Test) ... ok test_extract (test_Report.TestGembaseHMMReport) ... ok test_extract_concurent (test_Report.TestGembaseHMMReport) ... ok test_extract (test_Report.TestGeneralHMMReport) ... ok test_extract_concurent (test_Report.TestGeneralHMMReport) ... ok test_HMMReport (test_Report.TestHMMReport) ... ok test_best_hit (test_Report.TestHMMReport) ... ok test_build_my_db (test_Report.TestHMMReport) ... ok test_fill_my_db (test_Report.TestHMMReport) ... ok test_hit_start (test_Report.TestHMMReport) ... ok test_parse_hmm_body (test_Report.TestHMMReport) ... ok test_parse_hmm_header (test_Report.TestHMMReport) ... ok test_save_extract (test_Report.TestHMMReport) ... ok test_str (test_Report.TestHMMReport) ... ok test_extract (test_Report.TestOrderedHMMReport) ... ok test_extract_concurent (test_Report.TestOrderedHMMReport) ... ok test_ClusteSystemTracker (test_System.SystemTest) ... ok test_HitSystemTracker (test_System.SystemTest) ... ok test_count (test_System.SystemTest) ... ok test_hits (test_System.SystemTest) ... ok test_init (test_System.SystemTest) ... ok test_is_compatible (test_System.SystemTest) ... ok test_loci (test_System.SystemTest) ... ok test_multi_loci (test_System.SystemTest) ... ok test_occurrence (test_System.SystemTest) ... ok test_position (test_System.SystemTest) ... ok test_score (test_System.SystemTest) ... ok test_wholeness (test_System.SystemTest) ... ok test_build_clusters (test_cluster.TestBuildCluster) ... ok test_contains (test_cluster.TestCluster) ... ok test_fulfilled_function (test_cluster.TestCluster) ... ok test_init (test_cluster.TestCluster) ... ok test_len (test_cluster.TestCluster) ... ok test_loner (test_cluster.TestCluster) ... ok test_merge (test_cluster.TestCluster) ... ok test_replicon_name (test_cluster.TestCluster) ... ok test_score (test_cluster.TestCluster) ... ok test_str (test_cluster.TestCluster) ... ok test_filter_loners (test_cluster.TestHitFunc) ... ok test_get_loners (test_cluster.TestHitFunc) ... ok test_gembase (test_functional_test.Test) ... ok test_model_unknown (test_functional_test.Test) ... ok test_no_db_type (test_functional_test.Test) ... ok test_no_models (test_functional_test.Test) ... ok test_no_seq_db (test_functional_test.Test) ... ok test_only_loners (test_functional_test.Test) ... ok test_ordered_circular (test_functional_test.Test) ... ok test_ordered_linear (test_functional_test.Test) ... ok test_ordered_multi_loci (test_functional_test.Test) ... ok test_ordered_multi_system (test_functional_test.Test) ... ok test_ordered_multi_system_loner_in_clust (test_functional_test.Test) ... ok test_ordered_single_loci (test_functional_test.Test) ... ok test_unordered (test_functional_test.Test) ... ok test_working_dir_exists (test_functional_test.Test) ... ok test_working_dir_exists_and_not_dir (test_functional_test.Test) ... ok test_get_best_hits (test_hit.GetBestHitTest) ... ok test_cmp (test_hit.HitTest) ... ok test_eq (test_hit.HitTest) ... ok test_get_position (test_hit.HitTest) ... ok test_hash (test_hit.HitTest) ... ok test_str (test_hit.HitTest) ... ok test_hit_weight_default (test_hit.HitWeightTest) ... ok test_hit_weight_not_default (test_hit.HitWeightTest) ... ok test_delegation (test_hit.ValidHitTest) ... ok test_eq (test_hit.ValidHitTest) ... ok test_hash (test_hit.ValidHitTest) ... ok test_init (test_hit.ValidHitTest) ... ok test_available (test_macsydata.TestMacsydata) ... ok test_build_argparser (test_macsydata.TestMacsydata) ... ok test_check (test_macsydata.TestMacsydata) ... ok test_check_with_errors (test_macsydata.TestMacsydata) ... ok test_check_with_warnings (test_macsydata.TestMacsydata) ... ok test_cite (test_macsydata.TestMacsydata) ... ok test_cmd_name (test_macsydata.TestMacsydata) ... ok test_download (test_macsydata.TestMacsydata) ... ok test_freeze (test_macsydata.TestMacsydata) ... ok test_info (test_macsydata.TestMacsydata) ... ok test_install_installed_package_corrupted (test_macsydata.TestMacsydata) ... ok test_install_local (test_macsydata.TestMacsydata) ... ok test_install_local_already_installed (test_macsydata.TestMacsydata) ... ok test_install_local_already_installed_force (test_macsydata.TestMacsydata) ... ok test_install_remote (test_macsydata.TestMacsydata) ... ok test_install_remote_already_in_local (test_macsydata.TestMacsydata) ... ok test_install_remote_already_in_local_force (test_macsydata.TestMacsydata) ... ok test_install_remote_lower_in_local (test_macsydata.TestMacsydata) ... ok test_install_remote_permision_error (test_macsydata.TestMacsydata) ... ok test_install_remote_spec_not_found (test_macsydata.TestMacsydata) ... ok test_install_remote_upper_in_local (test_macsydata.TestMacsydata) ... ok test_list (test_macsydata.TestMacsydata) ... ok test_list_outdated (test_macsydata.TestMacsydata) ... ok test_list_uptodate (test_macsydata.TestMacsydata) ... ok test_list_verbose (test_macsydata.TestMacsydata) ... ok test_search_in_pack_desc (test_macsydata.TestMacsydata) ... ok test_search_in_pack_desc_match_case (test_macsydata.TestMacsydata) ... ok test_search_in_pack_name (test_macsydata.TestMacsydata) ... ok test_search_in_pack_name_match_case (test_macsydata.TestMacsydata) ... ok test_search_reach_limit (test_macsydata.TestMacsydata) ... ok test_uninstall (test_macsydata.TestMacsydata) ... ok test_verbosity_to_log_level (test_macsydata.TestMacsydata) ... ok test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_likely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_list_models (test_macsyfinder.TestMacsyfinder) ... ok test_parse_args (test_macsyfinder.TestMacsyfinder) ... ok test_rejected_clst_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems_model_unknown (test_macsyfinder.TestMacsyfinder) ... ok test_search_systems_unordered (test_macsyfinder.TestMacsyfinder) ... ok test_solutions_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_systems_to_tsv (test_macsyfinder.TestMacsyfinder) ... ok test_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_unnlikely_systems_to_txt (test_macsyfinder.TestMacsyfinder) ... ok test_init (test_package.TestLocalModelIndex) ... ok test_init (test_package.TestModelIndex) ... ok test_check (test_package.TestPackage) ... ok test_check_metadata (test_package.TestPackage) ... ok test_check_no_readme_n_no_license (test_package.TestPackage) ... ok test_check_structure (test_package.TestPackage) ... ok test_check_structure_bad_path (test_package.TestPackage) ... ok test_check_structure_no_def (test_package.TestPackage) ... ok test_check_structure_no_license (test_package.TestPackage) ... ok test_check_structure_no_metadata (test_package.TestPackage) ... ok test_check_structure_no_profiles (test_package.TestPackage) ... ok test_check_structure_no_readme (test_package.TestPackage) ... ok test_find_readme (test_package.TestPackage) ... ok test_help (test_package.TestPackage) ... ok test_info (test_package.TestPackage) ... ok test_init (test_package.TestPackage) ... ok test_metadata (test_package.TestPackage) ... ok test_parse_arch_path (test_package.TestPackageFunc) ... ok test_download (test_package.TestRemoteModelIndex) ... ok test_get_metadata (test_package.TestRemoteModelIndex) ... ok test_init (test_package.TestRemoteModelIndex) ... ok test_list_package_vers (test_package.TestRemoteModelIndex) ... ok test_list_packages (test_package.TestRemoteModelIndex) ... ok test_remote_exists (test_package.TestRemoteModelIndex) ... ok test_unarchive (test_package.TestRemoteModelIndex) ... ok test_url_json (test_package.TestRemoteModelIndex) ... ok test_url_json_reach_limit (test_package.TestRemoteModelIndex) ... ok test_DefinitionLocationn (test_registries.DefinitionLocationTest) ... ok test_add_submodel (test_registries.DefinitionLocationTest) ... ok test_all (test_registries.DefinitionLocationTest) ... ok test_eq (test_registries.DefinitionLocationTest) ... ok test_family_name (test_registries.DefinitionLocationTest) ... ok test_greater (test_registries.DefinitionLocationTest) ... ok test_hash (test_registries.DefinitionLocationTest) ... ok test_lesser (test_registries.DefinitionLocationTest) ... ok test_root_name (test_registries.DefinitionLocationTest) ... ok test_separator (test_registries.DefinitionLocationTest) ... ok test_split_fqn (test_registries.DefinitionLocationTest) ... ok test_str (test_registries.DefinitionLocationTest) ... ok test_ModelLocation (test_registries.ModelLocationTest) ... ok test_get_all_definitions (test_registries.ModelLocationTest) ... ok test_get_definition (test_registries.ModelLocationTest) ... ok test_get_definitions (test_registries.ModelLocationTest) ... ok test_get_profile (test_registries.ModelLocationTest) ... ok test_str (test_registries.ModelLocationTest) ... ok test_add_get (test_registries.ModelRegistryTest) ... ok test_models (test_registries.ModelRegistryTest) ... ok test_scan_models_dir (test_registries.ModelRegistryTest) ... ok test_str (test_registries.ModelRegistryTest) ... ok test_join_def_path (test_registries.RegitriesUtilsTest) ... ok test_split_def_name (test_registries.RegitriesUtilsTest) ... ok test_search (test_search_genes.TestSearchGenes) ... ok test_search_recover (test_search_genes.TestSearchGenes) ... ok test_LikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok test_SolutionSerializer_tsv (test_serialization.SerializationTest) ... ok test_SystemSerializer_str (test_serialization.SerializationTest) ... ok test_SystemSerializer_tsv (test_serialization.SerializationTest) ... ok test_UnlikelySystemSerializer_txt (test_serialization.SerializationTest) ... ok test_find_best_solution (test_solution.SolutionExplorerTest) ... ok test_get_def_to_detect (test_utils.TestUtils) ... ok ---------------------------------------------------------------------- Ran 304 tests in 43.749s OK (skipped=1) create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder running install running build running build_py running install_lib moving /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py.tmp -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9 creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/system.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/database.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/__init__.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/package.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/definition_parser.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/search_genes.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/profile.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/cluster.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/report.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/hit.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/gene.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/registries.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/solution.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/serialization.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/utils.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/config.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/error.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/model.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/__init__.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/macsydata.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/.pybuild/cpython3_3.9/build/macsypy/scripts/macsyfinder.py -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/system.py to system.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/database.py to database.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/__init__.py to __init__.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/package.py to package.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/search_genes.py to search_genes.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/profile.py to profile.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/cluster.py to cluster.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/report.py to report.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/hit.py to hit.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/gene.py to gene.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/registries.py to registries.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/solution.py to solution.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/serialization.py to serialization.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/utils.py to utils.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/config.py to config.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/error.py to error.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/model.py to model.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-39.pyc byte-compiling /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-39.pyc running install_data creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.topology -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/results.macsyfinder.json -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.fasta -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru.001.c01.11.prt -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/psae.001.c01.13.prt -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru_psae.001.c01.fasta -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/esco.030.p01.12.prt -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/data_replicons_topology_Prokaryotes_0213.dat -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/base creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/models copying data/models/readme -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/share/macsyfinder/data/models creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/etc creating /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/etc/macsyfinder copying etc/macsyfinder.conf -> /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/etc/macsyfinder running install_egg_info running egg_info writing macsyfinder.egg-info/PKG-INFO writing dependency_links to macsyfinder.egg-info/dependency_links.txt writing entry points to macsyfinder.egg-info/entry_points.txt writing requirements to macsyfinder.egg-info/requires.txt writing top-level names to macsyfinder.egg-info/top_level.txt reading manifest file 'macsyfinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' writing manifest file 'macsyfinder.egg-info/SOURCES.txt' Copying macsyfinder.egg-info to /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsyfinder-2.0rc1.egg-info Skipping SOURCES.txt running install_scripts Installing macsydata script to /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/bin Installing macsyfinder script to /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/bin I: pybuild pybuild:310: mv /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/usr/etc /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/macsyfinder/etc && cd /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/doc && make html latexpdf make[1]: Entering directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/doc' Running Sphinx v3.4.3 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 30 source files that are out of date updating environment: [new config] 30 added, 0 changed, 0 removed reading sources... [ 3%] developer_guide/api/cluster reading sources... [ 6%] developer_guide/api/config reading sources... [ 10%] developer_guide/api/database reading sources... [ 13%] developer_guide/api/definition_parser reading sources... [ 16%] developer_guide/api/error reading sources... [ 20%] developer_guide/api/gene reading sources... [ 23%] developer_guide/api/hit reading sources... [ 26%] developer_guide/api/index reading sources... [ 30%] developer_guide/api/model reading sources... [ 33%] developer_guide/api/package reading sources... [ 36%] developer_guide/api/profile reading sources... [ 40%] developer_guide/api/registries reading sources... [ 43%] developer_guide/api/report reading sources... [ 46%] developer_guide/api/search_genes reading sources... [ 50%] developer_guide/api/serialization reading sources... [ 53%] developer_guide/api/solution reading sources... [ 56%] developer_guide/api/system reading sources... [ 60%] developer_guide/api/utils reading sources... [ 63%] developer_guide/index reading sources... [ 66%] developer_guide/overview reading sources... [ 70%] index reading sources... [ 73%] user_guide/functioning reading sources... [ 76%] user_guide/gembase_convention reading sources... [ 80%] user_guide/index reading sources... [ 83%] user_guide/input reading sources... [ 86%] user_guide/installation reading sources... [ 90%] user_guide/model_definition reading sources... [ 93%] user_guide/new_v2 reading sources... [ 96%] user_guide/outputs reading sources... [100%] user_guide/quickstart /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 3%] developer_guide/api/cluster writing output... [ 6%] developer_guide/api/config writing output... [ 10%] developer_guide/api/database writing output... [ 13%] developer_guide/api/definition_parser writing output... [ 16%] developer_guide/api/error writing output... [ 20%] developer_guide/api/gene writing output... [ 23%] developer_guide/api/hit writing output... [ 26%] developer_guide/api/index writing output... [ 30%] developer_guide/api/model writing output... [ 33%] developer_guide/api/package writing output... [ 36%] developer_guide/api/profile writing output... [ 40%] developer_guide/api/registries writing output... [ 43%] developer_guide/api/report writing output... [ 46%] developer_guide/api/search_genes writing output... [ 50%] developer_guide/api/serialization writing output... [ 53%] developer_guide/api/solution writing output... [ 56%] developer_guide/api/system writing output... [ 60%] developer_guide/api/utils writing output... [ 63%] developer_guide/index writing output... [ 66%] developer_guide/overview writing output... [ 70%] index writing output... [ 73%] user_guide/functioning writing output... [ 76%] user_guide/gembase_convention writing output... [ 80%] user_guide/index writing output... [ 83%] user_guide/input writing output... [ 86%] user_guide/installation writing output... [ 90%] user_guide/model_definition writing output... [ 93%] user_guide/new_v2 writing output... [ 96%] user_guide/outputs writing output... [100%] user_guide/quickstart generating indices... genindex py-modindex done highlighting module code... [ 5%] collections highlighting module code... [ 10%] macsypy.cluster highlighting module code... [ 15%] macsypy.config highlighting module code... [ 21%] macsypy.database highlighting module code... [ 26%] macsypy.definition_parser highlighting module code... [ 31%] macsypy.error highlighting module code... [ 36%] macsypy.gene highlighting module code... [ 42%] macsypy.hit highlighting module code... [ 47%] macsypy.model highlighting module code... [ 52%] macsypy.package highlighting module code... [ 57%] macsypy.profile highlighting module code... [ 63%] macsypy.registries highlighting module code... [ 68%] macsypy.report highlighting module code... [ 73%] macsypy.search_genes highlighting module code... [ 78%] macsypy.serialization highlighting module code... [ 84%] macsypy.solution highlighting module code... [ 89%] macsypy.system highlighting module code... [ 94%] macsypy.utils highlighting module code... [100%] namedtuple_RepliconInfo writing additional pages... search done copying images... [ 10%] _static/gene_obj_interaction.svg copying images... [ 20%] _static/macsyfinder_classes.svg copying images... [ 30%] _static/figure_main-2.svg copying images... [ 40%] _static/msf_functionning_step1.svg copying images... [ 50%] _static/msf_functionning_step2.svg copying images... [ 60%] _static/msf_functionning_step3.svg copying images... [ 70%] _static/msf_functionning_step4.svg copying images... [ 80%] _static/msf_functionning_step5.svg copying images... [ 90%] _static/MSF_modelling.svg copying images... [100%] user_guide/../_static/under_construction.gif copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in build/html. Running Sphinx v3.4.3 making output directory... done loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found processing macsyfinder.tex... index user_guide/index user_guide/new_v2 user_guide/installation user_guide/quickstart user_guide/input user_guide/gembase_convention user_guide/outputs user_guide/model_definition user_guide/functioning developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/registries developer_guide/api/definition_parser developer_guide/api/model developer_guide/api/gene developer_guide/api/profile developer_guide/api/hit developer_guide/api/cluster developer_guide/api/system developer_guide/api/report developer_guide/api/search_genes developer_guide/api/solution developer_guide/api/serialization developer_guide/api/database developer_guide/api/error developer_guide/api/utils developer_guide/api/package resolving references... done writing... done copying images... [ 10%] _static/figure_main-2.png copying images... [ 20%] user_guide/../_static/under_construction.jpeg copying images... [ 30%] _static/MSF_modelling.pdf copying images... [ 40%] _static/msf_functionning_step1.pdf copying images... [ 50%] _static/msf_functionning_step2.pdf copying images... [ 60%] _static/msf_functionning_step3.pdf copying images... [ 70%] _static/msf_functionning_step4.pdf copying images... [ 80%] _static/msf_functionning_step5.pdf copying images... [ 90%] _static/macsyfinder_classes.pdf copying images... [100%] _static/gene_obj_interaction.pdf copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). make[2]: Entering directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/doc/build/latex' latexmk -pdf -dvi- -ps- 'macsyfinder.tex' Rc files read: /etc/LatexMk ./latexmkrc Latexmk: This is Latexmk, John Collins, 29 September 2020, version: 4.70b. Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./macsyfinder.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-01-09> xparse <2020-03-03> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2020/04/10 v1.4m Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.7182818 (TeX Live 2020/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.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 0.06943pt) Font metrics written on tcrm1000.tfm. 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Output written on tctt0900.600gf (128 characters, 17564 bytes). Transcript written on tctt0900.log. mktexpk: /build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/debian/.debhelper/generated/_source/home/.texlive2020/texmf-var/fonts/pk/ljfour/jknappen/ec/tctt0900.600pk: successfully generated. Output written on macsyfinder.pdf (97 pages, 1311924 bytes). Transcript written on macsyfinder.log. Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Missing input file: 'macsyfinder.ind' from line 'No file macsyfinder.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: List of undefined refs and citations: Reference `developer_guide/api/cluster:module-macsypy.cluster' on page 93 undefined on input line 7876 Reference `developer_guide/api/config:module-macsypy.config' on page 93 undefined on input line 7877 Reference `developer_guide/api/database:module-macsypy.database' on page 93 undefined on input line 7878 Reference `developer_guide/api/definition_parser:module-macsypy.definition_parser' on page 93 undefined on input line 7879 Reference `developer_guide/api/error:module-macsypy.error' on page 93 undefined on input line 7880 Reference `developer_guide/api/hit:module-macsypy.hit' on page 93 undefined on input line 7881 Reference `developer_guide/api/package:module-macsypy.package' on page 93 undefined on input line 7882 Reference `developer_guide/api/registries:module-macsypy.registries' on page 93 undefined on input line 7883 Reference `developer_guide/api/search_genes:module-macsypy.search_genes' on page 93 undefined on input line 7884 Reference `developer_guide/api/serialization:module-macsypy.serialization' on page 93 undefined on input line 7885 Reference `developer_guide/api/solution:module-macsypy.solution' on page 93 undefined on input line 7886 Reference `developer_guide/api/system:module-macsypy.system' on page 93 undefined on input line 7887 Reference `developer_guide/api/utils:module-macsypy.utils' on page 93 undefined on input line 7888 Rule 'makeindex macsyfinder.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'macsyfinder.idx' ------------ Run number 1 of rule 'makeindex macsyfinder.idx' ------------ ------------ Running 'makeindex -s python.ist -o "macsyfinder.ind" "macsyfinder.idx"' ------------ Latexmk: Examining 'macsyfinder.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex macsyfinder.idx'... 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[3] [4] [5] [6] [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/pcr/m/n/10 --sequence-db metagenome.fasta --models-dir my-models --models Underfull \hbox (badness 10000) in paragraph at lines 675--676 []\T1/pcr/m/n/10 macsyfinder --db-type ordered-replicon --sequence-db mygenome. fasta [11 <./under_construction.jpeg>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \vbox (badness 1874) detected at line 815 [13] Overfull \vbox (13.68166pt too high) detected at line 861 [14] Overfull \vbox (13.68166pt too high) detected at line 913 [15] [16] [17] Overfull \vbox (0.97772pt too high) detected at line 1222 [18] [19] [20] [21] Underfull \vbox (badness 10000) detected at line 1485 Overfull \vbox (16.52583pt too high) detected at line 1485 [22] [23] [24] [25] Underfull \vbox (badness 2351) detected at line 1758 Overfull \vbox (20.53116pt too high) detected at line 1758 [26] Overfull \vbox (13.98015pt too high) detected at line 1800 [27] [28] [29] [30] [31] [32 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2066--2067 []\T1/ptm/b/n/10 inter_gene_max_space\T1/ptm/m/n/10 : an \T1/ptm/m/it/10 in-te- ger \T1/ptm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- Overfull \vbox (1.72583pt too high) detected at line 2111 [33] [34] [35] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. 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[76] [77] [78] [79] [80] [81] [82] Overfull \hbox (27.20956pt too wide) in paragraph at lines 6995--6998 []\T1/ptm/m/n/10 replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_l oci\tsys_wholeness\tsys_score Overfull \hbox (44.58925pt too wide) in paragraph at lines 6995--6998 \T1/ptm/m/n/10 \tsys_occ\thit_gene_ref.alternate_of\thit_status\thit_seq_len\th it_i_eval\thit_score\thit_profile_cov [83] Underfull \hbox (badness 10000) in paragraph at lines 7214--7215 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by the con- Underfull \hbox (badness 10000) in paragraph at lines 7228--7230 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by con- [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 []\T1/pcr/b/n/10 models \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 list of tuple with the following structure: Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 \T1/pcr/m/sl/10 [(\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 model_1\TS1/pcr/m/sl/10 '\T 1/pcr/m/sl/10 , (\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 def1, def2, ..)), (\TS1/pcr/ m/sl/10 '\T1/pcr/m/sl/10 model_2\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , (\TS1/pcr/m /sl/10 '\T1/pcr/m/sl/10 def1\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , ..)), [86] [87] [88] [89] [90] Chapter 3. [91] [92] [93] (./macsyfinder.ind [94] Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databa se.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model. ModelBank Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/pcr/m/n/10 __eq__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databas e.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 21--22 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model.M odelBank Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/pcr/m/n/10 __getitem__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registr ies.ModelRegistry Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 __gt__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 36--38 []\T1/pcr/m/n/10 __hash__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .DefinitionLocation Overfull \hbox (8.23074pt too wide) in paragraph at lines 43--45 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.definition _parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 53--55 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Ab stractModelIndex Underfull \hbox (badness 10000) in paragraph at lines 55--56 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Lo calModelIndex Underfull \hbox (badness 10000) in paragraph at lines 57--58 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Re moteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 60--62 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .DefinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 62--63 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .ModelLocation Underfull \hbox (badness 10000) in paragraph at lines 63--64 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries .ModelRegistry Overfull \hbox (10.36pt too wide) in paragraph at lines 65--67 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.serializat ion.TsvSolutionSerializer Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Abs tractSetOfHits Underfull \hbox (badness 10000) in paragraph at lines 68--69 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Abs tractUnordered Underfull \hbox (badness 10000) in paragraph at lines 69--71 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Clu sterSystemTracker Underfull \hbox (badness 10000) in paragraph at lines 71--72 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Hit SystemTracker [95] Underfull \hbox (badness 10000) in paragraph at lines 73--74 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Ord eredMatchMaker Underfull \hbox (badness 10000) in paragraph at lines 74--75 []\T1/pcr/m/n/10 __init__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.system.Rej ectedClusters Underfull \hbox (badness 10000) in paragraph at lines 84--86 []\T1/pcr/m/n/10 __lt__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries.D efinitionLocation Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/pcr/m/n/10 __new__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Re pliconInfo static Underfull \hbox (badness 10000) in paragraph at lines 89--91 []\T1/pcr/m/n/10 __new__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Abs tractModelIndex Underfull \hbox (badness 10000) in paragraph at lines 97--99 []\T1/pcr/m/n/10 __str__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.registries. 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HMMReport Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 _fill_ordered_min_max() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 _find_readme() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.packag e.Package Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 _get_model_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/pcr/m/n/10 _load_metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.pack age.Package Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 _make() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Repl iconInfo class Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/pcr/m/n/10 _parse_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 175--177 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 177--179 []\T1/pcr/m/n/10 _parse_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 177--179 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/pcr/m/n/10 _parse_hmm_body() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.rep ort.HMMReport Underfull \hbox (badness 10000) in paragraph at lines 180--181 []\T1/pcr/m/n/10 _parse_hmm_header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 _profile_features() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.p rofile.Profile Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/pcr/m/n/10 _scan_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 185--187 []\T1/pcr/m/n/10 _scan_profiles() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\T1/pcr/m/n/10 _set_inter_gene_max_space() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 ma c- Underfull \hbox (badness 10000) in paragraph at lines 190--191 []\T1/pcr/m/n/10 _set_max_nb_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.c onfig.Config Underfull \hbox (badness 10000) in paragraph at lines 191--193 []\T1/pcr/m/n/10 _set_min_genes_required() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 193--195 []\T1/pcr/m/n/10 _set_min_mandatory_genes_required() Underfull \hbox (badness 10000) in paragraph at lines 196--197 []\T1/pcr/m/n/10 _set_models_dir() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.con fig.Config Underfull \hbox (badness 10000) in paragraph at lines 197--198 []\T1/pcr/m/n/10 _set_multi_loci() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.con fig.Config Underfull \hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 _set_replicon_topology() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 200--201 []\T1/pcr/m/n/10 _set_sequence_db() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.co nfig.Config Underfull \hbox (badness 10000) in paragraph at lines 201--202 []\T1/pcr/m/n/10 _set_topology_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. config.Config Underfull \hbox (badness 10000) in paragraph at lines 203--204 []\T1/pcr/m/n/10 _url_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.R emoteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 accessory_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 214--215 []\T1/pcr/m/n/10 add_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.ge ne.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 add_subdefinition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 sypy.registries.DefinitionLocation method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 allowed_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 219--221 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 221--222 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.E xchangeable Underfull \hbox (badness 10000) in paragraph at lines 222--223 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 check_consistency() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 233--235 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser [97] Underfull \hbox (badness 10000) in paragraph at lines 250--251 []\T1/pcr/m/n/10 DefinitionParser \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in mac- Underfull \hbox (badness 10000) in paragraph at lines 252--253 []\T1/pcr/m/n/10 download() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.Re moteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 260--261 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Gemb aseHMMReport Underfull \hbox (badness 10000) in paragraph at lines 261--262 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Gene ralHMMReport Underfull \hbox (badness 10000) in paragraph at lines 263--264 []\T1/pcr/m/n/10 extract() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.report.Orde redHMMReport Underfull \hbox (badness 10000) in paragraph at lines 271--272 []\T1/pcr/m/n/10 find_best_solutions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le mac- Underfull \hbox (badness 10000) in paragraph at lines 272--273 []\T1/pcr/m/n/10 find_my_indexes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.dat abase.Indexes Underfull \hbox (badness 10000) in paragraph at lines 273--275 []\T1/pcr/m/n/10 forbidden_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 273--275 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 275--276 []\T1/pcr/m/n/10 fulfilled_function() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. cluster.Cluster Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 get_all_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 get_definition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 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[3] [4] [5] [6] [7] [8] [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 667--669 \T1/pcr/m/n/10 --sequence-db metagenome.fasta --models-dir my-models --models Underfull \hbox (badness 10000) in paragraph at lines 675--676 []\T1/pcr/m/n/10 macsyfinder --db-type ordered-replicon --sequence-db mygenome. fasta [11 <./under_construction.jpeg>] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [12] Underfull \vbox (badness 1874) detected at line 815 [13] Overfull \vbox (13.68166pt too high) detected at line 861 [14] Overfull \vbox (13.68166pt too high) detected at line 913 [15] [16] [17] Overfull \vbox (0.97772pt too high) detected at line 1222 [18] [19] [20] [21] Underfull \vbox (badness 10000) detected at line 1485 Overfull \vbox (16.52583pt too high) detected at line 1485 [22] [23] [24] [25] Underfull \vbox (badness 2351) detected at line 1758 Overfull \vbox (20.53116pt too high) detected at line 1758 [26] Overfull \vbox (13.98015pt too high) detected at line 1800 [27] [28] [29] [30] [31] [32 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2066--2067 []\T1/ptm/b/n/10 inter_gene_max_space\T1/ptm/m/n/10 : an \T1/ptm/m/it/10 in-te- ger \T1/ptm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- Overfull \vbox (1.72583pt too high) detected at line 2111 [33] [34] [35] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. 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[58] [59] Underfull \hbox (badness 10000) in paragraph at lines 4336--4336 []\T1/ptm/m/it/10 fqn\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ter_gene_max_space\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 min_mandatory_genes_required=None\T1/ptm/m/n/10 , [60] [61] [62] [63] Underfull \hbox (badness 10000) in paragraph at lines 4798--4798 []\T1/ptm/m/it/10 gene\T1/ptm/m/n/10 , \T1/ptm/m/it/10 model\T1/ptm/m/n/10 , \T 1/ptm/m/it/10 loner=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 multi_system=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 in- [64] [65] [66] [67] [68] [69 <./gene_obj_interaction.pdf>] [70] [71] [72] [73 <./inheritance-8ba7a954ca815e13e62e2f63ee3be443ea836ee9.pdf>] [74] [75] Underfull \hbox (badness 10000) in paragraph at lines 6303--6305 [][][]\T1/pcr/m/sl/10 macsypy.system.System[][] \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 macsypy.cluster. [76] [77] [78] [79] [80] [81] [82] Overfull \hbox (27.20956pt too wide) in paragraph at lines 6995--6998 []\T1/ptm/m/n/10 replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_l oci\tsys_wholeness\tsys_score Overfull \hbox (44.58925pt too wide) in paragraph at lines 6995--6998 \T1/ptm/m/n/10 \tsys_occ\thit_gene_ref.alternate_of\thit_status\thit_seq_len\th it_i_eval\thit_score\thit_profile_cov [83] Underfull \hbox (badness 10000) in paragraph at lines 7214--7215 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by the con- Underfull \hbox (badness 10000) in paragraph at lines 7228--7230 []\T1/pcr/b/n/10 default_topology \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 string\T1/ptm /m/n/10 ) ^^U the topol-ogy pro-vided by con- [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 []\T1/pcr/b/n/10 models \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 list of tuple with the following structure: Underfull \hbox (badness 10000) in paragraph at lines 7502--7504 \T1/pcr/m/sl/10 [(\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 model_1\TS1/pcr/m/sl/10 '\T 1/pcr/m/sl/10 , (\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 def1, def2, ..)), (\TS1/pcr/ m/sl/10 '\T1/pcr/m/sl/10 model_2\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , (\TS1/pcr/m /sl/10 '\T1/pcr/m/sl/10 def1\TS1/pcr/m/sl/10 '\T1/pcr/m/sl/10 , ..)), [86] [87] [88] [89] [90] Chapter 3. [91] [92] [93] (./macsyfinder.ind [94] Underfull \hbox (badness 10000) in paragraph at lines 10--11 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.databa se.RepliconDB Underfull \hbox (badness 10000) in paragraph at lines 12--13 []\T1/pcr/m/n/10 __contains__() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.model. 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HMMReport Underfull \hbox (badness 10000) in paragraph at lines 166--168 []\T1/pcr/m/n/10 _fill_ordered_min_max() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 169--170 []\T1/pcr/m/n/10 _find_readme() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.packag e.Package Underfull \hbox (badness 10000) in paragraph at lines 170--172 []\T1/pcr/m/n/10 _get_model_node() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 170--172 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/pcr/m/n/10 _load_metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.pack age.Package Underfull \hbox (badness 10000) in paragraph at lines 174--175 []\T1/pcr/m/n/10 _make() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database.Repl iconInfo class Underfull \hbox (badness 10000) in paragraph at lines 175--177 []\T1/pcr/m/n/10 _parse_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 175--177 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 177--179 []\T1/pcr/m/n/10 _parse_genes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 177--179 \T1/ptm/m/it/10 sypy.definition_parser.DefinitionParser Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/pcr/m/n/10 _parse_hmm_body() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.rep ort.HMMReport Underfull \hbox (badness 10000) in paragraph at lines 180--181 []\T1/pcr/m/n/10 _parse_hmm_header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 181--182 []\T1/pcr/m/n/10 _profile_features() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.p rofile.Profile Underfull \hbox (badness 10000) in paragraph at lines 183--185 []\T1/pcr/m/n/10 _scan_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox 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\hbox (badness 10000) in paragraph at lines 198--200 []\T1/pcr/m/n/10 _set_replicon_topology() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 200--201 []\T1/pcr/m/n/10 _set_sequence_db() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.co nfig.Config Underfull \hbox (badness 10000) in paragraph at lines 201--202 []\T1/pcr/m/n/10 _set_topology_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. config.Config Underfull \hbox (badness 10000) in paragraph at lines 203--204 []\T1/pcr/m/n/10 _url_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.package.R emoteModelIndex Underfull \hbox (badness 10000) in paragraph at lines 210--212 []\T1/pcr/m/n/10 accessory_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 210--212 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 214--215 []\T1/pcr/m/n/10 add_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.ge ne.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/pcr/m/n/10 add_subdefinition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 217--219 \T1/ptm/m/it/10 sypy.registries.DefinitionLocation method\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 219--221 []\T1/pcr/m/n/10 allowed_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 219--221 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 221--222 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.E xchangeable Underfull \hbox (badness 10000) in paragraph at lines 222--223 []\T1/pcr/m/n/10 alternate_of() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 233--235 []\T1/pcr/m/n/10 check_consistency() 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[]\T1/pcr/m/n/10 find_best_solutions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le mac- Underfull \hbox (badness 10000) in paragraph at lines 272--273 []\T1/pcr/m/n/10 find_my_indexes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.dat abase.Indexes Underfull \hbox (badness 10000) in paragraph at lines 273--275 []\T1/pcr/m/n/10 forbidden_hits() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 273--275 \T1/ptm/m/it/10 sypy.system.AbstractUnordered prop-erty\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 275--276 []\T1/pcr/m/n/10 fulfilled_function() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy. cluster.Cluster Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/pcr/m/n/10 get_all_definitions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/pcr/m/n/10 get_definition() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac- Underfull \hbox (badness 10000) in paragraph at lines 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paragraph at lines 323--324 []\T1/pcr/m/n/10 is_accessory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene [98] Underfull \hbox (badness 10000) in paragraph at lines 325--326 []\T1/pcr/m/n/10 is_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gen e.Exchangeable Underfull \hbox (badness 10000) in paragraph at lines 326--327 []\T1/pcr/m/n/10 is_exchangeable() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gen e.ModelGene Underfull \hbox (badness 10000) in paragraph at lines 327--328 []\T1/pcr/m/n/10 is_forbidden() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 328--329 []\T1/pcr/m/n/10 is_mandatory() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.gene.M odelGene Underfull \hbox (badness 10000) in paragraph at lines 330--331 []\T1/pcr/m/n/10 iteritems() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 mac-sypy.database. 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Transcript written on macsyfinder.log. Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: Examining 'macsyfinder.log' === TeX engine is 'pdfTeX' Latexmk: All targets (macsyfinder.pdf) are up-to-date make[2]: Leaving directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/doc/build/latex' make[1]: Leaving directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1/doc' dh_installdocs -a -O--buildsystem=pybuild dh_sphinxdoc -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1' dh_fixperms find debian -name "test_*.fa" -executable -exec chmod -x \{\} \; find debian -name "*.prt" -executable -exec chmod -x \{\} \; make[1]: Leaving directory '/build/macsyfinder-lPXnIJ/macsyfinder-2.0-rc1' dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'macsyfinder' in '../macsyfinder_2.0~rc1-3+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../macsyfinder_2.0~rc1-3+b1_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/macsyfinder-lPXnIJ /tmp/macsyfinder-2.0~rc1-3+b1rx_ir3m_ I: cleaning package lists and apt cache... W: deleting files in /tmp: test_macsyfinder_search_genes I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.6P27rTaDWX... I: success in 777.6705 seconds md5: Value of 'md5' differs for macsyfinder_2.0~rc1-3+b1_amd64.deb md5: Size differs for macsyfinder_2.0~rc1-3+b1_amd64.deb sha1: Value of 'sha1' differs for macsyfinder_2.0~rc1-3+b1_amd64.deb sha1: Size differs for macsyfinder_2.0~rc1-3+b1_amd64.deb sha256: Value of 'sha256' differs for macsyfinder_2.0~rc1-3+b1_amd64.deb sha256: Size differs for macsyfinder_2.0~rc1-3+b1_amd64.deb Checksums: FAIL diffoscope run passed