Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/macsyfinder/macsyfinder_2.0~rc4-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/macsyfinder-2.0~rc4-1pask2mf8/macsyfinder_2.0~rc4-1_amd64.buildinfo Get source package info: macsyfinder=2.0~rc4-1 Source URL: http://snapshot.notset.fr/mr/package/macsyfinder/2.0~rc4-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b2 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 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=10.3.0-11 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 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=10.3.0-11 gcc=4:10.2.1-1 gcc-10=10.3.0-11 gcc-10-base=10.3.0-11 gcc-11-base=11.2.0-8 gettext=0.21-4 gettext-base=0.21-4 graphviz=2.42.2-5 grep=3.7-1 groff-base=1.22.4-7 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=1:4.75-0.1 libacl1=2.3.1-1 libann0=1.1.2+doc-7 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-8 libatomic1=11.2.0-8 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-7 libblas3=3.10.0-1 libblkid1=2.37.2-3 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-8 libcdt5=2.42.2-5 libcgraph6=2.42.2-5 libcom-err2=1.46.4-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate0=1.7-2 libdivsufsort3=2.0.1-5 libdpkg-perl=1.20.9 libelf1=0.185-2 libexpat1=2.4.1-2+b1 libffi8=3.4.2-2 libfile-stripnondeterminism-perl=1.12.0-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfontenc1=1:1.1.4-1 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.3.0-11 libgcc-s1=11.2.0-8 libgcrypt20=1.9.4-3+b1 libgd3=2.3.0-2 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgfortran5=11.2.0-8 libglib2.0-0=2.70.0-1+b1 libgmp10=2:6.2.1+dfsg-2 libgomp1=11.2.0-8 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 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=67.1-7 libisl23=0.23-1 libitm1=11.2.0-8 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=4.2.0-2 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkpathsea6=2021.20210626.59705-1 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblab-gamut1=2.42.2-5 liblapack3=3.10.0-1 liblsan0=11.2.0-8 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=2.37.2-3 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.2+20210905-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpango-1.0-0=1.48.10+ds1-1 libpangocairo-1.0-0=1.48.10+ds1-1 libpangoft2-1.0-0=1.48.10+ds1-1 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=5.32.1-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libptexenc1=2021.20210626.59705-1 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.7-4 libpython3.9-stdlib=3.9.7-4 libquadmath0=11.2.0-8 libreadline8=8.1-2 libseccomp2=2.5.2-2 libselinux1=3.1-3 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.37.2-3 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-11 libstdc++6=11.2.0-8 libsub-override-perl=0.09-2 libsynctex2=2021.20210626.59705-1 libsystemd0=247.9-4 libteckit0=2.5.10+ds1-3 libtexlua53=2021.20210626.59705-1 libtexluajit2=2021.20210626.59705-1 libthai-data=0.1.28-4.1 libthai0=0.1.28-4.1 libtiff5=4.3.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-8 libubsan1=11.2.0-8 libuchardet0=0.0.7-1 libudev1=247.9-4 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libwebp6=0.6.1-2.1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 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=2:1.3.4-1 libxi6=2:1.8-1 libxml2=2.9.12+dfsg-5 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=0.13.72+dfsg.1-1.1 linux-libc-dev=5.14.9-2 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+20210905-1 ncurses-bin=6.2+20210905-1 openssl=1.1.1l-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 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=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-colorlog=6.4.1-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-distutils=3.9.7-1 python3-docutils=0.16+dfsg-4 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=3.0.1-2 python3-lib2to3=3.9.7-1 python3-markupsafe=2.0.1-2 python3-minimal=3.9.2-3 python3-networkx=2.5+ds-2 python3-numpy=1:1.19.5-1 python3-packaging=20.9-2 python3-pandas=1.1.5+dfsg-2 python3-pandas-lib=1.1.5+dfsg-2 python3-pkg-resources=52.0.0-4 python3-pygments=2.7.1+dfsg-2.1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-setuptools=52.0.0-4 python3-six=1.16.0-2 python3-snowballstemmer=2.1.0-2 python3-sphinx=4.2.0-2 python3-sphinx-rtd-theme=1.0.0+dfsg-1 python3-tz=2021.3-1 python3-urllib3=1.26.5-1~exp1 python3-yaml=5.3.1-5 python3.9=3.9.7-4 python3.9-minimal=3.9.7-4 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.2.0-2 sphinx-rtd-theme-common=1.0.0+dfsg-1 sysvinit-utils=3.00-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 tex-gyre=20180621-3.1 texlive-base=2021.20210921-1 texlive-binaries=2021.20210626.59705-1 texlive-fonts-recommended=2021.20210921-1 texlive-latex-base=2021.20210921-1 texlive-latex-extra=2021.20210921-1 texlive-latex-recommended=2021.20210921-1 texlive-pictures=2021.20210921-1 texlive-plain-generic=2021.20210921-1 tzdata=2021c-1 ucf=3.0043 util-linux=2.37.2-3 x11-common=1:7.7+23 xdg-utils=1.1.3-4.1 xfonts-encodings=1:1.0.4-2.1 xfonts-utils=1:7.7+6 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/20211012T024642Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211012T024642Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211005T205147Z/ 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~rc4-1 && mkdir -p /build/macsyfinder-0Y4WeI && dpkg-source --no-check -x /*.dsc /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4 && chown -R builduser:builduser /build/macsyfinder-0Y4WeI" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4 && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633466292" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/macsyfinder-0Y4WeI /tmp/macsyfinder-2.0~rc4-1pask2mf8 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211005T205147Z 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.9c7j0ahU7W 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.9c7j0ahU7W Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). 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/20211005T205147Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211005T205147Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (811 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_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... 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/20211012T024642Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211012T024642Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211005T205147Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.9c7j0ahU7W Get:1 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211005T205147Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 20s (1179 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.9c7j0ahU7W I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d macsyfinder=2.0~rc4-1 && mkdir -p /build/macsyfinder-0Y4WeI && dpkg-source --no-check -x /*.dsc /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4 && chown -R builduser:builduser /build/macsyfinder-0Y4WeI"' exec /tmp/mmdebstrap.9c7j0ahU7W 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 29.9 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main macsyfinder 2.0~rc4-1 (dsc) [2423 B] Get:2 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main macsyfinder 2.0~rc4-1 (tar) [29.9 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211012T024642Z bookworm/main macsyfinder 2.0~rc4-1 (diff) [9340 B] Fetched 29.9 MB in 23s (1279 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'macsyfinder_2.0~rc4-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting macsyfinder in /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4 dpkg-source: info: unpacking macsyfinder_2.0~rc4.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.0~rc4-1.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 dpkg-source: info: applying fix-colorlog.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4 && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633466292" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.9c7j0ahU7W dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0~rc4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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-0Y4WeI/macsyfinder-2.0-rc4/.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-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/cluster.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/config.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/database.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/definition_parser.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/error.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/gene.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/hit.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/model.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/model_conf_parser.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/package.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/profile.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/registries.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/report.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/search_genes.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/serialization.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/solution.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/system.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/utils.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy copying macsypy/__init__.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/__init__.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsydata.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.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_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_cmd_config_file (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_model_conf (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_project_config_file (test_Config.TestConfig) ... ok test_save (test_Config.TestConfig) ... ok test_set_option (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_genes_fqn (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_index_dir (test_Indexes.Test) ... ok test_iter (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_hmm_protected_path (test_Profile.TestProfile) ... ok test_execute_hmm_w_GA_n_nocutga (test_Profile.TestProfile) ... ok test_execute_hmm_with_GA (test_Profile.TestProfile) ... skipped 'For some reason this fails to find hmmer_results - skipping' test_execute_hmm_wo_GA (test_Profile.TestProfile) ... ok 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_names (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_nb (test_System.SystemTest) ... ok test_loci_num (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_cfg_n_previous_run (test_functional_test.Test) ... ok test_degenerated_systems (test_functional_test.Test) ... ok test_gembase (test_functional_test.Test) ... ok test_index_dir (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_uncomplete_degenerated_systems (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_loner (test_hit.ValidHitTest) ... ok test_multi_system (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_help (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_summary_best_solution (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_LightHit (test_macsyprofile.TestMacsyprofile) ... ok test_build_my_db (test_macsyprofile.TestMacsyprofile) ... ok test_fill_my_db (test_macsyprofile.TestMacsyprofile) ... ok test_functional (test_macsyprofile.TestMacsyprofile) ... ok test_functional_best_score (test_macsyprofile.TestMacsyprofile) ... ok test_functional_coverage (test_macsyprofile.TestMacsyprofile) ... ok test_functional_evalue (test_macsyprofile.TestMacsyprofile) ... ok test_functional_no_hits (test_macsyprofile.TestMacsyprofile) ... ok test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile) ... ok test_functional_out_exists (test_macsyprofile.TestMacsyprofile) ... ok test_functional_pattern (test_macsyprofile.TestMacsyprofile) ... ok test_getProfile_len (test_macsyprofile.TestMacsyprofile) ... ok test_get_gene_name (test_macsyprofile.TestMacsyprofile) ... ok test_header (test_macsyprofile.TestMacsyprofile) ... ok test_hit_start (test_macsyprofile.TestMacsyprofile) ... ok test_parse (test_macsyprofile.TestMacsyprofile) ... ok test_parse_hmm_body (test_macsyprofile.TestMacsyprofile) ... ok test_parse_hmm_header (test_macsyprofile.TestMacsyprofile) ... ok test_pasre_args (test_macsyprofile.TestMacsyprofile) ... ok test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile) ... ok test_parse (test_model_conf_parser.TestModelConfParser) ... ok test_parse_bad_file (test_model_conf_parser.TestModelConfParser) ... ok test_parse_filtering (test_model_conf_parser.TestModelConfParser) ... ok test_parse_w_bad_value (test_model_conf_parser.TestModelConfParser) ... ok test_parse_w_unkown_tag (test_model_conf_parser.TestModelConfParser) ... ok test_parse_weights (test_model_conf_parser.TestModelConfParser) ... ok test_parse_wo_filtering (test_model_conf_parser.TestModelConfParser) ... ok test_parse_wo_weights (test_model_conf_parser.TestModelConfParser) ... 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_model_conf (test_package.TestPackage) ... ok test_check_model_conf_bad_conf (test_package.TestPackage) ... ok test_check_model_conf_no_conf (test_package.TestPackage) ... ok test_check_model_consistency (test_package.TestPackage) ... ok test_check_model_consistency_bad_definitions (test_package.TestPackage) ... ok test_check_model_consistency_extra_profile (test_package.TestPackage) ... ok test_check_model_consistency_lack_one_profile (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_get_profiles_names (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 359 tests in 29.574s OK (skipped=1) create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/macsyfinder/ -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder running install running build running build_py running install_lib moving /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/__init__.py.tmp -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/__init__.py creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9 creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/cluster.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/config.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/database.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/definition_parser.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/error.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/gene.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/hit.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/model.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/model_conf_parser.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/package.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/profile.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/registries.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/report.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/search_genes.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/serialization.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/solution.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/system.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/utils.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts/__init__.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts/macsyfinder.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts/macsydata.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/scripts/macsyprofile.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts copying /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/.pybuild/cpython3_3.9/build/macsypy/__init__.py -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/cluster.py to cluster.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/config.py to config.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/database.py to database.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/error.py to error.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/gene.py to gene.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/hit.py to hit.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/model.py to model.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/model_conf_parser.py to model_conf_parser.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/package.py to package.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/profile.py to profile.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/registries.py to registries.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/report.py to report.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/search_genes.py to search_genes.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/serialization.py to serialization.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/solution.py to solution.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/system.py to system.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/utils.py to utils.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/scripts/macsyprofile.py to macsyprofile.cpython-39.pyc byte-compiling /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsypy/__init__.py to __init__.cpython-39.pyc running install_data creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/data_replicons_topology_Prokaryotes_0213.dat -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/esco.030.p01.12.prt -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru.001.c01.11.prt -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/prru_psae.001.c01.fasta -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base copying data/base/psae.001.c01.13.prt -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/base creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/models copying data/models/readme -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/models creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.fasta -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/datatest_gembase.topology -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data copying data/sequence_data/results.macsyfinder.json -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/share/macsyfinder/data/sequence_data creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/etc creating /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/etc/macsyfinder copying etc/macsyfinder.conf -> /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/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-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/lib/python3.9/dist-packages/macsyfinder-2.0rc4.egg-info Skipping SOURCES.txt running install_scripts Installing macsydata script to /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/bin Installing macsyfinder script to /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/bin Installing macsyprofile script to /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/bin I: pybuild pybuild:310: mv /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/usr/etc /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/debian/macsyfinder/etc && cd /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/doc && make html latexpdf make[1]: Entering directory '/build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/doc' Running Sphinx v4.2.0 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 40 source files that are out of date updating environment: [new config] 40 added, 0 changed, 0 removed reading sources... [ 2%] developer_guide/api/cluster reading sources... [ 5%] developer_guide/api/config reading sources... [ 7%] developer_guide/api/database reading sources... [ 10%] developer_guide/api/definition_parser reading sources... [ 12%] developer_guide/api/error reading sources... [ 15%] developer_guide/api/gene reading sources... [ 17%] developer_guide/api/hit reading sources... [ 20%] developer_guide/api/index reading sources... [ 22%] developer_guide/api/model reading sources... [ 25%] developer_guide/api/model_conf_parser reading sources... [ 27%] developer_guide/api/package reading sources... [ 30%] developer_guide/api/profile reading sources... [ 32%] developer_guide/api/registries reading sources... [ 35%] developer_guide/api/report reading sources... [ 37%] developer_guide/api/search_genes reading sources... [ 40%] developer_guide/api/serialization reading sources... [ 42%] developer_guide/api/solution reading sources... [ 45%] developer_guide/api/system reading sources... 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[ 97%] user_guide/outputs reading sources... [100%] user_guide/quickstart /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: WARNING: Unexpected indentation. /build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/doc/source/user_guide/input.rst:421: WARNING: Inline substitution_reference start-string without end-string. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] developer_guide/api/cluster writing output... [ 5%] developer_guide/api/config writing output... [ 7%] developer_guide/api/database writing output... [ 10%] developer_guide/api/definition_parser writing output... [ 12%] developer_guide/api/error writing output... [ 15%] developer_guide/api/gene writing output... [ 17%] developer_guide/api/hit writing output... [ 20%] developer_guide/api/index writing output... 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[111] LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R epliconInfo' on page 112 undefined on input line 10336. LaTeX Warning: Hyper reference `developer_guide/api/config:macsypy.config.Confi g' on page 112 undefined on input line 10352. [112] Underfull \hbox (badness 10000) in paragraph at lines 10402--10405 []\T1/txtt/bx/n/10 default_topology \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 string\T1/ qtm/m/n/10 ) ^^U the topol-ogy pro-vided by con- LaTeX Warning: Hyper reference `developer_guide/api/database:macsypy.database.R epliconInfo' on page 113 undefined on input line 10441. [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 10710--10713 []\T1/txtt/bx/n/10 models \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 list of tuple with t he following structure: [(\TS1/txtt/m/sl/10 '\T1/txtt/m/sl/10 model_1\TS1/txtt/ m/sl/10 '\T1/txtt/m/sl/10 , LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.ModelRegistry' on page 115 undefined on input line 10716. LaTeX Warning: Hyper reference `developer_guide/api/registries:macsypy.registri es.DefinitionLocation' on page 115 undefined on input line 10726. Underfull \hbox (badness 10000) in paragraph at lines 10779--10782 []\T1/qtm/m/n/10 Unar-chive and un-com-press a pack-age un-der \T1/qtm/m/it/10 //< /usr/share/texmf/fonts/type1/public/tex-gyre/qtmr.pfb> Output written on macsyfinder.pdf (125 pages, 1410163 bytes). Transcript written on macsyfinder.log. Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Missing input file 'macsyfinder.ind' (or dependence on it) from following: '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 121 undefined on input line 11155 Reference `developer_guide/api/config:module-macsypy.config' on page 121 undefined on input line 11156 Reference `developer_guide/api/database:module-macsypy.database' on page 121 undefined on input line 11157 Reference `developer_guide/api/definition_parser:module-macsypy.definition_parser' on page 121 undefined on input line 11158 Reference `developer_guide/api/error:module-macsypy.error' on page 121 undefined on input line 11159 Reference `developer_guide/api/hit:module-macsypy.hit' on page 121 undefined on input line 11160 Reference `developer_guide/api/model_conf_parser:module-macsypy.model_conf_parser' on page 121 undefined on input line 11161 Reference `developer_guide/api/package:module-macsypy.package' on page 121 undefined on input line 11162 Reference `developer_guide/api/registries:module-macsypy.registries' on page 121 undefined on input line 11163 Reference `developer_guide/api/search_genes:module-macsypy.search_genes' on page 121 undefined on input line 11164 Reference `developer_guide/api/serialization:module-macsypy.serialization' on page 121 undefined on input line 11165 Reference `developer_guide/api/solution:module-macsypy.solution' on page 121 undefined on input line 11166 Reference `developer_guide/api/system:module-macsypy.system' on page 121 undefined on input line 11167 Reference `developer_guide/api/utils:module-macsypy.utils' on page 121 undefined on input line 11168 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'... This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file macsyfinder.idx....done (409 entries accepted, 0 rejected). Sorting entries......done (3679 comparisons). Generating output file macsyfinder.ind....done (588 lines written, 0 warnings). Output written in macsyfinder.ind. Transcript written in macsyfinder.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'macsyfinder.aux' 'macsyfinder.ind' 'macsyfinder.out' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -recorder "macsyfinder.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[6] Underfull \hbox (badness 6412) in paragraph at lines 536--539 []\T1/qtm/m/n/10 On a ^^Pmetage-nomic^^Q (un-ordered) dataset for ex-am-ple: \T 1/txtt/m/n/10 macsyfinder --db-type unordered [7] Underfull \hbox (badness 10000) in paragraph at lines 547--549 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db mygenome .fasta --models Underfull \hbox (badness 10000) in paragraph at lines 559--561 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db mygenome .fasta --models-dir [8] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [9] Overfull \vbox (2.72194pt too high) detected at line 749 [10] Overfull \vbox (5.6739pt too high) detected at line 802 [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 867--869 []\T1/qtm/m/n/10 $PRE-FIX/etc/macsyfinder/macsyfinder.conf < $(HOME)/.macsyfind er/macsyfinder.conf < mac-syfinder.conf < [13] [14] [15] [16] [17] Underfull \hbox (badness 5417) in paragraph at lines 1337--1339 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [18] [19] Underfull \vbox (badness 10000) detected at line 1538 Underfull \vbox (badness 10000) detected at line 1538 [20] [21] Underfull \vbox (badness 10000) detected at line 1664 Overfull \vbox (29.72195pt too high) detected at line 1664 [22] [23] Underfull \vbox (badness 4156) detected at line 1811 [24] Underfull \vbox (badness 10000) detected at line 1845 Overfull \vbox (8.67392pt too high) detected at line 1845 [25] Underfull \vbox (badness 10000) detected at line 1845 Underfull \vbox (badness 10000) detected at line 1845 [26] [27] [28] [29] [30] [31] Underfull \vbox (badness 10000) detected at line 2109 Overfull \vbox (23.67393pt too high) detected at line 2109 [32] Overfull \vbox (1.97241pt too high) detected at line 2161 [33] [34] [35] [36 <./msf_functionning_step1.pdf>] [37 <./msf_functionning_step 2.pdf>] [38] [39 <./msf_functionning_step3.pdf>] [40 <./msf_functionning_step4. pdf>] [41 <./msf_functionning_step5.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2690--2692 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2698--2700 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2706--2708 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2714--2716 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models [42] Underfull \hbox (badness 10000) in paragraph at lines 2725--2727 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --index-dir Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 2768. [43] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 2813. [44] [45] [46] Chapter 2. [47] [48] [49] [50] [51] [52 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 3403--3405 []\T1/qtm/b/n/10 in-ter_gene_max_space\T1/qtm/m/n/10 : an \T1/qtm/m/it/10 in-te -ger \T1/qtm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3711--3717 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [58] [59] [60] [61 <./T1SS_example.pdf>] [62] [63 <./T3SS_example.pdf>] [64] [65] [66] [67] [68] Chapter 3. [69] [70] [71 <./macsyfinder_classes.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4682--4687 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. [][]\T1/txtt/m/sl/10 macsypy.solution. 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[6] Underfull \hbox (badness 6412) in paragraph at lines 536--539 []\T1/qtm/m/n/10 On a ^^Pmetage-nomic^^Q (un-ordered) dataset for ex-am-ple: \T 1/txtt/m/n/10 macsyfinder --db-type unordered [7] Underfull \hbox (badness 10000) in paragraph at lines 547--549 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db mygenome .fasta --models Underfull \hbox (badness 10000) in paragraph at lines 559--561 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db mygenome .fasta --models-dir [8] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [9] Overfull \vbox (2.72194pt too high) detected at line 749 [10] Overfull \vbox (5.6739pt too high) detected at line 802 [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 867--869 []\T1/qtm/m/n/10 $PRE-FIX/etc/macsyfinder/macsyfinder.conf < $(HOME)/.macsyfind er/macsyfinder.conf < mac-syfinder.conf < [13] [14] [15] [16] [17] Underfull \hbox (badness 5417) in paragraph at lines 1337--1339 []\T1/qtm/m/n/10 To see po-ten-tial other best so-lu-tions (in case sev-eral ob -tained the same high-est score), see file [18] [19] Underfull \vbox (badness 10000) detected at line 1538 Underfull \vbox (badness 10000) detected at line 1538 [20] [21] Underfull \vbox (badness 10000) detected at line 1664 Overfull \vbox (29.72195pt too high) detected at line 1664 [22] [23] Underfull \vbox (badness 4156) detected at line 1811 [24] Underfull \vbox (badness 10000) detected at line 1845 Overfull \vbox (8.67392pt too high) detected at line 1845 [25] Underfull \vbox (badness 10000) detected at line 1845 Underfull \vbox (badness 10000) detected at line 1845 [26] [27] [28] [29] [30] [31] Underfull \vbox (badness 10000) detected at line 2109 Overfull \vbox (23.67393pt too high) detected at line 2109 [32] Overfull \vbox (1.97241pt too high) detected at line 2161 [33] [34] [35] [36 <./msf_functionning_step1.pdf>] [37 <./msf_functionning_step 2.pdf>] [38] [39 <./msf_functionning_step3.pdf>] [40 <./msf_functionning_step4. pdf>] [41 <./msf_functionning_step5.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 2690--2692 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2698--2700 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2706--2708 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models Underfull \hbox (badness 10000) in paragraph at lines 2714--2716 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --models [42] Underfull \hbox (badness 10000) in paragraph at lines 2725--2727 []\T1/txtt/m/n/10 macsyfinder --db-type ordered_replicon --sequence-db genome.f asta --index-dir Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 2768. [43] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 2813. [44] [45] [46] Chapter 2. [47] [48] [49] [50] [51] [52 <./MSF_modelling.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 3403--3405 []\T1/qtm/b/n/10 in-ter_gene_max_space\T1/qtm/m/n/10 : an \T1/qtm/m/it/10 in-te -ger \T1/qtm/m/n/10 that de-fines gene-wise value of sys-tem's ^^Pin- [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3711--3717 \T1/txtt/m/n/10 models in conf file XXX. May be these results have been generat ed with an old version [58] [59] [60] [61 <./T1SS_example.pdf>] [62] [63 <./T3SS_example.pdf>] [64] [65] [66] [67] [68] Chapter 3. [69] [70] [71 <./macsyfinder_classes.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4682--4687 []\T1/qtm/m/n/10 Among all this po-ten-tial sys-tems, MSF com-pute the best com -bi-na-tion. [][]\T1/txtt/m/sl/10 macsypy.solution. 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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-0Y4WeI/macsyfinder-2.0-rc4/doc/build/latex' make[1]: Leaving directory '/build/macsyfinder-0Y4WeI/macsyfinder-2.0-rc4/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-0Y4WeI/macsyfinder-2.0-rc4' 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-0Y4WeI/macsyfinder-2.0-rc4' dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -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~rc4-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../macsyfinder_2.0~rc4-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/macsyfinder-0Y4WeI /tmp/macsyfinder-2.0~rc4-1pask2mf8 I: cleaning package lists and apt cache... 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