Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/macsyfinder/macsyfinder_2.0~rc7-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/macsyfinder-2.0~rc7-14hv3oewm/macsyfinder_2.0~rc7-1_amd64.buildinfo Get source package info: macsyfinder=2.0~rc7-1 Source URL: http://snapshot.notset.fr/mr/package/macsyfinder/2.0~rc7-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-python=5.20220403 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 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=2.005-1 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-1 gettext=0.21-6 gettext-base=0.21-6 graphviz=2.42.2-6+b3 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hmmer=3.3.2+dfsg-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 latexmk=1:4.77-1 libacl1=2.3.1-1 libann0=1.1.2+doc-7 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12.1.0-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-4 libblas3=3.10.1-1 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12.1.0-1 libcdt5=2.42.2-6+b3 libcgraph6=2.42.2-6+b3 libcom-err2=1.46.5-2 libcommons-logging-java=1.2-3 libcommons-parent-java=43-1 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdeflate0=1.10-2 libdivsufsort3=2.0.1-5 libdpkg-perl=1.21.7 libelf1=0.187-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.4 libfontenc1=1:1.1.4-1 libfreetype6=2.12.0+dfsg-1 libfribidi0=1.0.8-2.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-1 libgcrypt20=1.10.1-2 libgd3=2.3.0-2+b1 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12.1.0-1 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12.1.0-1 libgpg-error0=1.45-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libgts-0.7-5=0.7.6+darcs121130-5 libgvc6=2.42.2-6+b3 libgvpr2=2.42.2-6+b3 libharfbuzz0b=2.7.4-1+b1 libice6=2:1.0.10-1 libicu71=71.1-3 libisl23=0.24-2 libitm1=12.1.0-1 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.1.2-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-sphinxdoc=4.5.0-3 libjs-underscore=1.13.3~dfsg+~1.11.4-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkpathsea6=2021.20210626.59705-1+b1 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblab-gamut1=2.42.2-6+b3 liblapack3=3.10.1-1 liblsan0=12.1.0-1 libltdl7=2.4.7-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3+20220423-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpango-1.0-0=1.50.7+ds-1 libpangocairo-1.0-0=1.50.7+ds-1 libpangoft2-1.0-0=1.50.7+ds-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpathplan4=2.42.2-6+b3 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libpdfbox-java=1:1.8.16-2 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-5 libptexenc1=2021.20210626.59705-1+b1 libpython3-stdlib=3.10.4-1+b1 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libpython3.9-minimal=3.9.12-1 libpython3.9-stdlib=3.9.12-1 libquadmath0=12.1.0-1 libreadline8=8.1.2-1.2 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsm6=2:1.2.3-1 libsmartcols1=2.38-4 libsqlite3-0=3.38.5-1 libssl1.1=1.1.1o-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-1 libsub-override-perl=0.09-2 libsynctex2=2021.20210626.59705-1+b1 libsystemd0=250.4-1 libteckit0=2.5.11+ds1-1 libtexlua53=2021.20210626.59705-1+b1 libtexluajit2=2021.20210626.59705-1+b1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtiff5=4.3.0-7 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-1 libubsan1=12.1.0-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunicode-escape-perl=0.0.2-4.1 libunicode-string-perl=2.10-1+b7 libunistring2=1.0-1 libuuid1=2.38-4 libwebp7=1.2.2-2+b1 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.14-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxi6=2:1.8-1 libxml2=2.9.14+dfsg-1 libxmu6=2:1.1.3-3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.1-1 libyaml-0-2=0.2.2-1 libzstd1=1.5.2+dfsg-1 libzzip-0-13=0.13.72+dfsg.1-1.1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 openssl=1.1.1o-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 po-debconf=1.0.21+nmu1 preview-latex-style=12.2-1 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.10.4-1+b1 python3-alabaster=0.7.12-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-2 python3-charset-normalizer=2.0.6-2 python3-colorama=0.4.4-1 python3-colorlog=6.6.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-distutils=3.9.12-1 python3-docutils=0.17.1+dfsg-2 python3-idna=3.3-1 python3-imagesize=1.3.0-1 python3-importlib-metadata=4.6.4-1 python3-jinja2=3.0.3-1 python3-lib2to3=3.9.12-1 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.10.4-1+b1 python3-more-itertools=8.10.0-2 python3-networkx=2.5+ds-2 python3-numpy=1:1.21.5-1 python3-packaging=21.3-1 python3-pandas=1.3.5+dfsg-4 python3-pandas-lib=1.3.5+dfsg-4 python3-pkg-resources=59.6.0-1.2 python3-pygments=2.11.2+dfsg-2 python3-pyparsing=3.0.7-2 python3-requests=2.27.1+dfsg-1 python3-roman=3.3-1 python3-setuptools=59.6.0-1.2 python3-six=1.16.0-3 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.5.0-3 python3-sphinx-rtd-theme=1.0.0+dfsg-1 python3-tz=2022.1-1 python3-urllib3=1.26.9-1 python3-yaml=5.4.1-1+b1 python3-zipp=1.0.0-3 python3.10=3.10.4-3 python3.10-minimal=3.10.4-3 python3.9=3.9.12-1 python3.9-minimal=3.9.12-1 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.5.0-3 sphinx-rtd-theme-common=1.0.0+dfsg-1 sysvinit-utils=3.03-1 t1utils=1.41-4 tar=1.34+dfsg-1 tex-common=6.17 tex-gyre=20180621-3.1 texlive-base=2021.20220204-1 texlive-binaries=2021.20210626.59705-1+b1 texlive-fonts-recommended=2021.20220204-1 texlive-latex-base=2021.20220204-1 texlive-latex-extra=2021.20220204-1 texlive-latex-recommended=2021.20220204-1 texlive-pictures=2021.20220204-1 texlive-plain-generic=2021.20220204-1 tzdata=2022a-1 ucf=3.0043 util-linux=2.38-4 util-linux-extra=2.38-4 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=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220515T040755Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220515T040755Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ 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~rc7-1 && mkdir -p /build/macsyfinder-TKcOu8 && dpkg-source --no-check -x /*.dsc /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7 && chown -R builduser:builduser /build/macsyfinder-TKcOu8" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652354106" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/macsyfinder-TKcOu8 /tmp/macsyfinder-2.0~rc7-14hv3oewm bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.gLyLQ4wIIU 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.gLyLQ4wIIU Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1041 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 ... 4628 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220515T040755Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220515T040755Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.gLyLQ4wIIU Get:1 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main amd64 Packages [11.4 MB] Fetched 23.5 MB in 20s (1185 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.gLyLQ4wIIU I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d macsyfinder=2.0~rc7-1 && mkdir -p /build/macsyfinder-TKcOu8 && dpkg-source --no-check -x /*.dsc /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7 && chown -R builduser:builduser /build/macsyfinder-TKcOu8"' exec /tmp/mmdebstrap.gLyLQ4wIIU 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 33.6 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main macsyfinder 2.0~rc7-1 (dsc) [2451 B] Get:2 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main macsyfinder 2.0~rc7-1 (tar) [33.6 MB] Get:3 http://snapshot.notset.fr/archive/debian/20220515T040755Z bookworm/main macsyfinder 2.0~rc7-1 (diff) [11.2 kB] Fetched 33.6 MB in 26s (1283 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'macsyfinder_2.0~rc7-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting macsyfinder in /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7 dpkg-source: info: unpacking macsyfinder_2.0~rc7.orig.tar.gz dpkg-source: info: unpacking macsyfinder_2.0~rc7-1.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 privacy dpkg-source: info: applying fix-test-parse.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652354106" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.gLyLQ4wIIU dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0~rc7-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:239: python3.10 setup.py clean running clean removing '/build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' 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:239: python3.10 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:239: /usr/bin/python3 setup.py build running build running build_py creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/__init__.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/cluster.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/config.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/database.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/definition_parser.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/error.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/gene.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/hit.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/model.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/model_conf_parser.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/package.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/profile.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/registries.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/report.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/search_genes.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/serialization.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/solution.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/system.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy copying macsypy/utils.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/__init__.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsy_gembase_split.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsyconfig.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsydata.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsyfinder.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" 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:239: /usr/bin/python3 setup.py install --root /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running install_lib creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10 creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/__init__.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/cluster.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/config.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/database.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/definition_parser.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/error.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/gene.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/hit.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/model.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/model_conf_parser.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/package.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/profile.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/registries.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/report.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/search_genes.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/serialization.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/solution.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/system.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/utils.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy creating /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/__init__.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsy_gembase_split.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsy_merge_results.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsyconfig.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsydata.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsyfinder.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts copying /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/.pybuild/cpython3_3.10/build/macsypy/scripts/macsyprofile.py -> /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/__init__.py to __init__.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/cluster.py to cluster.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/config.py to config.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/database.py to database.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/definition_parser.py to definition_parser.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/error.py to error.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/gene.py to gene.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/hit.py to hit.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/model.py to model.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/model_conf_parser.py to model_conf_parser.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/package.py to package.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/profile.py to profile.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/registries.py to registries.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/report.py to report.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/search_genes.py to search_genes.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/serialization.py to serialization.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/solution.py to solution.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/system.py to system.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/utils.py to utils.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/__init__.py to __init__.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsy_gembase_split.py to macsy_gembase_split.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsy_merge_results.py to macsy_merge_results.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsyconfig.py to macsyconfig.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsydata.py to macsydata.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsyfinder.py to macsyfinder.cpython-310.pyc byte-compiling /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/macsypy/scripts/macsyprofile.py to macsyprofile.cpython-310.pyc running install_egg_info 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 previously-included files matching '*' found under directory 'data' warning: no files found matching '*' under directory 'doc/build/html' warning: no files found matching 'doc/build/latex/macsyfinder.pdf' warning: no files found matching 'etc/macsyfinder.conf' warning: no previously-included files matching '*' found under directory 'tests/__pycache__/' warning: no previously-included files found matching 'tests/__init__.pyc' warning: no previously-included files found matching '.coverage' warning: no previously-included files found matching 'coverage_html/' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' warning: no files found matching 'CONTRIBUTORS' warning: no files found matching 'NEWS' adding license file 'COPYING' writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' Copying MacSyFinder.egg-info to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/lib/python3.10/dist-packages/MacSyFinder-2.0rc7.egg-info Skipping SOURCES.txt running install_scripts Installing macsyconfig script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin Installing macsydata script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin Installing macsyfinder script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin Installing macsymerge script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin Installing macsyprofile script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin Installing macsysplit script to /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/usr/bin I: pybuild pybuild:326: cp -a /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/etc /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/debian/macsyfinder/etc && cd /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/doc && make html latexpdf make[1]: Entering directory '/build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/doc' Running Sphinx v4.5.0 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 42 source files that are out of date updating environment: [new config] 42 added, 0 changed, 0 removed reading sources... [ 2%] developer_guide/api/cluster reading sources... [ 4%] developer_guide/api/config reading sources... [ 7%] developer_guide/api/database reading sources... [ 9%] developer_guide/api/definition_parser reading sources... [ 11%] developer_guide/api/error reading sources... [ 14%] developer_guide/api/gene reading sources... [ 16%] developer_guide/api/hit reading sources... [ 19%] developer_guide/api/index reading sources... [ 21%] developer_guide/api/model reading sources... [ 23%] developer_guide/api/model_conf_parser reading sources... [ 26%] developer_guide/api/package reading sources... [ 28%] developer_guide/api/profile reading sources... [ 30%] developer_guide/api/registries reading sources... [ 33%] developer_guide/api/report reading sources... [ 35%] developer_guide/api/scripts reading sources... [ 38%] developer_guide/api/search_genes reading sources... [ 40%] developer_guide/api/serialization reading sources... [ 42%] developer_guide/api/solution reading sources... 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[100%] user_guide/quickstart /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:3: ERROR: Unexpected indentation. /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/macsypy/serialization.py:docstring of macsypy.serialization.TsvSystemSerializer.serialize:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/macsypy/serialization.py:docstring of macsypy.serialization.TsvLikelySystemSerializer.serialize:3: WARNING: Definition list ends without a blank line; unexpected unindent. /build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/macsypy/serialization.py:docstring of macsypy.serialization.TxtLikelySystemSerializer.serialize:3: WARNING: Definition list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... 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[ 92%] user_guide/model_definition writing output... [ 95%] user_guide/new_v2 writing output... [ 97%] user_guide/outputs writing output... [100%] user_guide/quickstart generating indices... genindex py-modindex done highlighting module code... [ 4%] macsypy.cluster highlighting module code... [ 9%] macsypy.config highlighting module code... [ 13%] macsypy.database highlighting module code... [ 18%] macsypy.definition_parser highlighting module code... [ 22%] macsypy.error highlighting module code... [ 27%] macsypy.gene highlighting module code... [ 31%] macsypy.hit highlighting module code... [ 36%] macsypy.model highlighting module code... [ 40%] macsypy.model_conf_parser highlighting module code... [ 45%] macsypy.package highlighting module code... [ 50%] macsypy.profile highlighting module code... [ 54%] macsypy.registries highlighting module code... [ 59%] macsypy.report highlighting module code... [ 63%] macsypy.scripts.macsyconfig highlighting module code... [ 68%] macsypy.scripts.macsydata highlighting module code... [ 72%] macsypy.scripts.macsyfinder highlighting module code... [ 77%] macsypy.scripts.macsyprofile highlighting module code... [ 81%] macsypy.search_genes highlighting module code... [ 86%] macsypy.serialization highlighting module code... [ 90%] macsypy.solution highlighting module code... [ 95%] macsypy.system highlighting module code... [100%] macsypy.utils writing additional pages... search done copying images... [ 6%] _static/gene_obj_interaction.svg copying images... [ 12%] _static/macsyfinder_classes.svg copying images... [ 18%] _static/logo_macsyfinder.png copying images... [ 25%] _static/figure_main-2.svg copying images... [ 31%] _static/T1SS_example.svg copying images... [ 37%] _static/T3SS_example.svg copying images... [ 43%] _static/logo_macsymodels.png copying images... [ 50%] _static/MSF_modelling.svg copying images... [ 56%] _static/loner.svg copying images... [ 62%] _static/multi_system.svg copying images... 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Running Sphinx v4.5.0 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/big_data user_guide/model_definition user_guide/functioning user_guide/FAQ modeler_guide/index modeler_guide/package modeler_guide/modeling modeler_guide/helper_tools modeler_guide/publish_package modeler_guide/gallery modeler_guide/models_V1ToV2 modeler_guide/FAQ_modeler developer_guide/index developer_guide/overview developer_guide/api/index developer_guide/api/config developer_guide/api/model_conf_parser 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 developer_guide/api/scripts resolving references... done writing... done copying images... 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Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: applying rule 'makeindex macsyfinder.idx'... Rule 'makeindex macsyfinder.idx': File changes, etc: Changed files, or newly in use since previous run(s): macsyfinder.idx Rule 'makeindex macsyfinder.idx': The following rules & subrules became out-of-date: makeindex macsyfinder.idx ------------ Run number 1 of rule 'makeindex macsyfinder.idx' ------------ ------------ Running 'makeindex -s python.ist -o "macsyfinder.ind" "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 (553 entries accepted, 0 rejected). 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[8] Underfull \hbox (badness 6412) in paragraph at lines 674--677 []\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 Underfull \hbox (badness 10000) in paragraph at lines 685--687 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 697--699 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [9] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (4.7757pt too high) detected at line 795 [10] Overfull \vbox (5.6739pt too high) detected at line 859 [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 5417) in paragraph at lines 1505--1507 []\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 [20] [21] Underfull \vbox (badness 10000) detected at line 1712 Underfull \vbox (badness 10000) detected at line 1712 [22] [23] Underfull \vbox (badness 10000) detected at line 1842 Overfull \vbox (24.52194pt too high) detected at line 1842 [24] [25] Underfull \vbox (badness 1092) detected at line 1994 [26] Overfull \vbox (44.67392pt too high) detected at line 2028 [27] Underfull \vbox (badness 10000) detected at line 2028 Underfull \vbox (badness 10000) detected at line 2028 [28] [29] [30] Overfull \vbox (5.02042pt too high) detected at line 2193 [31] [32] [33] Overfull \vbox (1.92958pt too high) detected at line 2337 [34] Overfull \vbox (10.9724pt too high) detected at line 2381 [35] Overfull \vbox (1.97241pt too high) detected at line 2433 [36] [37] [38 <./graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.pdf>] [39] [40] [41] [42] [43] [44] [45] [46 <./msf_functionning_step1.pdf>] [47 <./m sf_functionning_step2.pdf>] [48] [49 <./msf_functionning_step3.pdf>] [50 <./msf _functionning_step4.pdf>] [51 <./msf_functionning_step5.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 3444--3446 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3452--3454 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3460--3462 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3468--3470 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models [52] Underfull \hbox (badness 10000) in paragraph at lines 3479--3481 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3522. [53] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3567. [54] [55] [56] Chapter 2. [57 <./logo_macsymodels.png>] [58] [59] [60] [61] [62] [63 <./MSF_modelling.pdf >] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4169. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 41 83. Package wrapfig Warning: Collision between wrapping environments on input line 4189. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4189. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 42 02. Package wrapfig Warning: Collision between wrapping environments on input line 4208. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4208. [64 <./loner.pdf>] Package wrapfig Warning: Stationary wrapfigure forced to float on input line 42 22. 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[8] Underfull \hbox (badness 6412) in paragraph at lines 674--677 []\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 Underfull \hbox (badness 10000) in paragraph at lines 685--687 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 697--699 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db my genome.fasta [][]models[]dir [9] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) Overfull \vbox (4.7757pt too high) detected at line 795 [10] Overfull \vbox (5.6739pt too high) detected at line 859 [11] [12] [13] [14] [15] [16] [17] [18] [19] Underfull \hbox (badness 5417) in paragraph at lines 1505--1507 []\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 [20] [21] Underfull \vbox (badness 10000) detected at line 1712 Underfull \vbox (badness 10000) detected at line 1712 [22] [23] Underfull \vbox (badness 10000) detected at line 1842 Overfull \vbox (24.52194pt too high) detected at line 1842 [24] [25] Underfull \vbox (badness 1092) detected at line 1994 [26] Overfull \vbox (44.67392pt too high) detected at line 2028 [27] Underfull \vbox (badness 10000) detected at line 2028 Underfull \vbox (badness 10000) detected at line 2028 [28] [29] [30] Overfull \vbox (5.02042pt too high) detected at line 2193 [31] [32] [33] Overfull \vbox (1.92958pt too high) detected at line 2337 [34] Overfull \vbox (10.9724pt too high) detected at line 2381 [35] Overfull \vbox (1.97241pt too high) detected at line 2433 [36] [37] [38 <./graphviz-c80ff5586733885cc13a7fe257e1d17e75060e46.pdf>] [39] [40] [41] [42] [43] [44] [45] [46 <./msf_functionning_step1.pdf>] [47 <./m sf_functionning_step2.pdf>] [48] [49 <./msf_functionning_step3.pdf>] [50 <./msf _functionning_step4.pdf>] [51 <./msf_functionning_step5.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 3444--3446 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3452--3454 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3460--3462 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models Underfull \hbox (badness 10000) in paragraph at lines 3468--3470 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]models [52] Underfull \hbox (badness 10000) in paragraph at lines 3479--3481 []\T1/txtt/m/n/10 macsyfinder [][]db[]type ordered_replicon [][]sequence[]db ge nome.fasta [][]index[]dir Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3522. [53] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\sphinxtitleref' on input line 3567. [54] [55] [56] Chapter 2. [57 <./logo_macsymodels.png>] [58] [59] [60] [61] [62] [63 <./MSF_modelling.pdf >] Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4169. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 41 83. Package wrapfig Warning: Collision between wrapping environments on input line 4189. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4189. Package wrapfig Warning: Stationary wrapfigure forced to float on input line 42 02. Package wrapfig Warning: Collision between wrapping environments on input line 4208. Package wrapfig Warning: wrapfigure used inside a conflicting environment on in put line 4208. [64 <./loner.pdf>] Package wrapfig Warning: Stationary wrapfigure forced to float on input line 42 22. 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[118] [119] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 11244--11246 []\T1/qtm/m/n/10 true_loners: a dict { str func-tion: :class:macsypy.hit.Loner | [122] [123 <./inheritance-c45e9d68e62b397a43153f505bd360af9eaa7a6c.pdf> <./inhe ritance-d38d58199ba0af98a545498012fba27f43247208.pdf pdfTeX warning: pdflatex (file ./inheritance-d38d58199ba0af98a545498012fba27f43 247208.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [124] [125] [126] [127] [128] [129] [130] Underfull \hbox (badness 10000) in paragraph at lines 12628--12631 []\T1/txtt/bx/n/10 h_grp \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 sequence of string (< itertools._grouper object at [131] [132] [133] [134] [135] [136] Underfull \hbox (badness 5105) in paragraph at lines 13382--13385 []\T1/qtm/m/n/10 Use only for un- [137] Underfull \hbox (badness 5105) in paragraph at lines 13508--13511 []\T1/qtm/m/n/10 Use only for un- [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 14020--14023 []\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- [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 14293--14296 []\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_fqn\TS1/txt t/m/sl/10 '\T1/txtt/m/sl/10 , [143] Underfull \hbox (badness 10000) in paragraph at lines 14434--14438 \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 (179 pages, 2427325 bytes). 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Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' Latexmk: Examining 'macsyfinder.log' Latexmk: Index file 'macsyfinder.idx' was written Latexmk: Log file says output to 'macsyfinder.pdf' Latexmk: All targets (macsyfinder.pdf) are up-to-date make[2]: Leaving directory '/build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/doc/build/latex' make[1]: Leaving directory '/build/macsyfinder-TKcOu8/macsyfinder-2.0-rc7/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-TKcOu8/macsyfinder-2.0-rc7' 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-TKcOu8/macsyfinder-2.0-rc7' 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~rc7-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../macsyfinder_2.0~rc7-1_amd64.buildinfo dpkg-genchanges --build=any -O../macsyfinder_2.0~rc7-1_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-TKcOu8 /tmp/macsyfinder-2.0~rc7-14hv3oewm I: cleaning package lists and apt cache... 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