Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/tombo/tombo_1.5.1-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/tombo-1.5.1-2srhv8d3h/tombo_1.5.1-2_all.buildinfo Get source package info: tombo=1.5.1-2 Source URL: http://snapshot.notset.fr/mr/package/tombo/1.5.1-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-3 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34.90.20200706-1 binutils-common=2.34.90.20200706-1 binutils-x86-64-linux-gnu=2.34.90.20200706-1 bsdextrautils=2.35.2-7 bsdutils=1:2.35.2-7 build-essential=12.8 bzip2=1.0.8-3 ca-certificates=20200601 coreutils=8.32-2 cpp=4:9.2.1-3.1 cpp-9=9.3.0-14 cython3=0.29.14-2 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2 debianutils=4.11 dh-autoreconf=19 dh-python=4.20200315 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 docutils-common=0.16+dfsg-2 docutils-doc=0.16+dfsg-2 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 fonts-font-awesome=5.0.10+really4.7.0~dfsg-2 fonts-lato=2.0-2 fonts-mathjax=2.7.8+dfsg-1 g++=4:9.2.1-3.1 g++-9=9.3.0-14 gcc=4:9.2.1-3.1 gcc-10-base=10.1.0-6 gcc-9=9.3.0-14 gcc-9-base=9.3.0-14 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libaec0=1.0.4-1 libarchive-zip-perl=1.68-1 libasan5=9.3.0-14 libatomic1=10.1.0-6 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34.90.20200706-1 libblas3=3.9.0-2 libblkid1=2.35.2-7 libbz2-1.0=1.0.8-3 libc-bin=2.30-8 libc-dev-bin=2.30-8 libc6=2.30-8 libc6-dev=2.30-8 libcap-ng0=0.7.9-2.2 libcc1-0=10.1.0-6 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34.90.20200706-1 libctf0=2.34.90.20200706-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.253 libdebhelper-perl=13.2 libdpkg-perl=1.20.5 libelf1=0.176-1.1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-9-dev=9.3.0-14 libgcc-s1=10.1.0-6 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgfortran5=10.1.0-6 libglib2.0-0=2.64.4-1 libgmp10=2:6.2.0+dfsg-6 libgomp1=10.1.0-6 libgpg-error0=1.38-2 libhdf5-103-1=1.10.6+repack-2 libhdf5-hl-100=1.10.6+repack-2 libicu67=67.1-3 libisl22=0.22.1-1 libitm1=10.1.0-6 libjs-jquery=3.5.1+dfsg-4 libjs-mathjax=2.7.8+dfsg-1 libjs-modernizr=2.6.2+ds1-3 libjs-sphinxdoc=2.4.3-4 libjs-underscore=1.9.1~dfsg-1 liblapack3=3.9.0-2 liblbfgsb0=3.0+dfsg.3-8 liblsan0=10.1.0-6 liblz4-1=1.9.2-2 liblzf1=3.6-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.35.2-7 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.0.2-1 libncursesw6=6.2-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.2-2 libpython3-all-dev=3.8.2-3 libpython3-dev=3.8.2-3 libpython3-stdlib=3.8.2-3 libpython3.8=3.8.4-1 libpython3.8-dev=3.8.4-1 libpython3.8-minimal=3.8.4-1 libpython3.8-stdlib=3.8.4-1 libquadmath0=10.1.0-6 libreadline8=8.0-4 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsmartcols1=2.35.2-7 libsqlite3-0=3.32.3-1 libssl1.1=1.1.1g-1 libstdc++-9-dev=9.3.0-14 libstdc++6=10.1.0-6 libsub-override-perl=0.09-2 libsystemd0=245.6-2 libsz2=1.0.4-1 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.1.0-6 libubsan1=10.1.0-6 libuchardet0=0.0.7-1 libudev1=245.6-2 libunistring2=0.9.10-4 libuuid1=2.35.2-7 libxml2=2.9.10+dfsg-5+b1 linux-libc-dev=5.7.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 node-jquery=3.5.1+dfsg-4 openssl=1.1.1g-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 python-babel-localedata=2.8.0+dfsg.1-3 python3=3.8.2-3 python3-alabaster=0.7.8-1.1 python3-all=3.8.2-3 python3-all-dev=3.8.2-3 python3-babel=2.8.0+dfsg.1-3 python3-certifi=2020.4.5.1-1 python3-chardet=3.0.4-7 python3-coverage=5.1+dfsg.1-1 python3-decorator=4.4.2-2 python3-dev=3.8.2-3 python3-distutils=3.8.3-2 python3-docutils=0.16+dfsg-2 python3-h5py=2.10.0-8 python3-h5py-serial=2.10.0-8 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-jinja2=2.11.2-1 python3-lib2to3=3.8.3-2 python3-mappy=2.17+dfsg-11 python3-markupsafe=1.1.1-1+b1 python3-minimal=3.8.2-3 python3-nose2=0.9.1-3 python3-numpy=1:1.19.0-1 python3-packaging=20.3-1.2 python3-pkg-resources=46.1.3-1 python3-pygments=2.3.1+dfsg-3 python3-pyparsing=2.4.7-1 python3-requests=2.23.0+dfsg-2 python3-roman=2.0.0-4 python3-scipy=1.4.1-2 python3-setuptools=46.1.3-1 python3-six=1.15.0-1 python3-sphinx=2.4.3-4 python3-sphinx-argparse=0.2.2-3 python3-sphinx-rtd-theme=0.4.3+dfsg-3 python3-tqdm=4.43.0-1 python3-tz=2020.1-2 python3-urllib3=1.25.9-1 python3.8=3.8.4-1 python3.8-dev=3.8.4-1 python3.8-minimal=3.8.4-1 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sgml-base=1.30 sphinx-common=2.4.3-4 sphinx-doc=2.4.3-4 sphinx-rtd-theme-common=0.4.3+dfsg-3 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 tzdata=2020a-1 util-linux=2.35.2-7 xml-core=0.18+nmu1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200720T204543Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200713T085630Z/ 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 tombo=1.5.1-2 && mkdir -p /build/tombo-3Sny7M && dpkg-source --no-check -x /*.dsc /build/tombo-3Sny7M/tombo-1.5.1 && chown -R builduser:builduser /build/tombo-3Sny7M" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tombo-3Sny7M/tombo-1.5.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1594813647" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/tombo-3Sny7M /tmp/tombo-1.5.1-2srhv8d3h bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200713T085630Z 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.Swoppb8oeN 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.Swoppb8oeN Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.2-7). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200713T085630Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200713T085630Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (1087 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 ... 4577 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-8) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200720T204543Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200713T085630Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Swoppb8oeN Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200720T204543Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200713T085630Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20200720T204543Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200720T204543Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200720T204543Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20200720T204543Z unstable/main amd64 Packages [11.3 MB] Fetched 34.0 MB in 31s (1084 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.Swoppb8oeN I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d tombo=1.5.1-2 && mkdir -p /build/tombo-3Sny7M && dpkg-source --no-check -x /*.dsc /build/tombo-3Sny7M/tombo-1.5.1 && chown -R builduser:builduser /build/tombo-3Sny7M"' exec /tmp/mmdebstrap.Swoppb8oeN Reading package lists... NOTICE: 'tombo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tombo.git Please use: git clone https://salsa.debian.org/med-team/tombo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.3 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tombo 1.5.1-2 (dsc) [2292 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tombo 1.5.1-2 (tar) [22.3 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tombo 1.5.1-2 (diff) [6344 B] Fetched 22.3 MB in 18s (1248 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'tombo_1.5.1-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting tombo in /build/tombo-3Sny7M/tombo-1.5.1 dpkg-source: info: unpacking tombo_1.5.1.orig.tar.gz dpkg-source: info: unpacking tombo_1.5.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_future.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying mathjax.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tombo-3Sny7M/tombo-1.5.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1594813647" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.Swoppb8oeN dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py clean running clean removing '/build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-indep dh binary-indep --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/tombo-3Sny7M/tombo-1.5.1' dh_auto_build I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/__init__.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_text_output_commands.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_plot_commands.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_preprocess.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_filter_reads.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/tombo_helper.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/resquiggle.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_default_parameters.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/__main__.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_event_resquiggle.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_version.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/tombo_stats.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_option_parsers.py -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt writing manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' copying tombo/_c_dynamic_programming.pyx -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo copying tombo/_c_helper.pyx -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo creating /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/R_scripts creating /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/tombo_models running build_ext cythoning tombo/_c_dynamic_programming.pyx to tombo/_c_dynamic_programming.cpp cythoning tombo/_c_helper.pyx to tombo/_c_helper.cpp building 'tombo._c_dynamic_programming' extension creating build creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/tombo x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/tombo-3Sny7M/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-3.8/tombo/_c_dynamic_programming.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from tombo/_c_dynamic_programming.cpp:612: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ tombo/_c_dynamic_programming.cpp: In function ‘PyObject* __pyx_pf_5tombo_22_c_dynamic_programming_2c_reg_z_scores(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, PyObject*)’: tombo/_c_dynamic_programming.cpp:3624:36: warning: ‘__pyx_v_np_max_half_z_score’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3624 | __pyx_t_28 = PyFloat_FromDouble(__pyx_v_np_max_half_z_score); if (unlikely(!__pyx_t_28)) __PYX_ERR(0, 93, __pyx_L1_error) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/tombo-3Sny7M/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tombo/_c_dynamic_programming.o -o /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/_c_dynamic_programming.cpython-38-x86_64-linux-gnu.so building 'tombo._c_helper' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/tombo-3Sny7M/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.8 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-3.8/tombo/_c_helper.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from tombo/_c_helper.cpp:612: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/tombo-3Sny7M/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/tombo/_c_helper.o -o /build/tombo-3Sny7M/tombo-1.5.1/.pybuild/cpython3_3.8/build/tombo/_c_helper.cpython-38-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tombo-3Sny7M/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tombo-3Sny7M/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) sphinx-build -N -bhtml docs docs/build Running Sphinx v2.4.3 Creating file ./tombo.rst. making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 54%] plotting reading sources... [ 63%] resquiggle reading sources... [ 72%] rna reading sources... [ 81%] text_output reading sources... [ 90%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 54%] plotting writing output... [ 63%] resquiggle writing output... [ 72%] rna writing output... [ 81%] text_output writing output... [ 90%] tombo writing output... [100%] tutorials generating indices... genindexdone writing additional pages... searchdone copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 8%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 21%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 34%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 47%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 56%] _images/pre_read_5mC.png copying images... [ 60%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 69%] _images/kmer_levels.png copying images... [ 73%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 82%] _images/begin_half_z_scores.png copying images... [ 86%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 95%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png copying static files... ... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 4 warnings. The HTML pages are in docs/build. /usr/lib/python3/dist-packages/sphinx_rtd_theme/search.html:21: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a