Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/cyvcf2/cyvcf2_0.30.4-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/cyvcf2-0.30.4-4jyq9b1c_/cyvcf2_0.30.4-4_amd64.buildinfo Get source package info: cyvcf2=0.30.4-4 Source URL: http://snapshot.notset.fr/mr/package/cyvcf2/0.30.4-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-6 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 cython3=0.29.21-3+b1 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.2 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20210126-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-2 help2man=1.47.17 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblas3=3.9.0-3 libblkid1=2.36.1-6 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.45.7-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libcurl3-gnutls=7.74.0-1 libcurl4-gnutls-dev=7.74.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.2 libdeflate-dev=1.7-1 libdeflate0=1.7-1 libdpkg-perl=1.20.7.1 libelf1=0.182-3 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.10.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libgfortran5=10.2.1-6 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhts-dev=1.11-4 libhts3=1.11-4 libicu67=67.1-6 libidn2-0=2.3.0-5 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 libldap-2.4-2=2.4.57+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-6 liblz4-1=1.9.3-1 liblzma-dev=5.2.5-1.0 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-6 libmpc3=1.2.0-1 libmpdec3=2.5.1-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libpython3-all-dev=3.9.1-1 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-3 libpython3.9-dev=3.9.1-3 libpython3.9-minimal=3.9.1-3 libpython3.9-stdlib=3.9.1-3 libquadmath0=10.2.1-6 libreadline8=8.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.13-1 libsmartcols1=2.36.1-6 libsqlite3-0=3.34.1-1 libssh2-1=1.9.0-2 libssl-dev=1.1.1i-3 libssl1.1=1.1.1i-3 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-5 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-5 libunistring2=0.9.10-4 libuuid1=2.36.1-6 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 python3=3.9.1-1 python3-all=3.9.1-1 python3-all-dev=3.9.1-1 python3-click=7.1.2-1 python3-colorama=0.4.4-1 python3-coloredlogs=7.3-2 python3-dev=3.9.1-1 python3-distutils=3.9.1-2 python3-humanfriendly=9.1-1 python3-lib2to3=3.9.1-2 python3-minimal=3.9.1-1 python3-nose=1.3.7-7 python3-numpy=1:1.19.5-1 python3-pkg-resources=52.0.0-1 python3-setuptools=52.0.0-1 python3.9=3.9.1-3 python3.9-dev=3.9.1-3 python3.9-minimal=3.9.1-3 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2021a-1 util-linux=2.36.1-6 xz-utils=5.2.5-1.0 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/20210203T203559Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210131T204918Z/ 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 cyvcf2=0.30.4-4 && mkdir -p /build/cyvcf2-tlNvyW && dpkg-source --no-check -x /*.dsc /build/cyvcf2-tlNvyW/cyvcf2-0.30.4 && chown -R builduser:builduser /build/cyvcf2-tlNvyW" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cyvcf2-tlNvyW/cyvcf2-0.30.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612355234" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/cyvcf2-tlNvyW /tmp/cyvcf2-0.30.4-4jyq9b1c_ bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210131T204918Z 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.xkkS9_wRzQ 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.xkkS9_wRzQ Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-6). 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/20210131T204918Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210131T204918Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (848 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 ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20210203T203559Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210131T204918Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.xkkS9_wRzQ Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210203T203559Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210131T204918Z 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/20210203T203559Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210203T203559Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210203T203559Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210203T203559Z unstable/main amd64 Packages [11.6 MB] Fetched 34.4 MB in 30s (1161 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.xkkS9_wRzQ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d cyvcf2=0.30.4-4 && mkdir -p /build/cyvcf2-tlNvyW && dpkg-source --no-check -x /*.dsc /build/cyvcf2-tlNvyW/cyvcf2-0.30.4 && chown -R builduser:builduser /build/cyvcf2-tlNvyW"' exec /tmp/mmdebstrap.xkkS9_wRzQ Reading package lists... NOTICE: 'cyvcf2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/cyvcf2.git Please use: git clone https://salsa.debian.org/med-team/cyvcf2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 414 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cyvcf2 0.30.4-4 (dsc) [2289 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cyvcf2 0.30.4-4 (tar) [405 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cyvcf2 0.30.4-4 (diff) [6332 B] Fetched 414 kB in 0s (1067 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'cyvcf2_0.30.4-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting cyvcf2 in /build/cyvcf2-tlNvyW/cyvcf2-0.30.4 dpkg-source: info: unpacking cyvcf2_0.30.4.orig.tar.gz dpkg-source: info: unpacking cyvcf2_0.30.4-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_htslib_link_dependency.patch dpkg-source: info: applying 188.patch dpkg-source: info: applying i386.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cyvcf2-tlNvyW/cyvcf2-0.30.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1612355234" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.xkkS9_wRzQ dpkg-buildpackage: info: source package cyvcf2 dpkg-buildpackage: info: source version 0.30.4-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from cyvcf2-0.30.4/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/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 debian/rules override_dh_clean make[1]: Entering directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' dh_clean rm -rf cyvcf2.egg-info cyvcf2/cyvcf2.c __o.vcf find . -name "*.so" -delete make[1]: Leaving directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' debian/rules binary-arch dh binary-arch --with python3 --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 Compiling cyvcf2/cyvcf2.pyx because it changed. [1/1] Cythonizing cyvcf2/cyvcf2.pyx 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/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_writer.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests running egg_info creating cyvcf2.egg-info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt writing manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/no-seq-len.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/no-seq-names.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-diff.csi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-invalid-header.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.bug.117.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests running build_ext building 'cyvcf2.cyvcf2' extension creating build creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/cyvcf2 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/cyvcf2-tlNvyW/cyvcf2-0.30.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.linux-x86_64-3.9/cyvcf2/cyvcf2.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers 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 cyvcf2/cyvcf2.c:651: /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 " \ | ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:14374:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 14374 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); | ^ cyvcf2/cyvcf2.c:14483:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 14483 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); | ^ cyvcf2/cyvcf2.c:14566:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 14566 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); | ^ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-QL8yo8/python3.9-3.9.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/cyvcf2-tlNvyW/cyvcf2-0.30.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/helpers.c -o build/temp.linux-x86_64-3.9/cyvcf2/helpers.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/cyvcf2-tlNvyW/cyvcf2-0.30.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/cyvcf2/cyvcf2.o build/temp.linux-x86_64-3.9/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cyvcf2.cpython-39-x86_64-linux-gnu.so debian/rules override_dh_auto_test make[1]: Entering directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' dh_auto_test I: pybuild base:232: cd /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build; python3.9 -m nose -v cyvcf2.tests.test_cli.test_version ... ok make sure that we are getting the correct gt_types ... ok cyvcf2.tests.test_reader.test_init ... ok cyvcf2.tests.test_reader.test_type ... ok cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_missing_samples ... ok cyvcf2.tests.test_reader.test_ibd ... ok cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 ok cyvcf2.tests.test_reader.test_pls ... ok cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok cyvcf2.tests.test_reader.test_str ... ok cyvcf2.tests.test_reader.test_region ... ok cyvcf2.tests.test_reader.test_empty_info ... ok cyvcf2.tests.test_reader.test_phases ... ok cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to open file "XXXXX" : No such file or directory ok cyvcf2.tests.test_reader.test_samples ... ok cyvcf2.tests.test_reader.test_next ... ok cyvcf2.tests.test_reader.test_variant ... ok cyvcf2.tests.test_reader.test_info_dict ... ok cyvcf2.tests.test_reader.test_attrs ... ok cyvcf2.tests.test_reader.test_empty ... ok cyvcf2.tests.test_reader.test_format_field ... ok cyvcf2.tests.test_reader.test_writer_from_string ... [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_writer ... ok cyvcf2.tests.test_reader.test_add_info_to_header ... ok cyvcf2.tests.test_reader.test_read_flag ... ok cyvcf2.tests.test_reader.test_add_flag ... ok cyvcf2.tests.test_reader.test_constants ... ok cyvcf2.tests.test_reader.test_add_filter_to_header ... ok cyvcf2.tests.test_reader.test_seqnames ... ok cyvcf2.tests.test_reader.test_different_index ... ok cyvcf2.tests.test_reader.test_var_type ... ok cyvcf2.tests.test_reader.test_header_info ... ok cyvcf2.tests.test_reader.test_snpeff_header ... ok cyvcf2.tests.test_reader.test_gt_types ... ok cyvcf2.tests.test_reader.test_raw_header ... ok cyvcf2.tests.test_reader.test_iterate ... ok cyvcf2.tests.test_reader.test_empty_call ... ok cyvcf2.tests.test_reader.test_haploid ... ok cyvcf2.tests.test_reader.test_diploid ... ok cyvcf2.tests.test_reader.test_format ... ok cyvcf2.tests.test_reader.test_header_stuff ... ok cyvcf2.tests.test_reader.test_bcf ... OK no intervals found for b'/build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf' at 1:69260-69438 ok cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok Ensure gt_bases works with more complex base representations. ... ok cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok test that we can handle multiple (in this case 3) values per sample ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_str_bytes_second_longer ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_str_bytes_first_longer ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_format_str_bytes_number3 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_info_del ... ok cyvcf2.tests.test_reader.test_filter_id ... ok cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_access_genotype ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_access_genotype_array ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_samples ... ok cyvcf2.tests.test_reader.test_hrec ... ok cyvcf2.tests.test_reader.test_issue44 ... ok cyvcf2.tests.test_reader.test_id_field_updates ... ok cyvcf2.tests.test_reader.test_set_pos ... ok cyvcf2.tests.test_reader.test_set_chrom_when_contig_not_in_header ... [cyvcf2]: added new contig NEW to headerok cyvcf2.tests.test_reader.test_set_chrom_after_contig_is_added_to_header ... ok cyvcf2.tests.test_reader.test_set_qual ... ok cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok cyvcf2.tests.test_reader.test_alt_repr ... ok cyvcf2.tests.test_reader.test_closed_iter ... ok cyvcf2.tests.test_reader.test_issue72 ... ok cyvcf2.tests.test_reader.test_is_transition ... ok cyvcf2.tests.test_reader.test_decomposed ... ok cyvcf2.tests.test_reader.test_fd ... ok cyvcf2.tests.test_reader.test_set_reference ... ok cyvcf2.tests.test_reader.test_set_alternates ... ok cyvcf2.tests.test_reader.test_no_seqlen ... ok cyvcf2.tests.test_reader.test_set_unknown_format ... ok cyvcf2.tests.test_reader.test_invalid_header ... [E::bcf_hdr_add_sample_len] Empty sample name: trailing spaces/tabs in the header line? ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithBcfFname_returnsCompressedBcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithCompressedBcfFname_returnsCompressedBcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithCompressedVcfFname_returnsCompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithHandle_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithIntFname_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithNonVcfName_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithPosixPath_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithStdOut_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_defaultModeWithVcfFname_returnsUncompressedVcf ... ok cyvcf2.tests.test_writer.TestFileModeInference.test_explicitMode_doesNotInferFromFname ... ok ---------------------------------------------------------------------- Ran 92 tests in 2.143s OK # clean up after testing find . -name out.vcf -delete make[1]: Leaving directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2 running install running build running build_py running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' running build_ext running install_lib creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9 creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cli.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/helpers.h -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cyvcf2.pxd -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/__init__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cyvcf2.cpython-39-x86_64-linux-gnu.so -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/__main__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/helpers.c -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cyvcf2.c -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/no-seq-len.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.bug.117.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__init__.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-invalid-header.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/empty.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-diff.csi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/no-seq-names.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_reader.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_writer.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_hemi.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__pycache__/test_reader.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__pycache__/test_writer.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__pycache__/test_hemi.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__pycache__/__init__.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/__pycache__/test_cli.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test_cli.py -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests creating /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/__pycache__/__init__.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/__pycache__/cli.cpython-39.pyc -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/relatedness.h -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 copying /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/.pybuild/cpython3_3.9_cyvcf2/build/cyvcf2/cyvcf2.pyx -> /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2 byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/cli.py to cli.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/__main__.py to __main__.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/test_reader.py to test_reader.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/test_writer.py to test_writer.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/test_hemi.py to test_hemi.cpython-39.pyc byte-compiling /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2/tests/test_cli.py to test_cli.cpython-39.pyc running install_egg_info Copying cyvcf2.egg-info to /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/cyvcf2-0.30.4.egg-info Skipping SOURCES.txt running install_scripts Installing cyvcf2 script to /build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' dh_numpy3 dh_install make[1]: Leaving directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' PATH=$PATH:/build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/bin \ PYTHONPATH=/build/cyvcf2-tlNvyW/cyvcf2-0.30.4/debian/python3-cyvcf2/usr/lib/python3.9/dist-packages/ \ help2man --no-info \ --name="fast parsing of VCF and BCF including region-queries" \ --version-string=0.30.4 cyvcf2 > debian/cyvcf2.1 dh_installman make[1]: Leaving directory '/build/cyvcf2-tlNvyW/cyvcf2-0.30.4' dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -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 dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'python3-cyvcf2' in '../python3-cyvcf2_0.30.4-4_amd64.deb'. dpkg-deb: building package 'python3-cyvcf2-dbgsym' in '../python3-cyvcf2-dbgsym_0.30.4-4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../cyvcf2_0.30.4-4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from cyvcf2-0.30.4/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/cyvcf2-tlNvyW /tmp/cyvcf2-0.30.4-4jyq9b1c_ I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.xkkS9_wRzQ... I: success in 459.1726 seconds md5: python3-cyvcf2-dbgsym_0.30.4-4_amd64.deb: OK md5: python3-cyvcf2_0.30.4-4_amd64.deb: OK sha1: python3-cyvcf2-dbgsym_0.30.4-4_amd64.deb: OK sha1: python3-cyvcf2_0.30.4-4_amd64.deb: OK sha256: python3-cyvcf2-dbgsym_0.30.4-4_amd64.deb: OK sha256: python3-cyvcf2_0.30.4-4_amd64.deb: OK Checksums: OK