Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/python-pyfaidx/python-pyfaidx_0.5.9.2-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/python-pyfaidx-0.5.9.2-1v84829p_/python-pyfaidx_0.5.9.2-1_all.buildinfo Get source package info: python-pyfaidx=0.5.9.2-1 Source URL: http://snapshot.notset.fr/mr/package/python-pyfaidx/0.5.9.2-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.1-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.1-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1+b1 libbinutils=2.35.1-4 libblas3=3.9.0-3 libblkid1=2.36.1-2 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libcurl3-gnutls=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.1-1 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhts3=1.11-2 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-1 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=2.4.56+dfsg-1 liblsan0=10.2.1-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-1 libncursesw6=6.2+20201114-1 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.21-2 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=10.35-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libpython3-stdlib=3.9.0-4 libpython3.9-minimal=3.9.1-1 libpython3.9-stdlib=3.9.1-1 libquadmath0=10.2.1-1 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=2.5.0-3+b1 libselinux1=3.1-2+b2 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libsqlite3-0=3.34.0-1 libssh2-1=1.9.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsystemd0=247.1-3 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libudev1=247.1-3 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 python3=3.9.0-4 python3-all=3.9.0-4 python3-coverage=5.1+dfsg.1-2+b2 python3-distutils=3.8.6-1 python3-lib2to3=3.8.6-1 python3-minimal=3.9.0-4 python3-mock=4.0.2-1 python3-nose=1.3.7-7 python3-numpy=1:1.19.4-1+b1 python3-pbr=5.5.0-2 python3-pkg-resources=50.3.0-1 python3-setuptools=50.3.0-1 python3-six=1.15.0-2 python3.9=3.9.1-1 python3.9-minimal=3.9.1-1 readline-common=8.1-1 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tabix=1.11-2 tar=1.32+dfsg-1 tzdata=2020d-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201210T083846Z/ 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 python-pyfaidx=0.5.9.2-1 && mkdir -p /build/python-pyfaidx-kAoxNT && dpkg-source --no-check -x /*.dsc /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2 && chown -R builduser:builduser /build/python-pyfaidx-kAoxNT" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607778023" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/python-pyfaidx-kAoxNT /tmp/python-pyfaidx-0.5.9.2-1v84829p_ bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201210T083846Z 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.inmBx4fZBx 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.inmBx4fZBx Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). 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/20201210T083846Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201210T083846Z 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 (827 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 ... 4616 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 (2.31-5) ... 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/20201210T083846Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.inmBx4fZBx Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201210T083846Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1146 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.inmBx4fZBx I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d python-pyfaidx=0.5.9.2-1 && mkdir -p /build/python-pyfaidx-kAoxNT && dpkg-source --no-check -x /*.dsc /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2 && chown -R builduser:builduser /build/python-pyfaidx-kAoxNT"' exec /tmp/mmdebstrap.inmBx4fZBx Reading package lists... NOTICE: 'python-pyfaidx' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pyfaidx.git Please use: git clone https://salsa.debian.org/med-team/python-pyfaidx.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 101 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pyfaidx 0.5.9.2-1 (dsc) [2337 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pyfaidx 0.5.9.2-1 (tar) [93.4 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main python-pyfaidx 0.5.9.2-1 (diff) [5140 B] Fetched 101 kB in 0s (506 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'python-pyfaidx_0.5.9.2-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting python-pyfaidx in /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2 dpkg-source: info: unpacking python-pyfaidx_0.5.9.2.orig.tar.gz dpkg-source: info: unpacking python-pyfaidx_0.5.9.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test-locale-to-c.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607778023" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.inmBx4fZBx dpkg-buildpackage: info: source package python-pyfaidx dpkg-buildpackage: info: source version 0.5.9.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . debian/rules clean LC_ALL=C.UTF-8 dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/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 rm -f .coverage rm -f tests/data/genes.fasta.gz rm -rf pyfaidx.egg-info make[1]: Leaving directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-indep LC_ALL=C.UTF-8 dh binary-indep --with python3 --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:232: python3.9 setup.py config running config dh_auto_build -i -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx copying pyfaidx/cli.py -> /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx copying pyfaidx/__init__.py -> /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' bgzip -c tests/data/genes.fasta > tests/data/genes.fasta.gz dh_auto_test -- --test --system=custom --test-args='set -e; \ {interpreter} -m "nose" --with-coverage --cover-package=pyfaidx' I: pybuild base:232: set -e; \ python3.9 -m "nose" --with-coverage --cover-package=pyfaidx Doctest: pyfaidx.Sequence.__eq__ ... ok Doctest: pyfaidx.Sequence.__getitem__ ... ok Doctest: pyfaidx.Sequence.__len__ ... ok Doctest: pyfaidx.Sequence.__neg__ ... ok Doctest: pyfaidx.Sequence.complement ... ok Doctest: pyfaidx.Sequence.fancy_name ... ok Doctest: pyfaidx.Sequence.gc ... ok Doctest: pyfaidx.Sequence.long_name ... ok Doctest: pyfaidx.Sequence.orientation ... ok Doctest: pyfaidx.Sequence.reverse ... ok Doctest: pyfaidx.check_bad_lines ... ok Doctest: pyfaidx.complement ... ok Doctest: pyfaidx.get_valid_filename ... ok Check for pathogenic FastaRecord.long_name behavior in mdshw5/pyfaidx#62 ... ok Test that deflines extracted using FastaRecord.long_name are ... ok Test the __array_interface__ ... ok Test that the sequence is always returned in ... ok test_unpadded_length (test_FastaRecord.TestFastaRecord) ... ok test_mutate_fasta_to_N (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_fasta_to_same (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_immutable_fasta (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_single_position (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_too_long (test_FastaRecord.TestMutableFastaRecord) ... ok test_fetch_whole_fasta (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_line_len (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_reverse_iter (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_all_diff (test_FastaVariant.TestFastaVariant) ... SKIP test_all_pos (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_het_variant (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_hom_variant (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_variant (test_FastaVariant.TestFastaVariant) ... SKIP seq[0:0] should return a blank string mdshw5/pyfaidx#53 ... SKIP Fetch past the end of a gene entry ... SKIP Fetch past the end of a gene entry ... SKIP test_fetch_end (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Fetch a key that does not exist ... SKIP test_fetch_middle (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Fetch starting with a negative coordinate ... SKIP Fetch past the end of a gene entry ... SKIP Fetch starting with a negative coordinate ... SKIP test_fetch_whole_entry (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_fetch_whole_fasta (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_integer_index (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_integer_slice (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_consistency (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_end_faidx (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_end_fasta (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_start (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_negate (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_one_based_false (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_one_based_false_negate (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_line_len (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Test that deflines extracted using FastaRecord.long_name are ... SKIP test_mutable_bgzf (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_rev (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_slice_from_beginning (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_slice_from_end (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Samtools BGZF index should be identical to pyfaidx BGZF index ... SKIP test_integer_index (test_Fasta_integer_index.TestFastaIntIndex) ... ok test_integer_slice (test_Fasta_integer_index.TestFastaIntIndex) ... ok Test that each read of a sequence range is atomic. ... ok Combine the above two tests to check that interleaved reads and writes don't conflict. ... ok Test that each write of a sequence range is atomic. ... ok test_fetch_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP test_revcomp_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP test_slice_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP Test that --auto-strand produces the same output as --reverse --complement ... ok test_fetch_error (test_faidx.TestCLI) ... ok test_fetch_whole_file (test_faidx.TestCLI) ... ok test_key_warning (test_faidx.TestCLI) ... warning: foo not found in file ok test_not_regexp (test_faidx.TestCLI) ... ok test_not_regexp_multi (test_faidx.TestCLI) ... ok test_regexp (test_faidx.TestCLI) ... ok test_short_line_lengths (test_faidx.TestCLI) ... ok test_split_entry (test_faidx.TestCLI) ... ok seq[0:0] should return a blank string mdshw5/pyfaidx#53 ... ok Fetch past the end of a gene entry ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_end ... ok Fetch a key that does not exist ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_middle ... ok Fetch starting with a negative coordinate ... ok Fetch past the end of a gene entry ... ok Fetch starting with a negative coordinate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_whole_entry ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_consistency ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_end_faidx ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_end_fasta ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_start ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_negate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_one_based_false ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_one_based_false_negate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_rev ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_slice_from_beginning ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_slice_from_end ... ok test_feature_bounds_check.TestFeatureZeroLength.test_fetch_zero_length ... ok test_feature_bounds_check.TestFeatureZeroLength.test_index_zero_length ... ok test_as_raw_zero_length_subsequence (test_feature_bounds_check.TestZeroLengthSequenceSubRange) ... ok test_zero_length_subsequence (test_feature_bounds_check.TestZeroLengthSequenceSubRange) ... ok Fetch past the end of a gene entry ... ok test_build (test_feature_indexing.TestIndexing) ... ok test_build_issue_111 (test_feature_indexing.TestIndexing) ... ok test_build_issue_141 (test_feature_indexing.TestIndexing) ... ok Ensure that blank lines between entries are treated in the ... ok Ensure that the fasta file is closed if construction of the 'Faidx' file ... ok Ensure that the fasta file is closed if construction of the 'Faidx' file ... ok Ensure that index file is not built when build_index=False. See mdshw5/pyfaidx#134. ... ok Ensure that an exception is raised when a file contains no deflines. See mdshw5/pyfaidx#144. ... ok test_order (test_feature_indexing.TestIndexing) ... ok Ensure that index files written with write_fai() can be read back ... ok This test ensures that the index is regenerated when the FASTA ... ok Makes all full-length lines blank and checks that error is raised ... ok Makes all full-length lines long and checks that error is raised ... ok Makes all full-length lines short and checks that error is raised ... ok test_duplicated_keys (test_feature_key_function.TestFeatureKeyFunction) ... ok test_duplicated_keys_longest (test_feature_key_function.TestFeatureKeyFunction) ... ok test_duplicated_keys_shortest (test_feature_key_function.TestFeatureKeyFunction) ... ok test_key_function_by_dictionary_get_key (test_feature_key_function.TestFeatureKeyFunction) ... ok test_key_function_by_fetch (test_feature_key_function.TestFeatureKeyFunction) ... ok test_keys (test_feature_key_function.TestFeatureKeyFunction) ... ok test_bounds_error (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_exceed (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_false (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_true (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_value (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_as_raw_false (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_false_error (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_true (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_true_error (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_type_when_blen_lt_0 (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok Check get_seq with rc argument ... ok Fetch sequence by blocks ... ok test_key_function_by_dictionary_get_key (test_feature_split_char.TestFeatureSplitChar) ... ok test_key_function_by_fetch (test_feature_split_char.TestFeatureSplitChar) ... ok test_keys (test_feature_split_char.TestFeatureSplitChar) ... ok test_stop (test_feature_split_char.TestFeatureSplitChar) ... ok test_sequence_class.test_negate ... ok test_sequence_class.test_negate_metadata ... ok test_sequence_class.test_seq_invalid ... ok test_sequence_class.test_integer_index ... ok test_sequence_class.test_slice_index ... ok test_sequence_class.test_comp_invalid ... ok test_sequence_class.test_check_coordinates ... ok test_sequence_class.test_comp_valid ... ok test_sequence_class.test_comp_empty ... ok Name Stmts Miss Cover Missing --------------------------------------------------- pyfaidx/__init__.py 730 149 80% 24-25, 169, 174, 303-305, 347-358, 361, 371-378, 388-392, 400, 404, 429-430, 455, 458, 494, 496, 502, 556-557, 601, 677-680, 726, 739, 741, 761, 776-787, 793, 818, 825, 865, 908-919, 942, 954, 958, 960, 962, 967, 1018, 1026-1027, 1030, 1037, 1068, 1078, 1081, 1084, 1106-1145, 1148, 1157-1177, 1198-1200, 1221-1226, 1234-1235, 1273, 1281, 1302-1303 pyfaidx/cli.py 255 128 50% 29-34, 45-48, 76, 78, 89-104, 118-138, 179-180, 184, 188, 190, 193, 200-205, 209-215, 229, 232, 238-240, 249-251, 257, 266-279, 283, 287-288, 291-294, 309-316, 322-329, 335-343, 349-359, 362 --------------------------------------------------- TOTAL 985 277 72% ---------------------------------------------------------------------- Ran 146 tests in 59.589s OK (SKIP=36) make[1]: Leaving directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx running install running build running build_py running install_lib creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9 creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages creating /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx copying /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx/cli.py -> /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx copying /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx/__init__.py -> /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx byte-compiling /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx/cli.py to cli.cpython-39.pyc byte-compiling /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx/__init__.py to __init__.cpython-39.pyc running install_egg_info running egg_info creating pyfaidx.egg-info writing pyfaidx.egg-info/PKG-INFO writing dependency_links to pyfaidx.egg-info/dependency_links.txt writing entry points to pyfaidx.egg-info/entry_points.txt writing requirements to pyfaidx.egg-info/requires.txt writing top-level names to pyfaidx.egg-info/top_level.txt writing manifest file 'pyfaidx.egg-info/SOURCES.txt' reading manifest file 'pyfaidx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'docs/build/html/*' writing manifest file 'pyfaidx.egg-info/SOURCES.txt' Copying pyfaidx.egg-info to /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx-0.5.9.2.egg-info Skipping SOURCES.txt running install_scripts Installing faidx script to /build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/bin dh_installdocs -i -O--buildsystem=pybuild dh_installchangelogs -i -O--buildsystem=pybuild dh_installexamples -i -O--buildsystem=pybuild dh_installman -i -O--buildsystem=pybuild dh_python3 -i -O--buildsystem=pybuild dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' dh_compress --exclude=gz.tbi make[1]: Leaving directory '/build/python-pyfaidx-kAoxNT/python-pyfaidx-0.5.9.2' dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyfaidx' in '../python3-pyfaidx_0.5.9.2-1_all.deb'. dpkg-deb: building package 'python-pyfaidx-examples' in '../python-pyfaidx-examples_0.5.9.2-1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../python-pyfaidx_0.5.9.2-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/python-pyfaidx-kAoxNT /tmp/python-pyfaidx-0.5.9.2-1v84829p_ I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.inmBx4fZBx... I: success in 528.4656 seconds md5: python-pyfaidx-examples_0.5.9.2-1_all.deb: OK md5: python3-pyfaidx_0.5.9.2-1_all.deb: OK sha1: python-pyfaidx-examples_0.5.9.2-1_all.deb: OK sha1: python3-pyfaidx_0.5.9.2-1_all.deb: OK sha256: python-pyfaidx-examples_0.5.9.2-1_all.deb: OK sha256: python3-pyfaidx_0.5.9.2-1_all.deb: OK Checksums: OK