I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 22 09:59:11 -12 2019 I: pbuilder-time-stamp: 1561240751 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-pyfaidx_0.5.5.2-1.dsc] I: copying [./python-pyfaidx_0.5.5.2.orig.tar.gz] I: copying [./python-pyfaidx_0.5.5.2-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 26 17:17:57 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pyfaidx_0.5.5.2-1.dsc dpkg-source: info: extracting python-pyfaidx in python-pyfaidx-0.5.5.2 dpkg-source: info: unpacking python-pyfaidx_0.5.5.2.orig.tar.gz dpkg-source: info: unpacking python-pyfaidx_0.5.5.2-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, python-all, python-coverage, python-setuptools, python-nose, python-numpy, python-six, python-mock, python3-all, python3-coverage, python3-setuptools, python3-nose, python3-numpy, python3-six, python3-mock dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python-all; however: Package python-all is not installed. pbuilder-satisfydepends-dummy depends on python-coverage; however: Package python-coverage is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python-nose; however: Package python-nose is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-six; however: Package python-six is not installed. pbuilder-satisfydepends-dummy depends on python-mock; however: Package python-mock is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-coverage; however: Package python3-coverage is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six is not installed. pbuilder-satisfydepends-dummy depends on python3-mock; however: Package python3-mock is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-all{a} python-coverage{a} python-funcsigs{a} python-minimal{a} python-mock{a} python-nose{a} python-numpy{a} python-pbr{a} python-pkg-resources{a} python-setuptools{a} python-six{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-all{a} python3-coverage{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-mock{a} python3-nose{a} python3-numpy{a} python3-pbr{a} python3-pkg-resources{a} python3-setuptools{a} python3-six{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libjs-jquery-isonscreen libjs-jquery-tablesorter libjs-jquery-throttle-debounce libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 158 MB will be used. Writing extended state information... Get: 1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://cdn-fastly.deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://cdn-fastly.deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://cdn-fastly.deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython2.7-minimal i386 2.7.16-2 [395 kB] Get: 8 http://cdn-fastly.deb.debian.org/debian buster/main i386 python2.7-minimal i386 2.7.16-2 [1383 kB] Get: 9 http://cdn-fastly.deb.debian.org/debian buster/main i386 python2-minimal i386 2.7.16-1 [41.4 kB] Get: 10 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-minimal i386 2.7.16-1 [21.0 kB] Get: 11 http://cdn-fastly.deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1c-1 [1532 kB] Get: 12 http://cdn-fastly.deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://cdn-fastly.deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-1 [102 kB] Get: 14 http://cdn-fastly.deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://cdn-fastly.deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython2.7-stdlib i386 2.7.16-2 [1935 kB] Get: 17 http://cdn-fastly.deb.debian.org/debian buster/main i386 python2.7 i386 2.7.16-2 [305 kB] Get: 18 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython2-stdlib i386 2.7.16-1 [20.8 kB] Get: 19 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython-stdlib i386 2.7.16-1 [20.8 kB] Get: 20 http://cdn-fastly.deb.debian.org/debian buster/main i386 python2 i386 2.7.16-1 [41.6 kB] Get: 21 http://cdn-fastly.deb.debian.org/debian buster/main i386 python i386 2.7.16-1 [22.8 kB] Get: 22 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython3.7-minimal i386 3.7.3-2 [590 kB] Get: 23 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3.7-minimal i386 3.7.3-2 [1746 kB] Get: 24 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-minimal i386 3.7.3-1 [36.6 kB] Get: 25 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmpdec2 i386 2.4.2-2 [83.2 kB] Get: 26 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython3.7-stdlib i386 3.7.3-2 [1751 kB] Get: 27 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3.7 i386 3.7.3-2 [330 kB] Get: 28 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpython3-stdlib i386 3.7.3-1 [20.0 kB] Get: 29 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3 i386 3.7.3-1 [61.5 kB] Get: 30 http://cdn-fastly.deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 31 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4 [242 kB] Get: 32 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4 [124 kB] Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 file i386 1:5.35-4 [66.3 kB] Get: 34 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 35 http://cdn-fastly.deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 36 http://cdn-fastly.deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 37 http://cdn-fastly.deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 38 http://cdn-fastly.deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://cdn-fastly.deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 40 http://cdn-fastly.deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 42 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 43 http://cdn-fastly.deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 44 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 45 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 46 http://cdn-fastly.deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 47 http://cdn-fastly.deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 48 http://cdn-fastly.deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2 [1333 kB] Get: 49 http://cdn-fastly.deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 50 http://cdn-fastly.deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 51 http://cdn-fastly.deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 52 http://cdn-fastly.deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2 [109 kB] Get: 53 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 54 http://cdn-fastly.deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 56 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 57 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 58 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-distutils all 3.7.3-1 [142 kB] Get: 59 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-python all 3.20190308 [99.3 kB] Get: 60 http://cdn-fastly.deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 61 http://cdn-fastly.deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 62 http://cdn-fastly.deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 63 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-all i386 2.7.16-1 [1044 B] Get: 64 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-pkg-resources all 40.8.0-1 [182 kB] Get: 65 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-coverage i386 4.5.2+dfsg.1-1 [145 kB] Get: 66 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-funcsigs all 1.0.2-4 [13.7 kB] Get: 67 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-setuptools all 40.8.0-1 [382 kB] Get: 68 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-six all 1.12.0-1 [15.7 kB] Get: 69 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-pbr all 4.2.0-5 [56.5 kB] Get: 70 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-mock all 2.0.0-4 [60.2 kB] Get: 71 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-nose all 1.3.7-4 [132 kB] Get: 72 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-numpy i386 1:1.16.2-1 [2096 kB] Get: 73 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-all i386 3.7.3-1 [1068 B] Get: 74 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 75 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-coverage i386 4.5.2+dfsg.1-1 [144 kB] Get: 76 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-setuptools all 40.8.0-1 [306 kB] Get: 77 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-six all 1.12.0-1 [15.7 kB] Get: 78 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-pbr all 4.2.0-5 [56.5 kB] Get: 79 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-mock all 2.0.0-4 [60.3 kB] Get: 80 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-nose all 1.3.7-4 [132 kB] Get: 81 http://cdn-fastly.deb.debian.org/debian buster/main i386 python3-numpy i386 1:1.16.2-1 [2115 kB] Fetched 39.1 MB in 42s (941 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:i386. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2_i386.deb ... Unpacking libpython2.7-minimal:i386 (2.7.16-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2_i386.deb ... Unpacking python2.7-minimal (2.7.16-2) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_i386.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_i386.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../10-libssl1.1_1.1.1c-1_i386.deb ... Unpacking libssl1.1:i386 (1.1.1c-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../12-libexpat1_2.2.6-1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:i386. Preparing to unpack .../14-libreadline7_7.0-5_i386.deb ... Unpacking libreadline7:i386 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:i386. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2_i386.deb ... Unpacking libpython2.7-stdlib:i386 (2.7.16-2) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2_i386.deb ... Unpacking python2.7 (2.7.16-2) ... Selecting previously unselected package libpython2-stdlib:i386. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_i386.deb ... Unpacking libpython2-stdlib:i386 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:i386. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_i386.deb ... Unpacking libpython-stdlib:i386 (2.7.16-1) ... Setting up libpython2.7-minimal:i386 (2.7.16-2) ... Setting up python2.7-minimal (2.7.16-2) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20696 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_i386.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20729 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_i386.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libpython3.7-minimal:i386. Preparing to unpack .../libpython3.7-minimal_3.7.3-2_i386.deb ... Unpacking libpython3.7-minimal:i386 (3.7.3-2) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.3-2_i386.deb ... Unpacking python3.7-minimal (3.7.3-2) ... Setting up libssl1.1:i386 (1.1.1c-1) ... Setting up libpython3.7-minimal:i386 (3.7.3-2) ... Setting up libexpat1:i386 (2.2.6-1) ... Setting up python3.7-minimal (3.7.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20983 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_i386.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../libmpdec2_2.4.2-2_i386.deb ... Unpacking libmpdec2:i386 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:i386. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2_i386.deb ... Unpacking libpython3.7-stdlib:i386 (3.7.3-2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2_i386.deb ... Unpacking python3.7 (3.7.3-2) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../libpython3-stdlib_3.7.3-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (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 ... 21395 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_i386.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_i386.deb ... Unpacking libmagic-mgc (1:5.35-4) ... 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Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:i386 (2.7.16-2) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython3-stdlib:i386 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2) ... Setting up liblapack3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2) ... Setting up libpython2-stdlib:i386 (2.7.16-1) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up libpython-stdlib:i386 (2.7.16-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python3-setuptools (40.8.0-1) ... 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Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/python-pyfaidx-0.5.5.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package python-pyfaidx dpkg-buildpackage: info: source version 0.5.5.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean LC_ALL=C.UTF-8 dh clean --with python2,python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean running clean removing '/build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build LC_ALL=C.UTF-8 dh build --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build/pyfaidx copying pyfaidx/cli.py -> /build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build/pyfaidx copying pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build/pyfaidx I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build/pyfaidx copying pyfaidx/cli.py -> /build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build/pyfaidx copying pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build/pyfaidx debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pyfaidx-0.5.5.2' dh_auto_test -- --test --system=custom --test-args='set -e; \ {interpreter} -m "nose" --with-coverage --cover-package=pyfaidx' I: pybuild base:217: set -e; \ python2.7 -m "nose" --with-coverage --cover-package=pyfaidx 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 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 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 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 712 149 79% 14-15, 24, 165, 170, 293, 336-347, 350, 360-367, 377-381, 389, 393, 418-419, 444, 447, 483, 485, 491, 545-546, 590, 597-600, 665-668, 711, 724, 726, 746, 761-772, 778, 803, 810, 850, 893-904, 927, 939, 943, 945, 947, 952, 1007, 1015-1016, 1019, 1054, 1061, 1083-1122, 1125, 1134-1154, 1172-1174, 1198-1203, 1211-1212, 1250, 1258, 1264-1265 pyfaidx/cli.py 256 128 50% 31-36, 47-50, 78, 80, 91-106, 120-140, 181-182, 186, 190, 192, 195, 202-207, 211-217, 231, 234, 240-242, 251-253, 259, 268-281, 285, 289-290, 293-296, 311-318, 324-331, 337-345, 351-361, 364 --------------------------------------------------- TOTAL 968 277 71% ---------------------------------------------------------------------- Ran 139 tests in 1405.065s OK (SKIP=36) I: pybuild base:217: set -e; \ python3.7 -m "nose" --with-coverage --cover-package=pyfaidx 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 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 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 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 712 146 79% 14-15, 165, 170, 293, 336-347, 350, 360-367, 377-381, 389, 393, 418-419, 444, 447, 483, 485, 491, 545-546, 590, 597-600, 665-668, 711, 724, 726, 746, 761-772, 778, 803, 810, 850, 893-904, 927, 939, 943, 945, 947, 952, 1007, 1015-1016, 1019, 1054, 1061, 1083-1122, 1125, 1134-1154, 1198-1203, 1211-1212, 1250, 1258, 1264-1265 pyfaidx/cli.py 256 128 50% 31-36, 47-50, 78, 80, 91-106, 120-140, 181-182, 186, 190, 192, 195, 202-207, 211-217, 231, 234, 240-242, 251-253, 259, 268-281, 285, 289-290, 293-296, 311-318, 324-331, 337-345, 351-361, 364 --------------------------------------------------- TOTAL 968 274 72% ---------------------------------------------------------------------- Ran 139 tests in 1184.166s OK (SKIP=36) make[1]: Leaving directory '/build/python-pyfaidx-0.5.5.2' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary LC_ALL=C.UTF-8 dh binary --with python2,python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx running install running build running build_py running install_lib creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7 creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages creating /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build/pyfaidx/cli.py -> /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.5.2/.pybuild/cpython2_2.7_pyfaidx/build/pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx byte-compiling /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx/cli.py to cli.pyc byte-compiling /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx/__init__.py to __init__.pyc running install_egg_info running egg_info creating pyfaidx.egg-info writing requirements to pyfaidx.egg-info/requires.txt writing pyfaidx.egg-info/PKG-INFO writing top-level names to pyfaidx.egg-info/top_level.txt writing dependency_links to pyfaidx.egg-info/dependency_links.txt writing entry points to pyfaidx.egg-info/entry_points.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-0.5.5.2/debian/python-pyfaidx/usr/lib/python2.7/dist-packages/pyfaidx-0.5.5.2.egg-info Skipping SOURCES.txt running install_scripts Installing faidx script to /build/python-pyfaidx-0.5.5.2/debian/python-pyfaidx/usr/bin I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx running install running build running build_py running install_lib creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7 creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages creating /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build/pyfaidx/cli.py -> /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.5.2/.pybuild/cpython3_3.7_pyfaidx/build/pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx byte-compiling /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx/cli.py to cli.cpython-37.pyc byte-compiling /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx/__init__.py to __init__.cpython-37.pyc running install_egg_info running 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 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-0.5.5.2/debian/python3-pyfaidx/usr/lib/python3.7/dist-packages/pyfaidx-0.5.5.2.egg-info Skipping SOURCES.txt running install_scripts Installing faidx script to /build/python-pyfaidx-0.5.5.2/debian/python3-pyfaidx/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/python-pyfaidx-0.5.5.2' dh_install # remove duplilcated wrapper script from Python2 package rm -rf debian/python-pyfaidx/usr/bin make[1]: Leaving directory '/build/python-pyfaidx-0.5.5.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/python-pyfaidx-0.5.5.2' dh_compress --exclude=gz.tbi make[1]: Leaving directory '/build/python-pyfaidx-0.5.5.2' dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-pyfaidx: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pyfaidx: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python-pyfaidx' in '../python-pyfaidx_0.5.5.2-1_all.deb'. dpkg-deb: building package 'python-pyfaidx-examples' in '../python-pyfaidx-examples_0.5.5.2-1_all.deb'. dpkg-deb: building package 'python3-pyfaidx' in '../python3-pyfaidx_0.5.5.2-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-pyfaidx_0.5.5.2-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/8730 and its subdirectories I: Current time: Sat Jun 22 10:57:43 -12 2019 I: pbuilder-time-stamp: 1561244263