Tue Jul 27 05:21:33 UTC 2021 I: starting to build python-gffutils/bullseye/i386 on jenkins on '2021-07-27 05:21' Tue Jul 27 05:21:33 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/13784/console.log Tue Jul 27 05:21:33 UTC 2021 I: Downloading source for bullseye/python-gffutils=0.10.1-2 --2021-07-27 05:21:33-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/python-gffutils/python-gffutils_0.10.1-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) Saving to: ‘python-gffutils_0.10.1-2.dsc’ 0K .. 100% 157M=0s 2021-07-27 05:21:34 (157 MB/s) - ‘python-gffutils_0.10.1-2.dsc’ saved [2331/2331] Tue Jul 27 05:21:34 UTC 2021 I: python-gffutils_0.10.1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: python-gffutils Binary: python3-gffutils Architecture: all Version: 0.10.1-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller Homepage: https://daler.github.io/gffutils Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/python-gffutils Vcs-Git: https://salsa.debian.org/med-team/python-gffutils.git Testsuite: autopkgtest Testsuite-Triggers: python3-nose Build-Depends: debhelper-compat (= 12), dh-python, bedtools, python3-all, python3-setuptools, python3-simplejson, python3-six, python3-argcomplete, python3-argh, python3-pyfaidx, python3-nose, python3-biopython, python3-pybedtools, help2man Package-List: python3-gffutils deb science optional arch=all Checksums-Sha1: 7b5c8697f5828042ea811f8ab78bab8697b1e9c8 1542433 python-gffutils_0.10.1.orig.tar.gz db5ad220474c1421c3c926468bfeb6686381ab8d 4996 python-gffutils_0.10.1-2.debian.tar.xz Checksums-Sha256: a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb 1542433 python-gffutils_0.10.1.orig.tar.gz 3c94175574f302c34900eadb71c24b03391b0e528be71e0186b075027b7824c7 4996 python-gffutils_0.10.1-2.debian.tar.xz Files: fb1de9379a29c37ab6f7f0613eba3128 1542433 python-gffutils_0.10.1.orig.tar.gz 5c00951e5d69596c3c4ebb59282a6b94 4996 python-gffutils_0.10.1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl5LsdcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHZEA/+MLIlDh8kx4MXRjuBynVt09/IaO9U39f3 9Kb9lgBgfoTnvRBOQ4xw7ken8ykwc1v4vkC6FKnNvc1eFfg9fYb+ReciajN5+o3+ U5kI6LFfn0kjoug+29Kg0s7zm/0DLYZXFyMJj/Tl2RipJsp77pKBi+MWVtmigFbL bAVKqKHXBPQRJh/kpmrZCpUfJUvCVl6tZqV6Rcwwh37vM/GaujvHYqS3aJXJAmTT 9W4RdR6toklIsuC1IlGxsGSCZCkjt2KGqix73X10FgVCHHG7MVUzAhYkz2uBTD2r gTMy8wqqVmG5IRqUcZaht2vdBYppOaW36eme1io062SpU7+EyYKBhPLuIYQ40rKC gLfZ1hFiguNSRS65sNCM06VOX0Z2TWSX/mvwOVaw/AJALzPAR2kbvy70IjoabPdO lP5lDKwYUQK1y19CxOhvXvOmeFl4kGO5dEbA6WsGLCjSx4aqqyH8ZcLthEtl6P+V SjSorlVO0GSbFoRSEv2t5d3HLETcCHobiYL73oWXDwFbzJJFTkXNyK9vhQnDDuUC sPIof2MRZw6+WFiIGmTgFZNNf21l2E5W+E9fSGj6PzHKUEINeIEbSKYpD4c1Ajf1 Ba4k56q0G7WSztCUf5exC7jRysMV6EC+zMzJ7wujCURruA/KOGe2d6rph+qOL8aS Yep4GKyLRCs= =HaRz -----END PGP SIGNATURE----- Tue Jul 27 05:21:34 UTC 2021 I: Checking whether the package is not for us Tue Jul 27 05:21:34 UTC 2021 I: Starting 1st build on remote node ionos2-i386.debian.net. Tue Jul 27 05:21:34 UTC 2021 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Tue Jul 27 05:26:46 UTC 2021 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 26 17:21:39 -12 2021 I: pbuilder-time-stamp: 1627363299 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-gffutils_0.10.1-2.dsc] I: copying [./python-gffutils_0.10.1.orig.tar.gz] I: copying [./python-gffutils_0.10.1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.a75eWlfi/trustedkeys.kbx': General error gpgv: Signature made Mon Feb 17 21:43:51 2020 -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-gffutils_0.10.1-2.dsc dpkg-source: info: extracting python-gffutils in python-gffutils-0.10.1 dpkg-source: info: unpacking python-gffutils_0.10.1.orig.tar.gz dpkg-source: info: unpacking python-gffutils_0.10.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying newer_bedtools dpkg-source: info: applying python3 dpkg-source: info: applying 99ba2581a184a6660ee6d8d8b6a422cd298eeee4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/453/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='9c7d50fb9007443f9cf135200307c84a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='453' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/pbuilderrc_WuLN --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/b1 --logfile b1/build.log python-gffutils_0.10.1-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos2-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-3 (2021-07-18) i686 GNU/Linux I: ls -l /bin total 5780 -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 21:26 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/453/tmp/hooks/D02_print_environment finished -> 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-compat (= 12), dh-python, bedtools, python3-all, python3-setuptools, python3-simplejson, python3-six, python3-argcomplete, python3-argh, python3-pyfaidx, python3-nose, python3-biopython, python3-pybedtools, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-simplejson; however: Package python3-simplejson is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six is not installed. pbuilder-satisfydepends-dummy depends on python3-argcomplete; however: Package python3-argcomplete is not installed. pbuilder-satisfydepends-dummy depends on python3-argh; however: Package python3-argh is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} bedtools{a} bsdextrautils{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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libhts3{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libnghttp2-14{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python3{a} python3-all{a} python3-argcomplete{a} python3-argh{a} python3-biopython{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pybedtools{a} python3-pyfaidx{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-simplejson{a} python3-six{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile python3-renderpm wget 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 52.8 MB of archives. After unpacking 175 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 liblocale-gettext-perl i386 1.07-4+b1 [19.4 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 mailcap all 3.69 [31.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 mime-support all 3.66 [10.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 bedtools i386 2.30.0+dfsg-1 [725 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 help2man i386 1.48.1 [190 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+b1 [368 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 liblcms2-2 i386 2.12~rc1-2 [161 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2.1 [269 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libwebpdemux2 i386 0.6.1-2.1 [88.2 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libwebpmux3 i386 0.6.1-2.1 [99.0 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 python3-all i386 3.9.2-3 [1060 B] Get: 82 http://deb.debian.org/debian bullseye/main i386 python3-argcomplete all 1.8.1-1.5 [29.7 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 python3-argh all 0.26.2-1.1 [25.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 python3-reportlab-accel i386 3.5.59-2 [39.9 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 python3-pil i386 8.1.2+dfsg-0.3 [445 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 python3-reportlab all 3.5.59-2 [575 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 python3-biopython i386 1.78+dfsg-4 [1401 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 python3-nose all 1.3.7-7 [133 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 python3-pysam i386 0.15.4+ds-3+b2 [1571 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-1 [17.1 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 python3-pybedtools i386 0.8.0-5 [12.1 MB] Get: 94 http://deb.debian.org/debian bullseye/main i386 python3-pyfaidx all 0.5.9.2-1 [26.4 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-4 [366 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 python3-simplejson i386 3.17.2-1 [62.8 kB] Fetched 52.8 MB in 12s (4590 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_i386.deb ... 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Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:i386 (3.9.2-1) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20557 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... 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Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 21002 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... 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Preparing to unpack .../28-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../29-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../30-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.48.1_i386.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../32-libblas3_3.9.0-3_i386.deb ... Unpacking libblas3:i386 (3.9.0-3) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../33-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../34-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../35-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../36-libsasl2-modules-db_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../37-libsasl2-2_2.1.27+dfsg-2.1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:i386. Preparing to unpack .../38-libldap-2.4-2_2.4.57+dfsg-3_i386.deb ... Unpacking libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../39-libnghttp2-14_1.43.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.43.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../40-libpsl5_0.21.0-1.2_i386.deb ... Unpacking libpsl5:i386 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../41-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../42-libssh2-1_1.9.0-2_i386.deb ... Unpacking libssh2-1:i386 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../43-libcurl3-gnutls_7.74.0-1.3+b1_i386.deb ... Unpacking libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../44-libdeflate0_1.7-1_i386.deb ... Unpacking libdeflate0:i386 (1.7-1) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../45-libpng16-16_1.6.37-3_i386.deb ... Unpacking libpng16-16:i386 (1.6.37-3) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../46-libfreetype6_2.10.4+dfsg-1_i386.deb ... Unpacking libfreetype6:i386 (2.10.4+dfsg-1) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../47-libgfortran5_10.2.1-6_i386.deb ... Unpacking libgfortran5:i386 (10.2.1-6) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../48-libhts3_1.11-4_i386.deb ... Unpacking libhts3:i386 (1.11-4) ... Selecting previously unselected package libimagequant0:i386. Preparing to unpack .../49-libimagequant0_2.12.2-1.1_i386.deb ... Unpacking libimagequant0:i386 (2.12.2-1.1) ... Selecting previously unselected package libjbig0:i386. Preparing to unpack .../50-libjbig0_2.1-3.1+b2_i386.deb ... Unpacking libjbig0:i386 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:i386. Preparing to unpack .../51-libjpeg62-turbo_1%3a2.0.6-4_i386.deb ... Unpacking libjpeg62-turbo:i386 (1:2.0.6-4) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../52-liblapack3_3.9.0-3_i386.deb ... Unpacking liblapack3:i386 (3.9.0-3) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../53-liblcms2-2_2.12~rc1-2_i386.deb ... Unpacking liblcms2-2:i386 (2.12~rc1-2) ... Selecting previously unselected package libwebp6:i386. Preparing to unpack .../54-libwebp6_0.6.1-2.1_i386.deb ... Unpacking libwebp6:i386 (0.6.1-2.1) ... Selecting previously unselected package libtiff5:i386. Preparing to unpack .../55-libtiff5_4.2.0-1_i386.deb ... Unpacking libtiff5:i386 (4.2.0-1) ... Selecting previously unselected package libwebpdemux2:i386. Preparing to unpack .../56-libwebpdemux2_0.6.1-2.1_i386.deb ... Unpacking libwebpdemux2:i386 (0.6.1-2.1) ... Selecting previously unselected package libwebpmux3:i386. Preparing to unpack .../57-libwebpmux3_0.6.1-2.1_i386.deb ... Unpacking libwebpmux3:i386 (0.6.1-2.1) ... 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Setting up file (1:5.39-3) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:i386 (3.9.0-3) ... 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 libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libimagequant0:i386 (2.12.2-1.1) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2.1) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up libtiff5:i386 (4.2.0-1) ... Setting up libwebpmux3:i386 (0.6.1-2.1) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.9.0-3) ... 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 libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:i386 (0.6.1-2.1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-six (1.16.0-1) ... Setting up python3-simplejson (3.17.2-1) ... Setting up python3-pil:i386 (8.1.2+dfsg-0.3) ... Setting up python3-reportlab-accel:i386 (3.5.59-2) ... Setting up python3-reportlab (3.5.59-2) ... Setting up python3-argcomplete (1.8.1-1.5) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-pyfaidx (0.5.9.2-1) ... Setting up python3-argh (0.26.2-1.1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-all (3.9.2-3) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-pybedtools (0.8.0-5) ... Processing triggers for libc-bin (2.31-13) ... 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 (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/python-gffutils-0.10.1/ && 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-gffutils dpkg-buildpackage: info: source version 0.10.1-2 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 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/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/python-gffutils-0.10.1' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/exceptions.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/gffwriter.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/helpers.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/create.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/pybedtools_integration.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/attributes.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/iterators.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/convert.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/interface.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/bins.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/version.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/merge_criteria.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/__init__.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/biopython_integration.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/inspect.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/constants.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/parser.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils copying gffutils/feature.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils package init file 'gffutils/scripts/__init__.py' not found (or not a regular file) creating /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/scripts copying gffutils/scripts/gffutils-flybase-convert.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/scripts creating /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/helpers_test.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/synth_test_base.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/expected.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/feature_test.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/attr_test_cases.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/performance_test.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/test_merge.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/test.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/parser_test.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/test_biopython_integration.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/__init__.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test copying gffutils/test/test_merge_all.py -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test package init file 'gffutils/test/data/__init__.py' not found (or not a regular file) creating /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/random-chr.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3.gz -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/ncbi_gff3.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/ensembl_gtf.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2_alt.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/download-large-annotation-files.sh -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/unsanitized.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/jgi_gff2.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/synthetic.gff3 -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/keyval_sep_in_attrs.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/intro_docs_example.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/F3-unique-3.v2.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/nonascii -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/dm6-chr2L.fa -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gtf -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/hybrid1.gff3 -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/FBgn0031208.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode-v19.gtf -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/mouse_extra_comma.gff3 -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/keep-order-test.gtf -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/glimmer_nokeyval.gff3 -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/wormbase_gff2.txt -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data copying gffutils/test/data/gff_example1.gff3 -> /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data running build_scripts creating build creating build/scripts-3.9 copying and adjusting gffutils/scripts/gffutils-cli -> build/scripts-3.9 changing mode of build/scripts-3.9/gffutils-cli from 644 to 755 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --name="Command line interface for python-gffutils." \ gffutils-cli > debian/gffutils-cli.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_fetch \- Fetch IDs") \ 'gffutils-cli fetch' > debian/gffutils-cli-fetch.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_children \- Fetch children from the database according to ID") \ 'gffutils-cli children' > debian/gffutils-cli-children.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_parents \- Fetch parents from the database according to ID") \ 'gffutils-cli parents' > debian/gffutils-cli-parents.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_region \- Returns features within provided genomic coordinates") \ 'gffutils-cli region' > debian/gffutils-cli-region.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_create \- Create a database") \ 'gffutils-cli create' > debian/gffutils-cli-create.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_common \- Identify child features in common") \ 'gffutils-cli common' > debian/gffutils-cli-common.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_clean \- Perform various QC operations to clean a GFF or GTF file") \ 'gffutils-cli clean' > debian/gffutils-cli-clean.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_sanitize \- Sanitize a GFF file") \ 'gffutils-cli sanitize' > debian/gffutils-cli-sanitize.1 PYTHONPATH=/build/python-gffutils-0.10.1 PATH=/build/python-gffutils-0.10.1/gffutils/scripts/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man --version-string=0.10.1 --no-info \ --include <(echo -e "[NAME]\ngffutils-cli_rmdups \- Remove duplicates from a GFF file") \ 'gffutils-cli rmdups' > debian/gffutils-cli-rmdups.1 make[1]: Leaving directory '/build/python-gffutils-0.10.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:232: cd /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build; python3.9 -m nose -v --with-doctest -a '!slow' Doctest: gffutils.attributes.Attributes.__init__ ... ok Doctest: gffutils.pybedtools_integration.tsses ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) /usr/lib/python3.9/subprocess.py:935: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:935: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:935: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:935: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:935: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) /usr/lib/python3.9/subprocess.py:946: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize) ok gffutils.test.feature_test.test_feature_from_line ... ok gffutils.test.feature_test.test_default_feature ... ok gffutils.test.feature_test.test_attributes_representations ... ok gffutils.test.feature_test.test_default_start_stop ... ok gffutils.test.feature_test.test_aliases ... ok gffutils.test.feature_test.test_string_representation ... ok gffutils.test.feature_test.test_pbt_interval_conversion ... ok gffutils.test.feature_test.test_hash ... ok gffutils.test.feature_test.test_repr ... ok gffutils.test.feature_test.test_attribute_order ... ok gffutils.test.feature_test.test_unjsonify ... ok test_merge_Attributes (gffutils.test.helpers_test.Test) ... ok Tests all possible cases of merging two dictionaries together ... ok gffutils.test.parser_test.test_directives ... ok gffutils.test.parser_test.test_split_attrs('count=1;gene=amx-2;sequence=SAGE:ggcagagtcttttggca;transcript=B0019.1', {'count': ['1'], 'gene': ['amx-2'], 'sequence': ['SAGE:ggcagagtcttttggca'], 'transcript': ['B0019.1']}, None) ... ok gffutils.test.parser_test.test_split_attrs('gene_id "Y74C9A.6"; transcript_id "Y74C9A.6"; exon_number "1"; gene_name "Y74C9A.6"; transcript_name "NR_001477.2";', {'gene_id': ['Y74C9A.6'], 'transcript_id': ['Y74C9A.6'], 'exon_number': ['1'], 'gene_name': ['Y74C9A.6'], 'transcript_name': ['NR_001477.2']}, None) ... ok gffutils.test.parser_test.test_split_attrs('g=A3233312322232122211;i=1;p=1.000;q=23,12,18,17,10,24,19,14,27,9,23,9,16,20,11,7,8,4,4,14;u=0,0,0,1', {'g': ['A3233312322232122211'], 'i': ['1'], 'p': ['1.000'], 'q': ['23', '12', '18', '17', '10', '24', '19', '14', '27', '9', '23', '9', '16', '20', '11', '7', '8', '4', '4', '14'], 'u': ['0', '0', '0', '1']}, None) ... ok gffutils.test.parser_test.test_split_attrs("ID=GL0000006;Name=GL0000006;Lack 3'-end;", {'ID': ['GL0000006'], 'Name': ['GL0000006'], "Lack 3'-end": []}, None) ... ok gffutils.test.parser_test.test_split_attrs('ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1', {'ID': ['A00469'], 'Dbxref': ['AFFX-U133:205840_x_at', 'Locuslink:2688', 'Genbank-mRNA:A00469', 'Swissprot:P01241', 'PFAM:PF00103', 'AFFX-U95:1332_f_at', 'Swissprot:SOMA_HUMAN'], 'Note': ['growth hormone 1'], 'Alias': ['GH1']}, 'ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth hormone 1;Alias=GH1') ... ok gffutils.test.parser_test.test_split_attrs('name "fgenesh1_pg.C_chr_1000007"; transcriptId 873', {'name': ['fgenesh1_pg.C_chr_1000007'], 'transcriptId': ['873']}, 'name "fgenesh1_pg.C_chr_1000007"; transcriptId "873"') ... ok gffutils.test.parser_test.test_split_attrs('Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,', {'Name': ['CDS:NC_000083.5:LOC100040603'], 'Parent': ['XM_001475631.1', '']}, None) ... ok gffutils.test.parser_test.test_split_attrs('ID=;Parent=XM_001475631.1', {'ID': [], 'Parent': ['XM_001475631.1']}, 'ID;Parent=XM_001475631.1') ... ok gffutils.test.parser_test.test_split_attrs('ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;exon_number=1', {'ID': ['NC_008596.1:speB:unknown_transcript_1'], 'Parent': ['NC_008596.1:speB'], 'locus_tag': ['MSMEG_1072'], 'EC_number': ['3.5.3.11'], 'note': ['identified by match to protein family HMM PF00491; match to protein family HMM TIGR01230'], 'transl_table': ['11'], 'product': ['agmatinase'], 'protein_id': ['YP_885468.1'], 'db_xref': ['GI:118469242', 'GeneID:4535378'], 'exon_number': ['1']}, 'ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified by match to protein family HMM PF00491%3B match to protein family HMM TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;exon_number=1') ... ok gffutils.test.parser_test.test_split_attrs('CDS "cr01.sctg102.wum.2.1"', {'CDS': ['cr01.sctg102.wum.2.1']}, None) ... ok Just confirm we can iterate completely through the test files.... ... ok reconstructing attributes with incomplete information returns empty string ... ok gffutils.test.parser_test.test_empty_split_keyvals ... ok if dialect says repeated keys, but len(vals) > 1, then the keys are not ... ok make sure from string and from file return identical results ... ok gffutils.test.parser_test.test_valid_line_count ... ok The second feature does not have a trailing semicolon (wormbase_gff2_alt is ... /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/create.py:733: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation warnings.warn( ok gffutils.test.parser_test.test_attributes ... ok gffutils.test.test.TestGFFClass.featurecount_test ... ok gffutils.test.test.TestGFFClass.table_test ... ok gffutils.test.test.TestGFFClass.test_bed12 ... ok gffutils.test.test.TestGFFClass.test_parents_level_1 ... ok gffutils.test.test.TestGFFClass.test_parents_level_2 ... ok gffutils.test.test.TestGTFClass.featurecount_test ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.TestGTFClass.table_test ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.TestGTFClass.test_bed12 ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.TestGTFClass.test_parents_level_1 ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.TestGTFClass.test_parents_level_2 ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.test_update ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok Test on GFF files with random chromosome events. ... ok Test GFFWriter. ... ok Test creation of FeatureDB from iterator. ... ok Test sanitization of GFF. Should be merged with GFF cleaning ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 1, 'end': 2000000000.0, 'completely_within': True}, 27),) ... ok gffutils.test.test.test_region(({'region': 'chr2L', 'start': 0}, ),) ... ok gffutils.test.test.test_region(({'region': 'chr2L', 'end': 0}, ),) ... ok gffutils.test.test.test_region(({'region': 'chr2L', 'seqid': 0}, ),) ... ok gffutils.test.test.test_region(({'region': 'chr2L:7529-12500'}, 27),) ... ok gffutils.test.test.test_region(({'region': 'chr2L:7529-12500', 'strand': '.'}, 0),) ... ok gffutils.test.test.test_region(({'region': 'chr2L:7529-12500', 'strand': '+'}, 21),) ... ok gffutils.test.test.test_region(({'region': 'chr2L:7529-12500', 'strand': '-'}, 6),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 11500, 'featuretype': 'exon'}, 1),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 9500, 'featuretype': 'exon', 'strand': '+'}, 1),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 7529, 'end': 12500}, 27),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 7680}, 26),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'start': 7680, 'completely_within': True}, 22),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'end': 7680}, 5),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L', 'end': 7680, 'completely_within': True}, 1),) ... ok gffutils.test.test.test_region(({'region': 'chr2L'}, 27),) ... ok gffutils.test.test.test_region(({'seqid': 'chr2L'}, 27),) ... ok gffutils.test.test.test_region(({'region': 'nowhere'}, 0),) ... ok gffutils.test.test.test_nonascii ... ok gffutils.test.test.test_feature_merge ... ok gffutils.test.test.test_add_relation ... ok Test creation of FeatureDB from URL iterator. ... 127.0.0.1 - - [26/Jul/2021 17:26:00] "GET /gff_example1.gff3 HTTP/1.1" 200 - 127.0.0.1 - - [26/Jul/2021 17:26:00] "GET /gff_example1.gff3.gz HTTP/1.1" 200 - ok gffutils.test.test.test_empty_files ... ok gffutils.test.test.test_false_function ... ok gffutils.test.test.test_inspect ... ok gffutils.test.test.test_delete ... ok gffutils.test.test.test_iterator_update ... ok gffutils.test.test.test_tempfiles ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 1 of 8 (12%) 3 of 8 (37%) 2 of 8 (25%) 4 of 8 (50%) 5 of 8 (62%) 3 of 8 (37%) 6 of 8 (75%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 1 of 8 (12%) 3 of 8 (37%) 2 of 8 (25%) 4 of 8 (50%) 3 of 8 (37%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 0 of 8 (0%) 3 of 8 (37%) 4 of 8 (50%) 1 of 8 (12%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 0 of 8 (0%) 5 of 8 (62%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 0 of 8 (0%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 2 of 8 (25%) 5 of 8 (62%) 3 of 8 (37%) 6 of 8 (75%) 0 of 8 (0%) 4 of 8 (50%) 5 of 8 (62%) 1 of 8 (12%) 2 of 8 (25%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 1 of 8 (12%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 0 of 8 (0%) 5 of 8 (62%) 6 of 8 (75%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 1 of 8 (12%) 3 of 8 (37%) 2 of 8 (25%) 4 of 8 (50%) 3 of 8 (37%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 1 of 8 (12%) 5 of 8 (62%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 4 of 8 (50%) 1 of 8 (12%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 0 of 8 (0%) 5 of 8 (62%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 0 of 8 (0%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 2 of 8 (25%) 5 of 8 (62%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 0 of 8 (0%) 3 of 8 (37%) 1 of 8 (12%) 1 of 8 (12%) 4 of 8 (50%) 2 of 8 (25%) 2 of 8 (25%) 5 of 8 (62%) 3 of 8 (37%) 3 of 8 (37%) 6 of 8 (75%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 0 of 8 (0%) 3 of 8 (37%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 1 of 8 (12%) 4 of 8 (50%) 5 of 8 (62%) 2 of 8 (25%) 6 of 8 (75%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 0 of 8 (0%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 0 of 8 (0%) 2 of 8 (25%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 0 of 8 (0%) 2 of 8 (25%) 5 of 8 (62%) 3 of 8 (37%) 1 of 8 (12%) 6 of 8 (75%) 4 of 8 (50%) 2 of 8 (25%) 5 of 8 (62%) 0 of 8 (0%) 3 of 8 (37%) 6 of 8 (75%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 1 of 8 (12%) 1 of 8 (12%) 3 of 8 (37%) 3 of 8 (37%) 2 of 8 (25%) 2 of 8 (25%) 4 of 8 (50%) 4 of 8 (50%) 3 of 8 (37%) 3 of 8 (37%) 5 of 8 (62%) 5 of 8 (62%) 4 of 8 (50%) 4 of 8 (50%) 6 of 8 (75%) 6 of 8 (75%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 0 of 8 (0%) 5 of 8 (62%) 6 of 8 (75%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 0 of 8 (0%) 4 of 8 (50%) 5 of 8 (62%) 1 of 8 (12%) 6 of 8 (75%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 1 of 8 (12%) 4 of 8 (50%) 2 of 8 (25%) 0 of 8 (0%) 5 of 8 (62%) 3 of 8 (37%) 0 of 8 (0%) 6 of 8 (75%) 4 of 8 (50%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 5 of 8 (62%) 2 of 8 (25%) 3 of 8 (37%) 6 of 8 (75%) 4 of 8 (50%) 3 of 8 (37%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 1 of 8 (12%) 2 of 8 (25%) 0 of 8 (0%) 3 of 8 (37%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 0 of 8 (0%) 4 of 8 (50%) 3 of 8 (37%) 5 of 8 (62%) 1 of 8 (12%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 2 of 8 (25%) 1 of 8 (12%) 5 of 8 (62%) 6 of 8 (75%) 3 of 8 (37%) 2 of 8 (25%) 4 of 8 (50%) 6 of 8 (75%) 5 of 8 (62%) 3 of 8 (37%) 6 of 8 (75%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 1 of 8 (12%) 3 of 8 (37%) 2 of 8 (25%) 4 of 8 (50%) 3 of 8 (37%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 3 of 8 (37%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 4 of 8 (50%) 6 of 8 (75%) 6 of 8 (75%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 3 of 8 (37%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 0 of 8 (0%) 1 of 8 (12%) 1 of 8 (12%) 2 of 8 (25%) 2 of 8 (25%) 3 of 8 (37%) 3 of 8 (37%) 4 of 8 (50%) 4 of 8 (50%) 5 of 8 (62%) 5 of 8 (62%) 6 of 8 (75%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok tests the new semantics for disabling gene/transcript inference ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/create.py:733: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation warnings.warn( 0 of 4 (0%) 1 of 4 (25%) 2 of 4 (50%) /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/create.py:724: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation warnings.warn( 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) 7 of 8 (87%) ok gffutils.test.test.test_deprecation_handler ... ok gffutils.test.test.test_nonsense_kwarg ... ok gffutils.test.test.test_infer_gene_extent ... ok gffutils.test.test.test_issue_79 ... 0 of 2 (0%) 1 of 2 (50%) ok gffutils.test.test.test_for_analyze ... 0 of 8 (0%) 1 of 8 (12%) 2 of 8 (25%) 3 of 8 (37%) 4 of 8 (50%) 5 of 8 (62%) 6 of 8 (75%) ok gffutils.test.test.test_issue_82 ... ok gffutils.test.test.test_sequence ... ok gffutils.test.test.test_issue_85 ... ok gffutils.test.test.test_unquoting ... ok gffutils.test.test.test_unreasonable_unquoting ... ok gffutils.test.test.test_unquoting_iter ... ok gffutils.test.test.test_db_unquoting ... ok gffutils.test.test.test_issue_107 ... ok gffutils.test.test.test_issue_119 ... ok gffutils.test.test.test_pr_131 ... ok gffutils.test.test.test_pr_133 ... ok gffutils.test.test.test_pr_139 ... ok gffutils.test.test.test_pr_144 ... ok gffutils.test.test.test_issue_105 ... ok Feature -> SeqFeature -> Feature should be invariant. ... ok test_adjacent_len1 (gffutils.test.test_merge.TestMerge) ... ok test_any_overlap (gffutils.test.test_merge.TestMerge) ... ok test_defaults (gffutils.test.test_merge.TestMerge) ... ok test_end_overlap (gffutils.test.test_merge.TestMerge) ... ok test_no_overlap (gffutils.test.test_merge.TestMerge) ... ok test_none (gffutils.test.test_merge.TestMerge) ... ok test_one (gffutils.test.test_merge.TestMerge) ... ok test_overlap (gffutils.test.test_merge.TestMerge) ... ok test_perfect_overlap (gffutils.test.test_merge.TestMerge) ... ok test_defaults (gffutils.test.test_merge_all.TestMerge_all) ... ok test_empty (gffutils.test.test_merge_all.TestMerge_all) ... ok test_exclude_components (gffutils.test.test_merge_all.TestMerge_all) ... ok test_merge_groups (gffutils.test.test_merge_all.TestMerge_all) ... ok test_no_overlap (gffutils.test.test_merge_all.TestMerge_all) ... ok test_one (gffutils.test.test_merge_all.TestMerge_all) ... ok ---------------------------------------------------------------------- Ran 113 tests in 4.509s OK I: pybuild pybuild:310: find . -name tmp.db -delete create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/python-gffutils-0.10.1/debian/python3-gffutils running install running build running build_py package init file 'gffutils/scripts/__init__.py' not found (or not a regular file) package init file 'gffutils/test/data/__init__.py' not found (or not a regular file) running build_scripts running install_lib creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9 creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/exceptions.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/helpers_test.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/synth_test_base.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/expected.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/random-chr.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gff_example1.gff3.gz -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/ncbi_gff3.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/ensembl_gtf.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/wormbase_gff2_alt.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/download-large-annotation-files.sh -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/unsanitized.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/jgi_gff2.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/synthetic.gff3 -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/keyval_sep_in_attrs.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/intro_docs_example.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gencode.vM8.chromsizes.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/F3-unique-3.v2.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/nonascii -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/dm6-chr2L.fa -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/c_elegans_WS199_ann_gff.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/c_elegans_WS199_shortened_gff.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/FBgn0031208.gtf -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/hybrid1.gff3 -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/FBgn0031208.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gencode-v19.gtf -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/mouse_extra_comma.gff3 -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/keep-order-test.gtf -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gencode.vM8.5000_transcript_ids.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/glimmer_nokeyval.gff3 -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gencode.vM8.5000_gene_ids.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/c_elegans_WS199_dna_shortened.fa -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/wormbase_gff2.txt -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/gff_example1.gff3 -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/data/dm6-chr2L.fa.fai -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/data copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/feature_test.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/attr_test_cases.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/test.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/__init__.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/attr_test_cases.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/synth_test_base.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/helpers_test.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/parser_test.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/test_merge.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/feature_test.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/performance_test.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/expected.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/test_merge_all.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__pycache__/test_biopython_integration.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/performance_test.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/test_merge.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/test.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/parser_test.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/test_biopython_integration.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/__init__.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/test/test_merge_all.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/gffwriter.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/scripts copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/scripts/gffutils-flybase-convert.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/scripts copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/helpers.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/create.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/pybedtools_integration.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/feature.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/interface.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/constants.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/convert.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/gffwriter.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/bins.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/__init__.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/create.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/pybedtools_integration.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/inspect.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/merge_criteria.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/parser.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/helpers.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/iterators.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/biopython_integration.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/exceptions.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/version.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__pycache__/attributes.cpython-39.pyc -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__pycache__ copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/attributes.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/iterators.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/convert.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/interface.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/bins.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/version.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/merge_criteria.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/__init__.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/biopython_integration.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/inspect.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/constants.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/parser.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils copying /build/python-gffutils-0.10.1/.pybuild/cpython3_3.9_gffutils/build/gffutils/feature.py -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/exceptions.py to exceptions.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/helpers_test.py to helpers_test.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/synth_test_base.py to synth_test_base.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/expected.py to expected.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/feature_test.py to feature_test.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/attr_test_cases.py to attr_test_cases.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/performance_test.py to performance_test.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/test_merge.py to test_merge.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/test.py to test.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/parser_test.py to parser_test.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/test_biopython_integration.py to test_biopython_integration.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/test/test_merge_all.py to test_merge_all.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/gffwriter.py to gffwriter.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/scripts/gffutils-flybase-convert.py to gffutils-flybase-convert.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/helpers.py to helpers.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/create.py to create.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/pybedtools_integration.py to pybedtools_integration.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/attributes.py to attributes.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/iterators.py to iterators.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/convert.py to convert.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/interface.py to interface.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/bins.py to bins.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/version.py to version.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/merge_criteria.py to merge_criteria.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/biopython_integration.py to biopython_integration.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/inspect.py to inspect.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/constants.py to constants.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/parser.py to parser.cpython-39.pyc byte-compiling /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils/feature.py to feature.cpython-39.pyc running install_egg_info running egg_info writing gffutils.egg-info/PKG-INFO writing dependency_links to gffutils.egg-info/dependency_links.txt writing requirements to gffutils.egg-info/requires.txt writing top-level names to gffutils.egg-info/top_level.txt reading manifest file 'gffutils.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs/source' warning: no files found matching '*.py' under directory 'docs/source' warning: no files found matching '*' under directory 'docs/source/images' warning: no files found matching 'docs/Makefile' warning: no files found matching 'docs/make.bat' warning: no files found matching 'gffutils/test/data/__init__.py' warning: no files found matching 'gffutils/test/data/t.py' writing manifest file 'gffutils.egg-info/SOURCES.txt' Copying gffutils.egg-info to /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/lib/python3.9/dist-packages/gffutils-0.10.1.egg-info Skipping SOURCES.txt running install_scripts creating /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/bin copying build/scripts-3.9/gffutils-cli -> /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/bin changing mode of /build/python-gffutils-0.10.1/debian/python3-gffutils/usr/bin/gffutils-cli to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-gffutils' in '../python3-gffutils_0.10.1-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-gffutils_0.10.1-2_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/453 and its subdirectories I: Current time: Mon Jul 26 17:26:45 -12 2021 I: pbuilder-time-stamp: 1627363605 Tue Jul 27 05:26:46 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Tue Jul 27 05:26:46 UTC 2021 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Tue Jul 27 05:27:30 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. Tue Jul 27 05:27:30 UTC 2021 I: python-gffutils_0.10.1-2_i386.changes: Format: 1.8 Date: Tue, 18 Feb 2020 10:38:32 +0100 Source: python-gffutils Binary: python3-gffutils Architecture: all Version: 0.10.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python3-gffutils - Work with GFF and GTF files in a flexible database framework Closes: 950853 Changes: python-gffutils (0.10.1-2) unstable; urgency=medium . * Team upload. . [ Stefano Rivera ] * Avoid deadlocks in tests under Python 3.8 Closes: #950853 . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * autopkgtest: - s/$ADTTMP/$AUTOPKGTEST_TMP/g - cleanup after running test suite - rename test script to run-unit-test - document how users can test installation Checksums-Sha1: c5eecb5d2cd7d247336652ba9b8c13f855196f32 6768 python-gffutils_0.10.1-2_i386.buildinfo 69be4602bad69dbd0fbd783f1a7823118572de77 1028480 python3-gffutils_0.10.1-2_all.deb Checksums-Sha256: 95dae4b4c87c370117049bcd7c00812871603c1123016644ac771a57c1fe1dd2 6768 python-gffutils_0.10.1-2_i386.buildinfo 7aad5a9886f219ca02d0b792e5bd4d56209d6e2edf3eb6a1d024c322ff106ebe 1028480 python3-gffutils_0.10.1-2_all.deb Files: ead852e884bcbf7a211a0d49e7c11c91 6768 science optional python-gffutils_0.10.1-2_i386.buildinfo 54d161dcddd675e897342f95753f500e 1028480 science optional python3-gffutils_0.10.1-2_all.deb Tue Jul 27 05:27:32 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/python-gffutils_0.10.1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/python-gffutils_0.10.1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/python-gffutils_0.10.1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/b1/python-gffutils_0.10.1-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.a41qKIT9it/b2/python-gffutils_0.10.1-2_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.791s) 1.791s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.029s) 0.029s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 27 05:27:35 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 27 05:27:35 UTC 2021 I: python-gffutils from bullseye built successfully and reproducibly on i386. Tue Jul 27 05:27:39 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 27 05:27:39 UTC 2021 I: Submitting 8.0K b1/python-gffutils_0.10.1-2_i386.buildinfo.asc Tue Jul 27 05:27:41 UTC 2021 I: Submitting 8.0K b2/python-gffutils_0.10.1-2_i386.buildinfo.asc Tue Jul 27 05:27:42 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 27 05:27:42 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 27 05:27:42 UTC 2021 I: Removing signed python-gffutils_0.10.1-2_i386.buildinfo.asc files: removed './b1/python-gffutils_0.10.1-2_i386.buildinfo.asc' removed './b2/python-gffutils_0.10.1-2_i386.buildinfo.asc'