unshare: unshare failed: Cannot allocate memory W: pbuilder: unshare CLONE_NEWNET not available I: pbuilder: network access is available during build! I: Current time: Mon Jun 28 03:47:45 -12 2021 I: pbuilder-time-stamp: 1624895265 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-pyfaidx_0.5.9.2-1.dsc] I: copying [./python-pyfaidx_0.5.9.2.orig.tar.gz] I: copying [./python-pyfaidx_0.5.9.2-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.j1Kz6qRt/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 12 04:15:33 2020 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pyfaidx_0.5.9.2-1.dsc dpkg-source: info: extracting python-pyfaidx in python-pyfaidx-0.5.9.2 dpkg-source: info: unpacking python-pyfaidx_0.5.9.2.orig.tar.gz dpkg-source: info: unpacking python-pyfaidx_0.5.9.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying test-locale-to-c.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29918/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=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='4fff74650cce4149a4708a8e7a056e54' 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='29918' 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.SSnf5NlGQL/pbuilderrc_rukK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.SSnf5NlGQL/b1 --logfile b1/build.log python-pyfaidx_0.5.9.2-1.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 4.19.194-2 (2021-06-21) i686 GNU/Linux I: ls -l /bin total 5784 -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 Jun 27 22:22 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/29918/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 (= 13), dh-python, python3-all, python3-coverage, python3-setuptools, python3-nose, python3-numpy, python3-six, python3-mock, samtools, tabix 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 (= 13); 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 python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-coverage; however: Package python3-coverage is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six is not installed. pbuilder-satisfydepends-dummy depends on python3-mock; however: Package python3-mock is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix 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} 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} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libicu67{a} liblapack3{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{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} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-coverage{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-mock{a} python3-nose{a} python3-numpy{a} python3-pbr{a} python3-pkg-resources{a} python3-setuptools{a} python3-six{a} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tabix{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libjs-jquery libjs-jquery-isonscreen libjs-jquery-tablesorter libjs-jquery-throttle-debounce libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 34.7 MB of archives. After unpacking 134 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 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1 [70.0 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1 [110 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3 [244 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.2 [367 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 python3-all i386 3.9.2-3 [1060 B] Get: 63 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-3 [189 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 python3-coverage i386 5.1+dfsg.1-2+b2 [169 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 python3-setuptools all 52.0.0-3 [441 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 python3-six all 1.16.0-1 [17.1 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 python3-pbr all 5.5.0-2 [60.4 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 python3-mock all 4.0.3-1 [34.6 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 python3-nose all 1.3.7-7 [133 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 tabix i386 1.11-4 [369 kB] Fetched 34.7 MB in 7s (4814 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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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 ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/python-pyfaidx-0.5.9.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package python-pyfaidx dpkg-buildpackage: info: source version 0.5.9.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean LC_ALL=C.UTF-8 dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-pyfaidx-0.5.9.2' dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/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 rm -f .coverage rm -f tests/data/genes.fasta.gz rm -rf pyfaidx.egg-info make[1]: Leaving directory '/build/python-pyfaidx-0.5.9.2' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary LC_ALL=C.UTF-8 dh binary --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 dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx copying pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx copying pyfaidx/cli.py -> /build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pyfaidx-0.5.9.2' bgzip -c tests/data/genes.fasta > tests/data/genes.fasta.gz dh_auto_test -- --test --system=custom --test-args='set -e; \ {interpreter} -m "nose" --with-coverage --cover-package=pyfaidx' I: pybuild base:232: set -e; \ python3.9 -m "nose" --with-coverage --cover-package=pyfaidx Doctest: pyfaidx.Sequence.__eq__ ... ok Doctest: pyfaidx.Sequence.__getitem__ ... ok Doctest: pyfaidx.Sequence.__len__ ... ok Doctest: pyfaidx.Sequence.__neg__ ... ok Doctest: pyfaidx.Sequence.complement ... ok Doctest: pyfaidx.Sequence.fancy_name ... ok Doctest: pyfaidx.Sequence.gc ... ok Doctest: pyfaidx.Sequence.long_name ... ok Doctest: pyfaidx.Sequence.orientation ... ok Doctest: pyfaidx.Sequence.reverse ... ok Doctest: pyfaidx.check_bad_lines ... ok Doctest: pyfaidx.complement ... ok Doctest: pyfaidx.get_valid_filename ... ok Check for pathogenic FastaRecord.long_name behavior in mdshw5/pyfaidx#62 ... ok Test that deflines extracted using FastaRecord.long_name are ... ok Test the __array_interface__ ... ok Test that the sequence is always returned in ... ok test_unpadded_length (test_FastaRecord.TestFastaRecord) ... ok test_mutate_fasta_to_N (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_fasta_to_same (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_immutable_fasta (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_single_position (test_FastaRecord.TestMutableFastaRecord) ... ok test_mutate_too_long (test_FastaRecord.TestMutableFastaRecord) ... ok test_fetch_whole_fasta (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_line_len (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_reverse_iter (test_FastaRecord_iter.TestFastaRecordIter) ... ok test_all_diff (test_FastaVariant.TestFastaVariant) ... SKIP test_all_pos (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_het_variant (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_hom_variant (test_FastaVariant.TestFastaVariant) ... SKIP test_fetch_variant (test_FastaVariant.TestFastaVariant) ... SKIP seq[0:0] should return a blank string mdshw5/pyfaidx#53 ... SKIP Fetch past the end of a gene entry ... SKIP Fetch past the end of a gene entry ... SKIP test_fetch_end (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Fetch a key that does not exist ... SKIP test_fetch_middle (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Fetch starting with a negative coordinate ... SKIP Fetch past the end of a gene entry ... SKIP Fetch starting with a negative coordinate ... SKIP test_fetch_whole_entry (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_fetch_whole_fasta (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_integer_index (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_integer_slice (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_consistency (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_end_faidx (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_end_fasta (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_74_start (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_negate (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_one_based_false (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_issue_79_fix_one_based_false_negate (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_line_len (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Test that deflines extracted using FastaRecord.long_name are ... SKIP test_mutable_bgzf (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_rev (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_slice_from_beginning (test_Fasta_bgzip.TestFastaBGZF) ... SKIP test_slice_from_end (test_Fasta_bgzip.TestFastaBGZF) ... SKIP Samtools BGZF index should be identical to pyfaidx BGZF index ... SKIP test_integer_index (test_Fasta_integer_index.TestFastaIntIndex) ... ok test_integer_slice (test_Fasta_integer_index.TestFastaIntIndex) ... ok Test that each read of a sequence range is atomic. ... ok Combine the above two tests to check that interleaved reads and writes don't conflict. ... ok Test that each write of a sequence range is atomic. ... ok test_fetch_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP test_revcomp_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP test_slice_whole_entry (test_bio_seqio.TestBioSeqIO) ... SKIP Test that --auto-strand produces the same output as --reverse --complement ... ok test_fetch_error (test_faidx.TestCLI) ... ok test_fetch_whole_file (test_faidx.TestCLI) ... ok test_key_warning (test_faidx.TestCLI) ... warning: foo not found in file ok test_not_regexp (test_faidx.TestCLI) ... ok test_not_regexp_multi (test_faidx.TestCLI) ... ok test_regexp (test_faidx.TestCLI) ... ok test_short_line_lengths (test_faidx.TestCLI) ... ok test_split_entry (test_faidx.TestCLI) ... ok seq[0:0] should return a blank string mdshw5/pyfaidx#53 ... ok Fetch past the end of a gene entry ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_end ... ok Fetch a key that does not exist ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_middle ... ok Fetch starting with a negative coordinate ... ok Fetch past the end of a gene entry ... ok Fetch starting with a negative coordinate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_fetch_whole_entry ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_consistency ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_end_faidx ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_end_fasta ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_74_start ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_negate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_one_based_false ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_issue_79_fix_one_based_false_negate ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_rev ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_slice_from_beginning ... ok test_feature_bounds_check.TestFeatureBoundsCheck.test_slice_from_end ... ok test_feature_bounds_check.TestFeatureZeroLength.test_fetch_zero_length ... ok test_feature_bounds_check.TestFeatureZeroLength.test_index_zero_length ... ok test_as_raw_zero_length_subsequence (test_feature_bounds_check.TestZeroLengthSequenceSubRange) ... ok test_zero_length_subsequence (test_feature_bounds_check.TestZeroLengthSequenceSubRange) ... ok Fetch past the end of a gene entry ... ok test_build (test_feature_indexing.TestIndexing) ... ok test_build_issue_111 (test_feature_indexing.TestIndexing) ... ok test_build_issue_141 (test_feature_indexing.TestIndexing) ... ok Ensure that blank lines between entries are treated in the ... ok Ensure that the fasta file is closed if construction of the 'Faidx' file ... ok Ensure that the fasta file is closed if construction of the 'Faidx' file ... ok Ensure that index file is not built when build_index=False. See mdshw5/pyfaidx#134. ... ok Ensure that an exception is raised when a file contains no deflines. See mdshw5/pyfaidx#144. ... ok test_order (test_feature_indexing.TestIndexing) ... ok Ensure that index files written with write_fai() can be read back ... ok This test ensures that the index is regenerated when the FASTA ... ok Makes all full-length lines blank and checks that error is raised ... ok Makes all full-length lines long and checks that error is raised ... ok Makes all full-length lines short and checks that error is raised ... ok test_duplicated_keys (test_feature_key_function.TestFeatureKeyFunction) ... ok test_duplicated_keys_longest (test_feature_key_function.TestFeatureKeyFunction) ... ok test_duplicated_keys_shortest (test_feature_key_function.TestFeatureKeyFunction) ... ok test_key_function_by_dictionary_get_key (test_feature_key_function.TestFeatureKeyFunction) ... ok test_key_function_by_fetch (test_feature_key_function.TestFeatureKeyFunction) ... ok test_keys (test_feature_key_function.TestFeatureKeyFunction) ... ok test_bounds_error (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_exceed (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_false (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_true (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_buffer_value (test_feature_read_ahead_buffer.TestFeatureBuffer) ... ok test_as_raw_false (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_false_error (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_true (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_true_error (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok test_as_raw_type_when_blen_lt_0 (test_feature_sequence_as_raw.TestFeatureSequenceAsRaw) ... ok Check get_seq with rc argument ... ok Fetch sequence by blocks ... ok test_key_function_by_dictionary_get_key (test_feature_split_char.TestFeatureSplitChar) ... ok test_key_function_by_fetch (test_feature_split_char.TestFeatureSplitChar) ... ok test_keys (test_feature_split_char.TestFeatureSplitChar) ... ok test_stop (test_feature_split_char.TestFeatureSplitChar) ... ok test_sequence_class.test_negate ... ok test_sequence_class.test_negate_metadata ... ok test_sequence_class.test_seq_invalid ... ok test_sequence_class.test_integer_index ... ok test_sequence_class.test_slice_index ... ok test_sequence_class.test_comp_invalid ... ok test_sequence_class.test_check_coordinates ... ok test_sequence_class.test_comp_valid ... ok test_sequence_class.test_comp_empty ... ok Name Stmts Miss Cover Missing --------------------------------------------------- pyfaidx/__init__.py 730 149 80% 24-25, 169, 174, 303-305, 347-358, 361, 371-378, 388-392, 400, 404, 429-430, 455, 458, 494, 496, 502, 556-557, 601, 677-680, 726, 739, 741, 761, 776-787, 793, 818, 825, 865, 908-919, 942, 954, 958, 960, 962, 967, 1018, 1026-1027, 1030, 1037, 1068, 1078, 1081, 1084, 1106-1145, 1148, 1157-1177, 1198-1200, 1221-1226, 1234-1235, 1273, 1281, 1302-1303 pyfaidx/cli.py 255 128 50% 29-34, 45-48, 76, 78, 89-104, 118-138, 179-180, 184, 188, 190, 193, 200-205, 209-215, 229, 232, 238-240, 249-251, 257, 266-279, 283, 287-288, 291-294, 309-316, 322-329, 335-343, 349-359, 362 --------------------------------------------------- TOTAL 985 277 72% ---------------------------------------------------------------------- Ran 146 tests in 205.044s OK (SKIP=36) make[1]: Leaving directory '/build/python-pyfaidx-0.5.9.2' create-stamp debian/debhelper-build-stamp 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-pyfaidx-0.5.9.2/debian/python3-pyfaidx running install running build running build_py running install_lib creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9 creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages creating /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx/__init__.py -> /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx copying /build/python-pyfaidx-0.5.9.2/.pybuild/cpython3_3.9_pyfaidx/build/pyfaidx/cli.py -> /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx byte-compiling /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx/cli.py to cli.cpython-39.pyc running install_egg_info running egg_info creating pyfaidx.egg-info writing pyfaidx.egg-info/PKG-INFO writing dependency_links to pyfaidx.egg-info/dependency_links.txt writing entry points to pyfaidx.egg-info/entry_points.txt writing requirements to pyfaidx.egg-info/requires.txt writing top-level names to pyfaidx.egg-info/top_level.txt writing manifest file 'pyfaidx.egg-info/SOURCES.txt' reading manifest file 'pyfaidx.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'docs/build/html/*' writing manifest file 'pyfaidx.egg-info/SOURCES.txt' Copying pyfaidx.egg-info to /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/lib/python3.9/dist-packages/pyfaidx-0.5.9.2.egg-info Skipping SOURCES.txt running install_scripts Installing faidx script to /build/python-pyfaidx-0.5.9.2/debian/python3-pyfaidx/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/python-pyfaidx-0.5.9.2' dh_compress --exclude=gz.tbi make[1]: Leaving directory '/build/python-pyfaidx-0.5.9.2' 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-pyfaidx' in '../python3-pyfaidx_0.5.9.2-1_all.deb'. dpkg-deb: building package 'python-pyfaidx-examples' in '../python-pyfaidx-examples_0.5.9.2-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-pyfaidx_0.5.9.2-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: 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/29918 and its subdirectories I: Current time: Mon Jun 28 03:55:31 -12 2021 I: pbuilder-time-stamp: 1624895731