Mon Jul 19 16:48:32 UTC 2021 I: starting to build pbh5tools/buster/amd64 on jenkins on '2021-07-19 16:48' Mon Jul 19 16:48:32 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/63487/console.log Mon Jul 19 16:48:32 UTC 2021 I: Downloading source for buster/pbh5tools=0.8.0+git20170929.58d54ff+dfsg-1 --2021-07-19 16:48:32-- http://deb.debian.org/debian/pool/main/p/pbh5tools/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2434 (2.4K) Saving to: ‘pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc’ 0K .. 100% 206M=0s 2021-07-19 16:48:32 (206 MB/s) - ‘pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc’ saved [2434/2434] Mon Jul 19 16:48:32 UTC 2021 I: pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: pbh5tools Binary: pbh5tools, python-pbh5tools, python-pbh5tools-doc Architecture: any all Version: 0.8.0+git20170929.58d54ff+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: https://github.com/PacificBiosciences/pbh5tools Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/pbh5tools Vcs-Git: https://salsa.debian.org/med-team/pbh5tools.git Testsuite: autopkgtest Testsuite-Triggers: python-nose Build-Depends: debhelper (>= 11~), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-h5py, python-cram Package-List: pbh5tools deb science optional arch=all python-pbh5tools deb python optional arch=any python-pbh5tools-doc deb doc optional arch=all Checksums-Sha1: 1d154aab6cf2bf537bc239a2ce5625594c4f1511 8532544 pbh5tools_0.8.0+git20170929.58d54ff+dfsg.orig.tar.xz e9b4a2cd8e73973a98a240b4b96db7063f399b3c 6804 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.debian.tar.xz Checksums-Sha256: 41ff9f72242f8de481191c93b0b083ac5848fbcf11e686898d1ae0b62e8fe989 8532544 pbh5tools_0.8.0+git20170929.58d54ff+dfsg.orig.tar.xz 20459211df6a2d73d0112f118ac6caf0b600c0d7d492024129ba00abd4baf04c 6804 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.debian.tar.xz Files: 1f61756105971df2f90895172753a6d2 8532544 pbh5tools_0.8.0+git20170929.58d54ff+dfsg.orig.tar.xz a2d7d84ce821534390a02744380522e2 6804 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltItBMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG1ZQ/+Ji5CKxZ57ps1e7M4QAHDyI3Dn6hHiR4d 0SHmejFiPeW+x9uFZ9kAmMuSqcL8veNBa51zD9HID9GHBqsTfb7/PYaIN0x2Lmik LgUhjOZLvlYuT8db4WnkHbGooYA5FgsrhfViuV2L/SyRtnwXEi53RFgxAVNYlMHw v17Iwft+rrzSbEsFEBfwfn7v1SPzDtHns8i+KGZd5Ta0O4erNgR61EMUXKvfD16b njCbUtSXtM9KtoYtIbgHOviubNUudRpcxD1CGxhx6TrRj0F7kh6RCNszh/5Unne+ tInJ7oXFmPJ4QVQZXJ5OqjTmNTL/sd7Jd9fMtbY+8nUeKJJ/j1ZBKelg6iA5swJ+ 5yTQWV9o0Xy5s1ZzVs8ria5YT+PIb8QI8Kt6cGfFm8ZmGgLB/axYUKhbKfMvgTbY RxTP6ApR9limQfR0QdGsMzSQ4QtLgm6lv6a/oghVXYEWKOh7CvyzHha7S/8n8ONg XZX+KeCIAn/2ulffu0Dn/VnqGPCJ7g4X+E4WNwU0ZBdwValuux5zCO58ptPfw4EW uln3Bh8R+vkeH4LBI3GGViZHwJdCOOnHzN8C+wgtZ+LGcwUBKZAci/E0FuT13Tru xfZypR4HIPYaewlck2Tj1oTGxblh7/amxhUZwMC3cgHk6kJnVDkG3KByYREI23sk i0lngG0HLNE= =cPrl -----END PGP SIGNATURE----- Mon Jul 19 16:48:32 UTC 2021 I: Checking whether the package is not for us Mon Jul 19 16:48:32 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Jul 19 16:48:32 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Jul 19 16:51:38 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 19 04:48:34 -12 2021 I: pbuilder-time-stamp: 1626713314 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc] I: copying [./pbh5tools_0.8.0+git20170929.58d54ff+dfsg.orig.tar.xz] I: copying [./pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Jul 13 02:15:47 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc dpkg-source: info: extracting pbh5tools in pbh5tools-0.8.0+git20170929.58d54ff+dfsg dpkg-source: info: unpacking pbh5tools_0.8.0+git20170929.58d54ff+dfsg.orig.tar.xz dpkg-source: info: unpacking pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying default-doc-theme dpkg-source: info: applying pbcore-change.patch dpkg-source: info: applying verbose-testing.patch dpkg-source: info: applying override-test-failure.patch dpkg-source: info: applying ignore-cram-results.patch dpkg-source: info: applying fix-type-in-test.patch dpkg-source: info: applying multiarch-module-path.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7852/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b014f61ae7124615a8bbd9e99a5603cc' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='7852' 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.zfoVdKzpOi/pbuilderrc_ZGfe --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zfoVdKzpOi/b1 --logfile b1/build.log pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos11-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 20:24 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/7852/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: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-h5py, python-cram dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python-pbcore; however: Package python-pbcore is not installed. pbuilder-satisfydepends-dummy depends on python-sphinx; however: Package python-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python-nose; however: Package python-nose is not installed. pbuilder-satisfydepends-dummy depends on python-h5py; however: Package python-h5py is not installed. pbuilder-satisfydepends-dummy depends on python-cram; however: Package python-cram is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhdf5-103{a} libhts2{a} libicu63{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} python{a} python-alabaster{a} python-babel{a} python-babel-localedata{a} python-certifi{a} python-chardet{a} python-cram{a} python-docutils{a} python-h5py{a} python-idna{a} python-imagesize{a} python-jinja2{a} python-markupsafe{a} python-minimal{a} python-nose{a} python-numpy{a} python-packaging{a} python-pbcore{a} python-pkg-resources{a} python-pygments{a} python-pyparsing{a} python-pysam{a} python-requests{a} python-roman{a} python-setuptools{a} python-six{a} python-sphinx{a} python-typing{a} python-tz{a} python-urllib3{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl docutils-doc javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python-cryptography python-enum34 python-ipaddress python-openssl python-pil shared-mime-info wget xdg-user-dirs 0 packages upgraded, 118 newly installed, 0 to remove and 0 not upgraded. Need to get 59.3 MB of archives. After unpacking 220 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u6 [844 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 docutils-common all 0.14+dfsg-4 [167 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get: 84 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libjs-underscore all 1.9.1~dfsg-1+deb10u1 [100.0 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 python-alabaster all 0.7.8-1 [18.4 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 python-babel all 2.6.0+dfsg.1-1 [97.3 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 python-certifi all 2018.8.24-1 [140 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 python-chardet all 3.0.4-3 [80.6 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 python-cram all 0.7-3 [17.0 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 python-roman all 2.0.0-3 [8688 B] Get: 99 http://deb.debian.org/debian buster/main amd64 python-docutils all 0.14+dfsg-4 [379 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 python-h5py amd64 2.8.0-3 [693 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 python-idna all 2.6-1 [34.1 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 python-imagesize all 1.0.0-1 [4888 B] Get: 105 http://deb.debian.org/debian buster/main amd64 python-markupsafe amd64 1.1.0-1 [14.0 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 python-jinja2 all 2.10-2 [106 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 python-nose all 1.3.7-4 [132 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 python-pyparsing all 2.2.0+dfsg1-2 [89.5 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 python-packaging all 19.0-1 [20.4 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 python-pygments all 2.3.1+dfsg-1+deb10u2 [596 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 python-typing all 3.6.6-1 [22.7 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 sphinx-common all 1.8.4-1 [500 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 python-sphinx all 1.8.4-1 [482 kB] Fetched 59.3 MB in 1s (46.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... 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 ... 20945 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21357 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... 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Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../18-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../19-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../20-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../21-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../22-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../23-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../25-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../26-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. 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Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up python-babel-localedata (2.6.0+dfsg.1-1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up sgml-base (1.29) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up openssl (1.1.1d-0+deb10u6) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libjs-underscore (1.9.1~dfsg-1+deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up libhts2:amd64 (1.9-11) ... Setting up python-typing (3.6.6-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python-cram (0.7-3) ... Setting up python-certifi (2018.8.24-1) ... Setting up python-pygments (2.3.1+dfsg-1+deb10u2) ... Setting up python-six (1.12.0-1) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up python-imagesize (1.0.0-1) ... Setting up python-idna (2.6-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-markupsafe (1.1.0-1) ... Setting up python-roman (2.0.0-3) ... Setting up python-tz (2019.1-1) ... Setting up python-alabaster (0.7.8-1) ... Setting up python-chardet (3.0.4-3) ... Setting up python-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python-packaging (19.0-1) ... Setting up python-urllib3 (1.24.1-1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-nose (1.3.7-4) ... Setting up python-jinja2 (2.10-2) ... Setting up python-requests (2.21.0-1) ... Setting up python-h5py (2.8.0-3) ... Setting up python-pbcore (1.6.5+dfsg-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package pbh5tools dpkg-buildpackage: info: source version 0.8.0+git20170929.58d54ff+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean LC_ALL=C.UTF-8 dh clean --with python2 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' dh_auto_clean I: pybuild base:217: python2.7 setup.py clean running clean removing '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it /usr/bin/make clean make[2]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' cd doc && rm -rf modules.rst pbtools.* bash5lib.* cmph5tools.* \ bash5tools.* _templates _static _build searchindex.js objects.inv rm -rf build/;\ find . -name "*.egg-info" | xargs rm -rf;\ find . -name "*.pyc" | xargs rm -rf;\ rm -rf dist/ rm -f nosetests.xml make[2]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' make[1]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build LC_ALL=C.UTF-8 dh build --with python2 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' dh_auto_build I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/Indexer.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/mlab.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/cbook.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/_version.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/__init__.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/PBH5ToolsException.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/Metrics.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Utils.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Stats.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Sort.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Select.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Merge.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Format.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools copying ./pbh5tools/CmpH5Compare.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools running build_ext building 'pbh5tools/ci' extension creating build creating build/temp.linux-amd64-2.7 creating build/temp.linux-amd64-2.7/pbh5tools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pbh5tools/ci.c -o build/temp.linux-amd64-2.7/pbh5tools/ci.o -O3 -shared x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/pbh5tools/ci.o -o /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.so running build_scripts creating build/scripts-2.7 copying and adjusting bin/bash5tools.py -> build/scripts-2.7 copying and adjusting bin/cmph5tools.py -> build/scripts-2.7 changing mode of build/scripts-2.7/bash5tools.py from 644 to 755 changing mode of build/scripts-2.7/cmph5tools.py from 644 to 755 /usr/bin/make -C doc html make[2]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.8.4 making output directory... loading intersphinx inventory from http://docs.python.org/objects.inv... WARNING: failed to reach any of the inventories with the following issues: WARNING: intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : ('intersphinx inventory %r not fetchable due to %s: %s', 'http://docs.python.org/objects.inv', , ConnectionError(...)) building [mo]: targets for 0 po files that are out of date building [html]: targets for 2 source files that are out of date updating environment: 2 added, 0 changed, 0 removed reading sources... [ 50%] cmph5tools-examples reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 50%] cmph5tools-examples writing output... [100%] index generating indices... genindex writing additional pages... search copying static files... WARNING: html_static_path entry u'/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/doc/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 3 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/doc' make[1]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="PATH=/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7:$PATH /usr/bin/make test" \ dh_auto_test I: pybuild base:217: PATH=/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make test make[2]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' cram -v doc/examples.t doc/examples.t: passed # Ran 1 tests, 0 skipped, 0 failed. sed 's/^ / /' doc/examples.t > doc/examples.md find tests -name "*.py" | xargs nosetests -v test_cmph5lib_CmpH5Sort.TestCmpH5Format.test___init__ ... ok test_cmph5lib_CmpH5Sort.TestComputeIndices.test_compute_indices ... ok test_cmph5lib_CmpH5Sort.TestComputeIndicesDP.test_compute_indices_d_p ... ok test_cmph5lib_CmpH5Sort.TestComputeRefIndexTable.test_compute_ref_index_table ... ok test_cmph5lib_CmpH5Sort.TestGetOverlappingRanges.test_get_overlapping_ranges ... ok test_cmph5lib_CmpH5Sort.TestGetReadsInRange.test_get_reads_in_range ... ok test_cmph5lib_CmpH5Sort.TestNumberWithinRange.test_number_within_range ... ok test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Merge) ... ok test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Select) ... ok test_output_file_in_inputs (test_cmph5lib_CmpH5Merge.TestMergeException) ... ok ---------------------------------------------------------------------- Ran 10 tests in 10.182s OK find tests/cram -name "*.t" | xargs cram -v tests/cram/valid.t: passed tests/cram/stats.t: failed --- tests/cram/stats.t +++ tests/cram/stats.t.err @@ -71,15 +71,15 @@ Generate whitelist for other pipelines. **zmw's not unique, includes header** $ $CMD --what WhiteList --where "ReadLength > 400" --outFile out.csv $ tail -n +2 out.csv | uniq - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/3008 - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/1000 - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/2006 - m110818_075520_42141_c100129202555500000315043109121112_s1_p0/1007 - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/4007 - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/1002 - m110818_075520_42141_c100129202555500000315043109121112_s2_p0/9 - m110818_075520_42141_c100129202555500000315043109121112_s1_p0/9 - m110818_075520_42141_c100129202555500000315043109121112_s1_p0/2003 + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/3008\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/1000\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/2006\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s1_p0/1007\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/4007\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/1002\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s2_p0/9\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s1_p0/9\r (esc) + m110818_075520_42141_c100129202555500000315043109121112_s1_p0/2003\r (esc) Test 'select' subtool commands $ SCMD="cmph5tools.py select $INH5" Generate new cmp.h5 files per movie with length/accuracy filtering @@ -153,7 +153,7 @@ $ linecount out.csv 85 $ tail -n 1 out.csv - m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011,182,0.1538,0.3418 + m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011,182,0.1538,0.3418\r (esc) Export to csv file (2) $ $CMD --what "Tbl(readlength = ReadLength, errorRate = 1 - Accuracy, ipd = Mean(IPD))" --groupBy "Movie * Reference" --where "Accuracy > .85" --outFile out.csv $ linecount out.csv tests/cram/sort.t: failed --- tests/cram/sort.t +++ tests/cram/sort.t.err @@ -1,14 +1,74 @@ $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"` $ cmph5tools.py sort --deep --outFile tmp.cmp.h5 $INH5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ echo $? 0 $ cmph5tools.py sort --deep --inPlace tmp.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ echo $? 0 $ cmph5tools.py sort --deep tmp.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ echo $? 0 $ cmph5tools.py sort --outFile ftmp.cmp.h5 $INH5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ echo $? 0 $ python -c "from pbcore.io import CmpH5Reader; a = CmpH5Reader('tmp.cmp.h5'); b = CmpH5Reader('ftmp.cmp.h5'); print(all([a[i] == b[i] for i in xrange(len(a))]));" tests/cram/sort-extended.t: failed --- tests/cram/sort-extended.t +++ tests/cram/sort-extended.t.err @@ -1,9 +1,39 @@ $ export INCMP=$TESTDIR/../../etc/aligned_reads_ss.cmp.h5 $ cmph5tools.py sort $INCMP --outFile out.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py select --groupBy Barcode \ > --where "(Barcode == 'F_42--R_42') | (Barcode == 'F_28--R_28')" $INCMP $ cmph5tools.py sort --inPlace F_42--R_42.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py merge --outFile m1.cmp.h5 F_42--R_42.cmp.h5 \ > F_28--R_28.cmp.h5 @@ -13,8 +43,40 @@ * alignments differ (glob) [1] $ cmph5tools.py sort --inPlace m1.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py sort --inPlace m2.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py equal m1.cmp.h5 m2.cmp.h5 + 56 alignments differ + [1] $ cmph5tools.py select --where "SubSample(.05)" $INCMP \ > --outFile ss1.cmp.h5 tests/cram/select.t: passed tests/cram/merge.t: failed --- tests/cram/merge.t +++ tests/cram/merge.t.err @@ -12,7 +12,37 @@ $ echo $? 0 $ cmph5tools.py sort merged.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py sort tot.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ cmph5tools.py equal tot.cmp.h5 merged.cmp.h5 $ echo $? 0 @@ -20,6 +50,21 @@ $ echo $? 0 $ cmph5tools.py sort --inPlace merged1.cmp.h5 + Traceback (most recent call last): + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 240, in + sys.exit(CmpH5ToolsRunner().start()) + File "/usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py", line 85, in start + return self.run() + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/build/scripts-2.7/cmph5tools.py", line 188, in run + inPlace = self.args.inPlace) + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py", line 368, in cmpH5Sort + myIndexer = Indexer.Indexer().compute + File "/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py", line 40, in __init__ + self._dll = ctypes.CDLL(self.SW_DLL_PATH) + File "/usr/lib/python2.7/ctypes/__init__.py", line 366, in __init__ + self._handle = _dlopen(self._name, mode) + OSError: /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.x86_64-linux-gnu.so: cannot open shared object file: No such file or directory + [1] $ echo $? 0 $ cmph5tools.py equal merged1.cmp.h5 $INH5 tests/cram/groupcsv.t: passed tests/cram/bash5tools.t: passed # Ran 8 tests, 0 skipped, 4 failed. make[2]: [Makefile:21: test] Error 123 (ignored) make[2]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' make[1]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary LC_ALL=C.UTF-8 dh binary --with python2 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools running install running build running build_py running build_ext running build_scripts running install_lib creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7 creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/_version.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Compare.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/cbook.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/mlab.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Stats.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Merge.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Metrics.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Utils.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Format.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/PBH5ToolsException.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/__init__.pyc -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/ci.so -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Compare.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Format.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Merge.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Select.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Sort.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Stats.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/CmpH5Utils.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Metrics.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/PBH5ToolsException.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/__init__.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/_version.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/cbook.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/mlab.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools copying /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/.pybuild/cpython2_2.7_pbh5tools/build/pbh5tools/Indexer.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Compare.py to CmpH5Compare.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Format.py to CmpH5Format.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Merge.py to CmpH5Merge.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Select.py to CmpH5Select.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Sort.py to CmpH5Sort.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Stats.py to CmpH5Stats.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Utils.py to CmpH5Utils.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/Metrics.py to Metrics.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/PBH5ToolsException.py to PBH5ToolsException.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/__init__.py to __init__.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/_version.py to _version.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/cbook.py to cbook.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/mlab.py to mlab.pyc byte-compiling /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/Indexer.py to Indexer.pyc running install_egg_info running egg_info creating pbh5tools.egg-info writing requirements to pbh5tools.egg-info/requires.txt writing pbh5tools.egg-info/PKG-INFO writing top-level names to pbh5tools.egg-info/top_level.txt writing dependency_links to pbh5tools.egg-info/dependency_links.txt writing manifest file 'pbh5tools.egg-info/SOURCES.txt' reading manifest file 'pbh5tools.egg-info/SOURCES.txt' writing manifest file 'pbh5tools.egg-info/SOURCES.txt' Copying pbh5tools.egg-info to /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info Skipping SOURCES.txt running install_scripts creating /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/bin copying build/scripts-2.7/cmph5tools.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/bin copying build/scripts-2.7/bash5tools.py -> /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/bin changing mode of /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/bin/cmph5tools.py to 755 changing mode of /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/python-pbh5tools/usr/bin/bash5tools.py to 755 debian/rules override_dh_install make[1]: Entering directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' dh_install # We do this here rather than in .install files so that debhelper # takes care of the #!/usr/bin/env lines for us mkdir -p /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/pbh5tools/usr/bin mv debian/python-pbh5tools/usr/bin/bash5tools.py /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/pbh5tools/usr/bin/bash5tools mv debian/python-pbh5tools/usr/bin/cmph5tools.py /build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg/debian/pbh5tools/usr/bin/cmph5tools make[1]: Leaving directory '/build/pbh5tools-0.8.0+git20170929.58d54ff+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 tools:114: replacing shebang in debian/pbh5tools/usr/bin/cmph5tools I: dh_python2 tools:114: replacing shebang in debian/pbh5tools/usr/bin/bash5tools I: dh_python2 fs:343: renaming ci.so to ci.x86_64-linux-gnu.so dh_installinit -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_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/ci.x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-pbh5tools: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pbh5tools: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python-pbh5tools: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pbh5tools: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pbh5tools' in '../pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb'. dpkg-deb: building package 'python-pbh5tools' in '../python-pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb'. dpkg-deb: building package 'python-pbh5tools-doc' in '../python-pbh5tools-doc_0.8.0+git20170929.58d54ff+dfsg-1_all.deb'. dpkg-deb: building package 'python-pbh5tools-dbgsym' in '../python-pbh5tools-dbgsym_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.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/7852 and its subdirectories I: Current time: Mon Jul 19 04:51:38 -12 2021 I: pbuilder-time-stamp: 1626713498 Mon Jul 19 16:51:39 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon Jul 19 16:51:39 UTC 2021 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon Jul 19 16:54:07 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon Jul 19 16:54:08 UTC 2021 I: pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.changes: Format: 1.8 Date: Fri, 13 Jul 2018 15:58:44 +0200 Source: pbh5tools Binary: pbh5tools python-pbh5tools python-pbh5tools-dbgsym python-pbh5tools-doc Architecture: all amd64 Version: 0.8.0+git20170929.58d54ff+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: pbh5tools - tools for manipulating Pacific Biosciences HDF5 files python-pbh5tools - tools for manipulating Pacific Biosciences HDF5 files -- Python 2 python-pbh5tools-doc - tools for manipulating HDF5 files produced by Pacific Biosciences Changes: pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) unstable; urgency=medium . * Team upload. * d/watch: use git mode * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 * Build-Depends: python-h5py * DEP3 Checksums-Sha1: 6805b54b429d8c509212ea0e03b23b9fca1e0387 8796 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb 8c05415b8954bc334185784fd1666f04dbe1820e 8568 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo b60a4a8337fd855231d51c9207fd38bf1603817f 5896 python-pbh5tools-dbgsym_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb 361c414aa5996bd4434d335d4e88aecce21b58ea 36968 python-pbh5tools-doc_0.8.0+git20170929.58d54ff+dfsg-1_all.deb 39d4aeeac0f304c2d8954f69b8fcd250eeec6d25 29236 python-pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb Checksums-Sha256: ca022f2906df9872db86343bdfbb83b5ac00e3d85a8aee0fd694048de83baa07 8796 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb 695dabbdece12740ea0639c644a51d2aeba0cc51344d0935c9421ad5e132f579 8568 pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo 7d50a2a0803cf75a254e6866fb2b461cb6ac779ebe851471ab796c609d650e74 5896 python-pbh5tools-dbgsym_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb b5ae5818737336a5ae4d492d3483bb03b113b8b9b051b56c37169939d1110f8a 36968 python-pbh5tools-doc_0.8.0+git20170929.58d54ff+dfsg-1_all.deb c208b60a2720f0027fdae3cc4b6a512a33d909691fe73a1fb4bdaa66f41949e3 29236 python-pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb Files: f020dfdd8b170f14da9b4f9c7e198bcf 8796 science optional pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb 584975d707221b953be79f8e64967e08 8568 science optional pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo 557ddf53673c0cb96ed1fd3eebf42133 5896 debug optional python-pbh5tools-dbgsym_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb bf576343eb1d93ac2968d88a3b572213 36968 doc optional python-pbh5tools-doc_0.8.0+git20170929.58d54ff+dfsg-1_all.deb 6459c34a35e026b1974930393b3e01b3 29236 python optional python-pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.deb Mon Jul 19 16:54:09 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.zfoVdKzpOi/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.zfoVdKzpOi/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.zfoVdKzpOi/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.zfoVdKzpOi/b1/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.zfoVdKzpOi/b2/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.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: 0.268s) 0.268s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.070s) 0.069s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 19 16:54:12 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 19 16:54:12 UTC 2021 I: pbh5tools from buster built successfully and reproducibly on amd64. Mon Jul 19 16:54:13 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 19 16:54:13 UTC 2021 I: Submitting 12K b1/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo.asc Mon Jul 19 16:54:14 UTC 2021 I: Submitting 12K b2/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo.asc Mon Jul 19 16:54:15 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 19 16:54:15 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 19 16:54:15 UTC 2021 I: Removing signed pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo.asc files: removed './b1/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo.asc' removed './b2/pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_amd64.buildinfo.asc'