iva →
1.0.9+ds-11 →
armhf → 2021-01-24 22:44:40
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| iva 1.0.9+ds-11 (armhf) Sun, 24 Jan 2021 22:14:13 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.9+ds-11
Source Version: 1.0.9+ds-11
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-1339eaef-60e9-45a4-b94c-2e74d96c2570' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 25.2 MB in 25s (995 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'iva' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/iva.git
Please use:
git clone https://salsa.debian.org/med-team/iva.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8684 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-11 (dsc) [2292 B]
Get:2 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-11 (tar) [8675 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-11 (diff) [5864 B]
Fetched 8684 kB in 1s (6023 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-JkGSDM/iva-1.0.9+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-JkGSDM' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-7lzX4U/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-7lzX4U/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7lzX4U/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2768 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 80 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12564 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
Filtered Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<<BUILDDIR>>/resolver-7lzX4U/apt_archive/sbuild-build-depends-iva-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-iva-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Sources [605 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ Packages [686 B]
Fetched 2624 B in 1s (3580 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install iva build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bioperl ca-certificates
ca-certificates-java cpp-10 debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz
fastaq file fontconfig-config fonts-dejavu-core g++-10 gawk gcc-10
gcc-10-base gettext gettext-base groff-base help2man intltool-debian
java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasan6
libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data
libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0
libcapture-tiny-perl libcc1-0 libclass-data-inheritable-perl libcups2
libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0
libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-10-dev
libgcc-s1 libgfortran5 libglib2.0-0 libgnutls30 libgomp1 libgraphite2-3
libharfbuzz0b libhts3 libicu67 libio-string-perl libjpeg62-turbo liblapack3
liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6
libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1
libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libstdc++-10-dev libstdc++6 libsub-override-perl libsub-uplevel-perl
libtest-deep-perl libtest-differences-perl libtest-exception-perl
libtest-most-perl libtest-warn-perl libtext-diff-perl libtinfo6 libtool
libubsan1 libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 mailcap man-db media-types
mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless openssl
po-debconf python3 python3-decorator python3-distutils python3-lib2to3
python3-minimal python3-networkx python3-nose python3-numpy
python3-packaging python3-pkg-resources python3-pyparsing python3-pysam
python3-setuptools python3.9 python3.9-minimal samtools smalt ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-10-locales dh-make
default-jre gcc-10-doc gawk-doc gettext-doc libasprintf-dev libgettextpo-dev
groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl cups-common
gnutls-bin liblcms2-utils pcscd libssl-doc libstdc++-10-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
openjdk-11-demo openjdk-11-source libnss-mdns fonts-dejavu-extra
fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei
| fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk
python3-venv python-networkx-doc python-nose-doc gfortran python-numpy-doc
python3-dev python3-pytest python3-numpy-dbg python-pyparsing-doc
python-setuptools-doc python3.9-venv python3.9-doc binfmt-support cwltool
Recommended packages:
bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl
libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl
liburi-perl libxml-simple-perl libyaml-perl libace-perl
liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget
| lynx libalgorithm-diff-xs-perl alsa-ucm-conf alsa-topology-conf
bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl
libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
libsort-naturally-perl libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl
libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk
libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl
libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl
python3-gdal python3-matplotlib python3-pydot python3-pygraphviz
python3-scipy python3-yaml
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bioperl ca-certificates
ca-certificates-java debhelper default-jdk-headless default-jre-headless
dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file
fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base
help2man intltool-debian java-common kmc libalgorithm-diff-perl
libarchive-zip-perl libasound2 libasound2-data libavahi-client3
libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3
libbrotli1 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl
libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl
libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl
libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libicu67
libio-string-perl libjpeg62-turbo liblapack3 liblcms2-2
liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libpsl5
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libsub-override-perl libsub-uplevel-perl
libtest-deep-perl libtest-differences-perl libtest-exception-perl
libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2
libxrender1 libxtst6 m4 mailcap man-db media-types mime-support mummer
openjdk-11-jdk-headless openjdk-11-jre-headless openssl po-debconf python3
python3-decorator python3-distutils python3-lib2to3 python3-minimal
python3-networkx python3-nose python3-numpy python3-packaging
python3-pkg-resources python3-pyparsing python3-pysam python3-setuptools
python3.9 python3.9-minimal samtools sbuild-build-depends-iva-dummy smalt
ucf x11-common
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgnutls30 libgomp1 libncursesw6 libssl1.1 libstdc++-10-dev
libstdc++6 libtinfo6 libubsan1
17 upgraded, 131 newly installed, 0 to remove and 63 not upgraded.
Need to get 294 MB of archives.
After this operation, 166 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7lzX4U/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4+b1 [18.3 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.1-6+rpi1 [746 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.1-6+rpi1 [202 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.1-6+rpi1 [36.1 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.1-6+rpi1 [84.1 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.1-6+rpi1 [8212 B]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.1-6+rpi1 [1986 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.1-6+rpi1 [6688 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.1-6+rpi1 [38.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.1-6+rpi1 [7341 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.1-6+rpi1 [13.4 MB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.1-6+rpi1 [682 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.1-6+rpi1 [1751 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.1-6+rpi1 [408 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf gawk armhf 1:5.0.1+dfsg-1 [540 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1i-2 [1272 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-2+rpi1 [790 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1-2+rpi1 [1623 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.68 [31.6 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-2 [328 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-2 [105 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1-2+rpi1 [1658 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.1-2+rpi1 [464 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.1-1 [64.1 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.7.0-5 [1275 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libio-string-perl all 1.08-3.1 [11.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libbio-perl-perl all 1.7.7-2 [2607 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libexception-class-perl all 1.44-1 [32.3 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libtest-deep-perl all 1.130-1 [49.3 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libtest-differences-perl all 0.67-1 [18.7 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libsub-uplevel-perl all 0.2800-1.1 [16.5 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libtest-exception-perl all 0.43-1 [18.7 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libtest-warn-perl all 0.36-1 [16.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libtest-most-perl all 0.37-1 [24.9 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf bioperl all 1.7.7-2 [246 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1i-2 [813 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf java-common all 0.72 [14.5 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common-data armhf 0.8-3+b2 [127 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common3 armhf 0.8-3+b2 [55.3 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libdbus-1-3 armhf 1.12.20-1+b3 [192 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libavahi-client3 armhf 0.8-3+b2 [58.0 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libcups2 armhf 2.3.3op1-7 [311 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-2 [120 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [353 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libnspr4 armhf 2:4.29-1 [89.9 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libnss3 armhf 2:3.60-1 [1086 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libasound2-data all 1.2.4-1.1 [38.2 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libasound2 armhf 1.2.4-1.1 [303 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.4-1 [1182 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpcsclite1 armhf 1.9.0-1 [56.7 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2.1 [136 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.7.0-2 [310 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.0-2 [706 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libxi6 armhf 2:1.7.10-1 [77.9 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+21 [252 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jre-headless armhf 11.0.10+8-1 [32.8 MB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.1 [188 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.10.0-1 [25.6 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.10.0-1 [15.3 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210118-1 [163 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.1 [1010 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jdk-headless armhf 11.0.10+8-1 [174 MB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf default-jdk-headless armhf 2:1.11-72+b4 [1100 B]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.9.1-2 [77.2 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.9.1-2 [143 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102 [99.3 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 51.1.0-1 [203 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1 [301 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf fastaq all 3.17.0-3 [47.8 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.17 [189 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf kmc armhf 3.1.1+dfsg-3 [692 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libbambamc0 armhf 0.0.50-4 [30.2 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1i-2 [1575 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf mummer armhf 3.23+dfsg-7 [618 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf python3-decorator all 4.4.2-2 [15.8 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf python3-networkx all 2.5+ds-2 [900 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf python3-nose all 1.3.7-7 [133 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.19.4-1+b2 [2930 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.7-1 [109 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 20.8-1 [32.6 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf python3-pysam armhf 0.15.4+ds-3+b1 [1344 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 51.1.0-1 [1099 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf smalt armhf 0.7.6-9 [93.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.14-2.1) ...
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Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
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Setting up libhts3:armhf (1.11-2) ...
Setting up libstdc++-10-dev:armhf (10.2.1-6+rpi1) ...
Setting up g++-10 (10.2.1-6+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libtest-most-perl (0.37-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.3-1.1) ...
Setting up python3 (3.9.1-1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.11-1) ...
Setting up python3-decorator (4.4.2-2) ...
Setting up python3-pyparsing (2.4.7-1) ...
Setting up libcups2:armhf (2.3.3op1-7) ...
Setting up python3-lib2to3 (3.9.1-2) ...
Setting up python3-pkg-resources (51.1.0-1) ...
Setting up python3-distutils (3.9.1-2) ...
Setting up dh-python (4.20201102) ...
Setting up bioperl (1.7.7-2) ...
Setting up python3-pysam (0.15.4+ds-3+b1) ...
Setting up python3-setuptools (51.1.0-1) ...
Setting up libxi6:armhf (2:1.7.10-1) ...
Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up fastaq (3.17.0-3) ...
Setting up python3-networkx (2.5+ds-2) ...
Setting up python3-nose (1.3.7-7) ...
Setting up python3-packaging (20.8-1) ...
Setting up python3-numpy (1:1.19.4-1+b2) ...
Setting up dh-autoreconf (19) ...
Setting up default-jre-headless (2:1.11-72+b4) ...
Setting up openjdk-11-jre-headless:armhf (11.0.10+8-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up debhelper (13.3.1) ...
Setting up openjdk-11-jdk-headless:armhf (11.0.10+8-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jdk-headless (2:1.11-72+b4) ...
Setting up ca-certificates-java (20190909) ...
head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:EC-ACC.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Sonera_Class_2_Root_CA.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
done.
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-5+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-5+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-5+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-1 binutils_2.35.1-5+rpi1 binutils-arm-linux-gnueabihf_2.35.1-5+rpi1 binutils-common_2.35.1-5+rpi1 bioperl_1.7.7-2 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20210119 ca-certificates-java_20190909 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.1 debianutils_4.11.2 default-jdk-headless_2:1.11-72+b4 default-jre-headless_2:1.11-72+b4 dh-autoreconf_19 dh-python_4.20201102 dh-strip-nondeterminism_1.10.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20210118-1 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fastaq_3.17.0-3 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.1-6+rpi1 gawk_1:5.0.1+dfsg-1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-5+rpi1 gettext_0.21-3 gettext-base_0.21-3 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.17 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 java-common_0.72 kmc_3.1.1+dfsg-3 krb5-locales_1.18.3-4 libacl1_2.2.53-8 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libasound2_1.2.4-1.1 libasound2-data_1.2.4-1.1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libavahi-client3_0.8-3+b2 libavahi-common-data_0.8-3+b2 libavahi-common3_0.8-3+b2 libbambamc0_0.0.50-4 libbinutils_2.35.1-5+rpi1 libbio-perl-perl_1.7.7-2 libblas3_3.9.0-3 libblkid1_2.36.1-2 libbrotli1_1.0.9-2+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-5+rpi1 libc6_2.31-5+rpi1 libc6-dev_2.31-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcapture-tiny-perl_0.48-1 libcc1-0_10.2.1-6+rpi1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-5+rpi1 libctf0_2.35.1-5+rpi1 libcups2_2.3.3op1-7 libcurl3-gnutls_7.74.0-1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.20-1+b3 libdebconfclient0_0.255+b1 libdebhelper-perl_13.3.1 libdeflate0_1.7-1 libdevel-stacktrace-perl_2.0400-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-3 libexception-class-perl_1.44-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.10.0-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.4+dfsg-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.66.4-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.18.3-4 libharfbuzz0b_2.7.4-1 libhogweed6_3.6-2 libhts3_1.11-2 libicu67_67.1-6 libidn2-0_2.3.0-4 libio-string-perl_1.08-3.1 libisl23_0.23-1 libjpeg62-turbo_1:2.0.5-2 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-2 liblapack3_3.9.0-3 liblcms2-2_2.12~rc1-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnspr4_2:4.29-1 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnss3_2:3.60-1 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libpcsclite1_1.9.0-1 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libpsl5_0.21.0-1.1 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-2+rpi1 libpython3.9-stdlib_3.9.1-2+rpi1 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsmartcols1_2.36.1-2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-2 libssl-dev_1.1.1i-2 libssl1.1_1.1.1i-2 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsub-uplevel-perl_0.2800-1.1 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libtest-deep-perl_1.130-1 libtest-differences-perl_0.67-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.37-1 libtest-warn-perl_0.36-1 libtext-diff-perl_1.45-1 libtinfo6_6.2+20201114-2 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2.1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxi6_2:1.7.10-1 libxml2_2.9.10+dfsg-6.3 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 mailcap_3.68 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mime-support_3.66 mount_2.36.1-2 mummer_3.23+dfsg-7 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 openjdk-11-jdk-headless_11.0.10+8-1 openjdk-11-jre-headless_11.0.10+8-1 openssl_1.1.1i-2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.1-1 python3-decorator_4.4.2-2 python3-distutils_3.9.1-2 python3-lib2to3_3.9.1-2 python3-minimal_3.9.1-1 python3-networkx_2.5+ds-2 python3-nose_1.3.7-7 python3-numpy_1:1.19.4-1+b2 python3-packaging_20.8-1 python3-pkg-resources_51.1.0-1 python3-pyparsing_2.4.7-1 python3-pysam_0.15.4+ds-3+b1 python3-setuptools_51.1.0-1 python3.9_3.9.1-2+rpi1 python3.9-minimal_3.9.1-2+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 smalt_0.7.6-9 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 ucf_3.0043 util-linux_2.36.1-2 x11-common_1:7.7+21 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.daETKk2B/trustedkeys.kbx': General error
gpgv: Signature made Tue Dec 22 10:23:23 2020 UTC
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 ./iva_1.0.9+ds-11.dsc
dpkg-source: info: extracting iva in /<<BUILDDIR>>/iva-1.0.9+ds
dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.9+ds-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-multithreaded-test.patch
dpkg-source: info: applying perl-shebang.patch
dpkg-source: info: applying samtools1.10
dpkg-source: info: applying disable-ram-test.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-1339eaef-60e9-45a4-b94c-2e74d96c2570
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.9+ds-11
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
rm -rf .pybuild
rm -f iva/gage/*.class
rm -rf /<<BUILDDIR>>/iva-1.0.9+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:232: python3.9 setup.py config
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
chmod a-x /<<BUILDDIR>>/iva-1.0.9+ds/iva/read_trim/adapters.fasta
chmod a+x /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /<<BUILDDIR>>/iva-1.0.9+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/*.java
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/GetFastaStats.java]]
[parsing completed 483ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.java]]
[parsing completed 38ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 23ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.java]]
[parsing completed 151ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 449ms]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.scripting.nashorn.shell/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/java.base/module-info.class]
[loading /modules/java.management/module-info.class]
[loading /modules/java.desktop/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/jdk.pack/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/jdk.rmic/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/jdk.scripting.nashorn/module-info.class]
[loading /modules/jdk.naming.ldap/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/java.compiler/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[search path for source files: .]
[search path for class files: /usr/lib/jvm/java-11-openjdk-armhf/lib/modules,.]
[loading /modules/java.base/java/io/BufferedReader.class]
[loading /modules/java.base/java/io/FileInputStream.class]
[loading /modules/java.base/java/io/InputStreamReader.class]
[loading /modules/java.base/java/text/DecimalFormat.class]
[loading /modules/java.base/java/text/NumberFormat.class]
[loading /modules/java.base/java/util/ArrayList.class]
[loading /modules/java.base/java/util/Arrays.class]
[loading /modules/java.base/java/util/HashMap.class]
[loading /modules/java.base/java/lang/Object.class]
[loading /modules/java.base/java/lang/String.class]
[loading /modules/java.base/java/lang/Integer.class]
[loading /modules/java.base/java/lang/Exception.class]
[loading /modules/java.base/java/lang/StringBuffer.class]
[loading /modules/java.management/java/lang/management/ManagementFactory.class]
[loading /modules/java.management/java/lang/management/MemoryMXBean.class]
[loading /modules/java.base/java/io/File.class]
[loading /modules/java.base/java/io/FileReader.class]
[loading /modules/java.base/java/lang/Boolean.class]
[loading /modules/java.base/java/lang/Enum.class]
[loading /modules/java.base/java/lang/Comparable.class]
[loading /modules/java.base/java/io/Serializable.class]
[loading /modules/java.base/java/util/Collections.class]
[loading /modules/java.base/java/lang/Deprecated.class]
[loading /modules/java.base/java/lang/annotation/Retention.class]
[loading /modules/java.base/java/lang/annotation/RetentionPolicy.class]
[loading /modules/java.base/java/lang/annotation/Target.class]
[loading /modules/java.base/java/lang/annotation/ElementType.class]
[checking GetFastaStats]
[loading /modules/java.base/java/lang/AutoCloseable.class]
[loading /modules/java.base/java/util/Map.class]
[loading /modules/java.base/java/lang/Throwable.class]
[loading /modules/java.base/java/lang/CharSequence.class]
[loading /modules/java.base/java/io/Reader.class]
[loading /modules/java.base/java/lang/Readable.class]
[loading /modules/java.base/java/io/Closeable.class]
[loading /modules/java.base/java/lang/Number.class]
[loading /modules/java.base/java/lang/Cloneable.class]
[loading /modules/java.base/java/util/AbstractMap.class]
[loading /modules/java.base/java/lang/AbstractStringBuilder.class]
[loading /modules/java.base/java/lang/Appendable.class]
[loading /modules/java.base/java/lang/Byte.class]
[loading /modules/java.base/java/lang/Character.class]
[loading /modules/java.base/java/lang/Short.class]
[loading /modules/java.base/java/lang/Long.class]
[loading /modules/java.base/java/lang/Float.class]
[loading /modules/java.base/java/lang/Double.class]
[loading /modules/java.base/java/lang/Void.class]
[loading /modules/java.base/java/io/FileDescriptor.class]
[loading /modules/java.base/java/lang/System.class]
[loading /modules/java.base/java/io/PrintStream.class]
[loading /modules/java.base/java/io/FilterOutputStream.class]
[loading /modules/java.base/java/io/OutputStream.class]
[loading /modules/java.base/java/io/Flushable.class]
[loading /modules/java.base/java/util/Set.class]
[loading /modules/java.base/java/lang/Iterable.class]
[loading /modules/java.base/java/util/Collection.class]
[loading /modules/java.base/java/lang/Math.class]
[loading /modules/java.base/java/util/List.class]
[loading /modules/java.base/java/util/RandomAccess.class]
[loading /modules/java.base/java/util/AbstractList.class]
[loading /modules/java.base/java/util/AbstractCollection.class]
[loading /modules/java.base/java/util/function/IntFunction.class]
[loading /modules/java.base/java/util/Comparator.class]
[loading /modules/java.base/java/text/Format.class]
[loading /modules/java.base/java/lang/Error.class]
[loading /modules/java.base/java/lang/RuntimeException.class]
[loading /modules/java.base/java/io/IOException.class]
[loading /modules/java.base/java/lang/NumberFormatException.class]
[loading /modules/java.base/java/lang/IllegalArgumentException.class]
[loading /modules/java.base/java/io/FileNotFoundException.class]
[loading /modules/java.base/java/util/Iterator.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/GetFastaStats$ContigAt.class]
[loading /modules/java.base/java/lang/invoke/StringConcatFactory.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class]
[loading /modules/java.base/java/lang/invoke/MethodType.class]
[loading /modules/java.base/java/io/InputStream.class]
[loading /modules/java.base/java/lang/invoke/CallSite.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/GetFastaStats.class]
[checking SizeFasta]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.class]
[checking SplitFastaByLetter]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class]
[checking Utils]
[loading /modules/java.base/java/lang/CloneNotSupportedException.class]
[loading /modules/java.base/java/lang/Class.class]
[loading /modules/java.base/java/net/URI.class]
[loading /modules/java.base/java/lang/Process.class]
[loading /modules/java.base/java/lang/Runtime.class]
[loading /modules/java.base/java/lang/StringBuilder.class]
[loading /modules/java.base/java/lang/reflect/GenericDeclaration.class]
[loading /modules/java.base/java/lang/reflect/AnnotatedElement.class]
[loading /modules/java.base/java/lang/reflect/Type.class]
[loading /modules/java.base/java/lang/AssertionError.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$Pair.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$Translate.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.class]
[checking getScaffoldStats]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class]
[wrote /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.class]
[total 13806ms]
dh_auto_build --
I: pybuild base:232: /usr/bin/python3 setup.py build
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running build
running build_py
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.9
copying and adjusting scripts/iva -> build/scripts-3.9
copying and adjusting scripts/iva_qc -> build/scripts-3.9
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.9
changing mode of build/scripts-3.9/iva from 644 to 755
changing mode of build/scripts-3.9/iva_qc from 644 to 755
changing mode of build/scripts-3.9/iva_qc_make_db from 644 to 755
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
python3 setup.py test
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
running egg_info
creating iva.egg-info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
writing manifest file 'iva.egg-info/SOURCES.txt'
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
running build_ext
/<<BUILDDIR>>/iva-1.0.9+ds/iva/mapping.py:159: DeprecationWarning: invalid escape sequence \^
s = re.sub('\^.', '', s)
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \(
'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \(
'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \(
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \(
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d
'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \.
self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
/<<BUILDDIR>>/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W
return re.sub('\W', '_', s).strip('_')
test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly)
Test _contig_contained_in_nucmer_hits ... ok
test_contig_names_size_order (assembly_test.TestAssembly)
Test _contig_names_size_order ... ok
test_contig_worth_extending (assembly_test.TestAssembly)
Test _contig_worth_extending ... ok
test_coords_to_new_contig (assembly_test.TestAssembly)
Test _coords_to_new_contig ... ok
test_extend_contigs_with_bam (assembly_test.TestAssembly)
test _extend_contigs_with_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_get_contig_order_by_orfs (assembly_test.TestAssembly)
Test get_contig_order_by_orfs ... ok
test_get_ref_length (assembly_test.TestAssembly)
Test _get_ref_length ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam'
ok
test_get_ref_length_sam_pair (assembly_test.TestAssembly)
Test _get_ref_length_sam_pair ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam'
ok
test_get_unmapped_pairs (assembly_test.TestAssembly)
Test _get_unmapped_pairs ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.bam'
ok
test_good_intervals_from_strand_coverage (assembly_test.TestAssembly)
Test good_intervals_from_strand_coverage ... ok
test_init_and_write (assembly_test.TestAssembly)
test assembly initialise and write to file ... ok
test_map_reads (assembly_test.TestAssembly)
test _map_reads ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.assembly_test.out.bam'
ok
test_merge_overlapping_contigs (assembly_test.TestAssembly)
Test _merge_overlapping_contigs ... ok
test_read_pair_extend (assembly_test.TestAssembly)
Test read_pair_extend ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.4.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.5.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.4.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.5.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/tmp.filter_reads.p9omi_8g/out.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/tmp.trim_strand_biased_ends._zfrpq2q/out.unsorted.bam'
ok
test_remove_contained_contigs (assembly_test.TestAssembly)
Test _remove_contained_contigs ... ok
test_remove_contig (assembly_test.TestAssembly)
Test _remove_contig ... ok
test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly)
Test _remove_contig_from_nucmer_hits ... ok
test_subcontigs_from_strand_bias (assembly_test.TestAssembly)
Test _subcontigs_from_strand_bias ... ok
test_trim_contig_for_strand_bias (assembly_test.TestAssembly)
Test _trim_contig_for_strand_bias ... ok
test_trim_contigs (assembly_test.TestAssembly)
Test trim_contigs ... ok
test_trim_strand_biased_ends (assembly_test.TestAssembly)
Test _trim_strand_biased_ends ... ok
test_worth_extending (assembly_test.TestAssembly)
Test worth_extending ... ok
test_add_left_kmer (contig_test.TestContig)
Test add_left_kmer ... ok
test_add_right_kmer (contig_test.TestContig)
Test add_right_kmer ... ok
test_extend (contig_test.TestContig)
Test extend ... ok
test_init (contig_test.TestContig)
Test init ... ok
test_len (contig_test.TestContig)
Test len ... ok
test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim)
Test _coverage_to_trimmed_coords ... ok
test_trim_ends (contig_trim_test.TestContigTrim)
Test _trim_ends ... ok
test_trim_primers_and_adapters (contig_trim_test.TestContigTrim)
Test trim_primers_and_adapters ... ok
test_change_hit_coords_with_intersection (edge_test.TestEdge)
test test_change_hit_coords_with_intersection ... ok
test_make_contig_first (edge_test.TestEdge)
test make_contig_first ... ok
test_make_contig_forwards (edge_test.TestEdge)
test make_contig_forwards ... ok
test_merge_into (edge_test.TestEdge)
test merge_into ... ok
test_open_end (edge_test.TestEdge)
test open_end ... ok
test_reverse (edge_test.TestEdge)
test reverse ... ok
test_copy_dir (egg_extract_test.TestEggExtract)
test copy_dir ... ok
test_copy_dir_unzipped (egg_extract_test.TestEggExtract)
test copy_dir_unzipped ... ok
test_copy_dir_zipped (egg_extract_test.TestEggExtract)
test copy_dir_zipped ... ok
test_copy_file (egg_extract_test.TestEggExtract)
test copy_file ... ok
test_copy_file_unzipped (egg_extract_test.TestEggExtract)
test _copy_file_unzipped ... ok
test_copy_file_zipped (egg_extract_test.TestEggExtract)
test _copy_file_zipped ... ok
test_init_and_write (egg_extract_test.TestEggExtract)
test __init__ ... ok
test_blastn_version (external_progs_test.TestExternalProgs)
Test blastn version ... ok
test_delta_filter_in_path (external_progs_test.TestExternalProgs)
Test delta-filter in path ... ok
test_kmc_dump_in_path (external_progs_test.TestExternalProgs)
Test kmc_dump in path ... ok
test_kmc_dump_version (external_progs_test.TestExternalProgs)
Test kmc_dump version ... ok
test_kmc_in_path (external_progs_test.TestExternalProgs)
Test kmc in path ... ok
test_kmc_version (external_progs_test.TestExternalProgs)
Test kmc version ... ok
test_makeblastdb_version (external_progs_test.TestExternalProgs)
Test makeblastdb version ... ok
test_nucmer_in_path (external_progs_test.TestExternalProgs)
Test nucmer in path ... ok
test_nucmer_version (external_progs_test.TestExternalProgs)
Test nucmer version ... ok
test_r_version (external_progs_test.TestExternalProgs)
Test R versions ... ok
test_samtools_in_path (external_progs_test.TestExternalProgs)
Test samtools in path ... ok
test_samtools_original_version (external_progs_test.TestExternalProgs)
Test samtools original version ... ok
test_samtools_version (external_progs_test.TestExternalProgs)
Test samtools version ... ok
test_show_coords_in_path (external_progs_test.TestExternalProgs)
Test show-coords in path ... ok
test_smalt_in_path (external_progs_test.TestExternalProgs)
Test smalt in path ... ok
test_smalt_version (external_progs_test.TestExternalProgs)
Test smalt version ... ok
test_add_and_get_edges (graph_test.TestGraph)
test adding and getting edges ... ok
test_connected_components (graph_test.TestGraph)
test connected_components ... ok
test_degree (graph_test.TestGraph)
test degree ... ok
test_edges_are_consistent (graph_test.TestGraph)
test edges_are_consistent ... ok
test_find_simple_path (graph_test.TestGraph)
test find_simple_path ... ok
test_get_nodes (graph_test.TestGraph)
test get_nodes ... ok
test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph)
test merged_coords_from_simple_nonredundant_path ... ok
test_node_to_coords (graph_test.TestGraph)
test _node_to_coords ... ok
test_remove_middle_node (graph_test.TestGraph)
test remove_middle_node ... ok
test_remove_node (graph_test.TestGraph)
test remove_node ... ok
test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph)
test remove_redundant_nodes_from_simple_path ... ok
test_simple_path_is_consistent (graph_test.TestGraph)
test simple_path_is_consistent ... ok
test_counts_file_to_fasta (kcount_test.TestKcount)
Test _counts_file_to_fasta ... ok
test_head_fastaq_fa (kcount_test.TestKcount)
Test head_fastaq with FASTA input ... ok
test_head_fastaq_fq (kcount_test.TestKcount)
Test head_fastaq with FASTQ input ... ok
test_kmc_to_kmer_counts (kcount_test.TestKcount)
Test _kmc_to_kmer_counts ... ok
test_median (kcount_test.TestKcount)
Test _median() ... ok
test_append (kmers_test.TestKmers)
Test append ... ok
test_commonest_kmers (kmers_test.TestKmers) ... ok
test_extend (kmers_test.TestKmers)
Test extend ... ok
test_extension (kmers_test.TestKmers)
Test extension ... ok
test_init (kmers_test.TestKmers)
Test __init__ ... ok
test_kmer_dict (kmers_test.TestKmers)
Test kmer_dict ... ok
test_append_to_file (kraken_test.TestKraken)
test _append_to_file ... ok
test_count_cds_from_embl (kraken_test.TestKraken)
test count_cds_from_embl ... ok
test_genbank_to_taxon_and_gi (kraken_test.TestKraken)
test _genbank_to_taxon_and_gi ... ok
test_get_most_common_species_dir (kraken_test.TestKraken)
Test get_most_common_species ... ok
test_get_parent_taxons (kraken_test.TestKraken)
test _get_parent_taxons ... ok
test_load_extra_ref_info (kraken_test.TestKraken)
test _load_extra_ref_info ... ok
test_replace_fasta_header (kraken_test.TestKraken)
test _replace_fasta_header ... ok
test_species_to_dir (kraken_test.TestKraken)
test species_to_dir ... ok
test_bam_file_to_fasta_pair_files (mapping_test.TestMapping)
Test bam_file_to_fasta_pair_files ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping)
Test bam_file_to_fasta_pair_files with a region ... ok
test_bam_file_to_region_fasta (mapping_test.TestMapping)
Test bam_file_to_region_fasta ... ok
test_bam_to_fasta (mapping_test.TestMapping)
Test bam_to_fasta ... ok
test_can_extend (mapping_test.TestMapping)
Test can_extend ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_consensus_base (mapping_test.TestMapping)
Test consensus_base ... ok
test_consensus_base_both_strands (mapping_test.TestMapping)
Test consensus_base_both_strands ... ok
test_find_incorrect_ref_bases (mapping_test.TestMapping)
Test find_incorrect_ref_bases ... ok
test_get_bam_region_coverage_fwd (mapping_test.TestMapping)
Test get_bam_region_coverage forward strand ... ok
test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping)
Test get_bam_region_coverage both strands ... ok
test_get_bam_region_coverage_rev (mapping_test.TestMapping)
Test get_bam_region_coverage reverse strand ... ok
test_get_pair_type (mapping_test.TestMapping)
Test get_pair_type ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_get_ref_name (mapping_test.TestMapping)
Test get_ref_name ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_map_reads (mapping_test.TestMapping)
Test mapping reads ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam'
ok
test_map_reads_and_sort (mapping_test.TestMapping)
Test mapping reads and sort BAM ... ok
test_map_reads_wth_flag (mapping_test.TestMapping)
Test map_reads with required flag ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.flag12.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam'
ok
test_remove_indels (mapping_test.TestMapping)
Test _remove_indels ... ok
test_sam_to_fasta (mapping_test.TestMapping)
Test sam_to_fasta ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_smalt_in_path (mapping_test.TestMapping)
Test that samtools is in the user's path ... ok
test_soft_clipped (mapping_test.TestMapping)
Test soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_strip_mpileup_coverage_string (mapping_test.TestMapping)
Test strip_mpileup_coverage_string ... ok
test_total_ref_length_from_bam (mapping_test.TestMapping)
Test _total_ref_length_from_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/mapping_test.total_ref_length_from_bam.bam'
ok
test_file_read (mummer_test.TestMummer)
test file_read ... ok
test_is_at_ends (mummer_test.TestMummer)
Test is_at_ends ... ok
test_is_self_hit (mummer_test.TestMummer)
Test is_self_hit ... ok
test_on_same_strand (mummer_test.TestMummer)
test on_same_strand ... ok
test_qry_coords (mummer_test.TestMummer)
Test qry_coords ... ok
test_ref_coords (mummer_test.TestMummer)
Test ref_coords ... ok
test_run_nucmer (mummer_test.TestMummer)
test run_nucmer ... ok
test_sort (mummer_test.TestMummer)
test sort ... ok
test_swap (mummer_test.TestMummer)
test swap ... ok
test_to_graph_edge (mummer_test.TestMummer)
Test to_graph_edge ... ok
test_run_gage (qc_external_test.TestQcExternal)
test run_gage ... ok
test_run_ratt (qc_external_test.TestQcExternal)
test run_ratt ... ok
test_calculate_cds_assembly_stats (qc_test.TestQc)
test _calculate_cds_assembly_stats ... ok
test_calculate_contig_placement (qc_test.TestQc)
test calculate_contig_placement ... ok
test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc)
test _calculate_ref_positions_covered_by_contigs ... ok
test_calculate_ref_read_coverage (qc_test.TestQc)
test _calculate_ref_read_coverage ... ok
test_calculate_ref_read_region_coverage (qc_test.TestQc)
test _calculate_ref_read_region_coverage ... ok
test_calculate_refseq_assembly_stats (qc_test.TestQc)
test _calculate_refseq_assembly_stats ... ok
test_calculate_should_have_assembled (qc_test.TestQc)
test _calculate_should_have_assembled ... ok
test_contig_placement_in_reference (qc_test.TestQc)
test _contig_placement_in_reference ... ok
test_contigs_and_bases_that_hit_ref (qc_test.TestQc)
test _contigs_and_bases_that_hit_ref ... ok
test_cov_to_R_string (qc_test.TestQc)
test _cov_to_R_string ... ok
test_coverage_list_to_low_cov_intervals (qc_test.TestQc)
test _coverage_list_to_low_cov_intervals ... ok
test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc)
test _get_R_plot_contig_order_from_contig_placement ... ok
test_get_contig_hits_to_reference (qc_test.TestQc)
test _get_contig_hits_to_reference ... ok
test_get_overlapping_qry_hits (qc_test.TestQc)
test _get_overlapping_qry_hits ... ok
test_get_ref_cds_from_gff (qc_test.TestQc)
test _get_ref_cds_from_gff ... ok
test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc)
test _get_unique_and_repetitive_from_contig_hits ... ok
test_gff_and_fasta_to_cds (qc_test.TestQc)
test _gff_and_fasta_to_cds ... ok
test_has_orf (qc_test.TestQc)
test _has_orf ... ok
test_hash_nucmer_hits_by_ref (qc_test.TestQc)
test _hash_nucmer_hits_by_ref ... ok
test_ids_in_order_from_fai (qc_test.TestQc)
test _ids_in_order_from_fai ... ok
test_invert_list (qc_test.TestQc)
test _invert_list ... ok
test_map_cds_to_assembly (qc_test.TestQc)
test _map_cds_to_assembly ... ok
test_mummer_coords_file_to_dict (qc_test.TestQc)
test _mummer_coords_file_to_dict ... ok
test_write_cds_seqs (qc_test.TestQc)
test _write_cds_seqs ... ok
test_write_fasta_contigs_hit_ref (qc_test.TestQc)
test _write_fasta_contigs_hit_ref ... ok
test_write_fasta_contigs_not_hit_ref (qc_test.TestQc)
test _write_fasta_contigs_not_hit_ref ... ok
test_write_ref_coverage_to_files_for_R (qc_test.TestQc)
test _write_ref_coverage_to_files_for_R ... ok
test_run_trimmomatic (read_trim_test.TestReadTrim)
Test run_trimmomatic ... ok
test_extend (seed_test.TestSeed)
Test extend ... ok
test_extend_with_reads_as_single_end (seed_test.TestSeed)
Test _extend_with_reads_as_single_end ... ok
test_extension_from_read (seed_test.TestSeed)
Test _test_extension_from_read ... ok
test_extensions_from_reads_file (seed_test.TestSeed)
Test _extensions_from_reads_file ... ok
test_init (seed_test.TestSeed)
test init ... ok
test_kmc_in_path (seed_test.TestSeed)
Test that kmc is in the user's path ... ok
test_len (seed_test.TestSeed)
Test len ... ok
test_write_fasta (seed_test.TestSeed)
Test write_fasta ... ok
----------------------------------------------------------------------
Ran 160 tests in 43.325s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running install
running build
running build_py
running build_scripts
running install_lib
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/assembly.py to assembly.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/common.py to common.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig.py to contig.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig_trim.py to contig_trim.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/edge.py to edge.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/egg_extract.py to egg_extract.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/external_progs.py to external_progs.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/graph.py to graph.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kcount.py to kcount.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kmers.py to kmers.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kraken.py to kraken.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mummer.py to mummer.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc.py to qc.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc_external.py to qc_external.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim.py to read_trim.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed.py to seed.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed_processor.py to seed_processor.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mapping.py to mapping.cpython-39.pyc
running install_egg_info
running egg_info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
Copying iva.egg-info to /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva-1.0.9.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.9/iva -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.9/iva_qc -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.9/iva_qc_make_db -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva to 755
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 755
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
mkdir -p /<<BUILDDIR>>/iva-1.0.9+ds/debian/man
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva.1 \
-n 'iterative virus assembler' \
--no-discard-stderr ./scripts/iva
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva_qc.1 \
-n 'compare an assembly to a reference' \
--no-discard-stderr ./scripts/iva_qc
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva_qc_make_db.1 \
-n 'make a database as input for iva_qc' \
--no-discard-stderr ./scripts/iva_qc_make_db
dh_installman --
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
dh_python3 -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -O--buildsystem=pybuild
dh_dwz -a -a -O--buildsystem=pybuild
dh_strip -a -a -O--buildsystem=pybuild
dh_makeshlibs -a -a -O--buildsystem=pybuild
dh_shlibdeps -a -a -O--buildsystem=pybuild
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-11_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../iva_1.0.9+ds-11_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-01-24T22:44:31Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
iva_1.0.9+ds-11_armhf.changes:
------------------------------
Format: 1.8
Date: Tue, 22 Dec 2020 09:12:41 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.9+ds-11
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
iva - iterative virus sequence assembler
Changes:
iva (1.0.9+ds-11) unstable; urgency=medium
.
* Rebuild to reflect versioned Build-Depends: kmc (>= 3.1). This will
invalidate iva on several architectures as long kmc 3.x is only
available on amd64
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit.
* Restrictions: skip-not-installable
Checksums-Sha1:
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25f32beaf119424a7ff84680b60ce2cbf1f79ffe 8578708 iva_1.0.9+ds-11_armhf.deb
Checksums-Sha256:
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6b5a23ac5643078c7ce6e030abc160fc6010b50cc87a40731e8dd02ed37d0dc6 8578708 iva_1.0.9+ds-11_armhf.deb
Files:
9188bcfe252481be7329112dc0c52c38 8000 science optional iva_1.0.9+ds-11_armhf.buildinfo
ba0beb5b2dbd8b028e7acfc79428f959 8578708 science optional iva_1.0.9+ds-11_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
iva_1.0.9+ds-11_armhf.deb
-------------------------
new Debian package, version 2.0.
size 8578708 bytes: control archive=3008 bytes.
941 bytes, 21 lines control
5477 bytes, 64 lines md5sums
231 bytes, 12 lines * postinst #!/bin/sh
380 bytes, 12 lines * prerm #!/bin/sh
Package: iva
Version: 1.0.9+ds-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8765
Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless
Recommends: r-base-core, bioperl, trimmomatic
Section: science
Priority: optional
Homepage: https://github.com/sanger-pathogens/iva
Description: iterative virus sequence assembler
IVA is a de novo assembler designed to assemble
virus genomes that have no repeat sequences,
using Illumina read pairs sequenced from mixed
populations at extremely high depth.
.
IVA's main algorithm works by iteratively extending
contigs using aligned read pairs. Its input can be
just read pairs, or additionally you can provide an
existing set of contigs to be extended. Alternatively,
it can take reads together with a reference sequence.
drwxr-xr-x root/root 0 2020-12-22 08:12 ./
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/bin/
-rwxr-xr-x root/root 17240 2020-12-22 08:12 ./usr/bin/iva
-rwxr-xr-x root/root 6228 2020-12-22 08:12 ./usr/bin/iva_qc
-rwxr-xr-x root/root 2406 2020-12-22 08:12 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root 483 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root 4 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/
-rw-r--r-- root/root 1033 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/__init__.py
-rw-r--r-- root/root 28055 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/assembly.py
-rw-r--r-- root/root 1856 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/common.py
-rw-r--r-- root/root 1960 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig.py
-rw-r--r-- root/root 4391 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig_trim.py
-rw-r--r-- root/root 4903 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/edge.py
-rw-r--r-- root/root 3077 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/egg_extract.py
-rw-r--r-- root/root 4110 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/external_progs.py
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root 508 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root 10192 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root 14839 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root 3689 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root 3611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root 2898 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root 2229 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root 640 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root 4583 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root 1244 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root 5920 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/Utils.class
-rw-r--r-- root/root 9230 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/Utils.java
-rwxr-xr-x root/root 80 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl
-rwxr-xr-x root/root 1773 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh
-rwxr-xr-x root/root 1430 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh
-rw-r--r-- root/root 814 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root 13703 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class
-rw-r--r-- root/root 19111 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java
-rw-r--r-- root/root 7133 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/graph.py
-rw-r--r-- root/root 9487 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kcount.py
-rw-r--r-- root/root 3466 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kmers.py
-rw-r--r-- root/root 16961 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kraken.py
-rw-r--r-- root/root 13294 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/mapping.py
-rw-r--r-- root/root 8365 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/mummer.py
-rw-r--r-- root/root 36646 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc.py
-rw-r--r-- root/root 8190 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc_external.py
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root 1008 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root 1045 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl
-rwxr-xr-x root/root 41988 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl
-rw-r--r-- root/root 90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config
-rw-r--r-- root/root 90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv
-rw-r--r-- root/root 57611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm
-rwxr-xr-x root/root 13201 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh
-rw-r--r-- root/root 1428 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim.py
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/read_trim/
-rw-r--r-- root/root 3143 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta
-rw-r--r-- root/root 6056 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed.py
-rw-r--r-- root/root 5586 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed_processor.py
-rw-r--r-- root/root 2443 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_data_runner.py
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/test_run_data/
-rw-r--r-- root/root 672 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa
-rw-r--r-- root/root 9981 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta
-rw-r--r-- root/root 9200 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta
-rw-r--r-- root/root 3813239 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root 4661713 2020-12-22 08:12 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz
-rw-r--r-- root/root 9217 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/share/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/share/doc/iva/
-rw-r--r-- root/root 1435 2020-12-22 08:12 ./usr/share/doc/iva/changelog.Debian.gz
-rw-r--r-- root/root 1488 2020-12-22 08:12 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/share/man/
drwxr-xr-x root/root 0 2020-12-22 08:12 ./usr/share/man/man1/
-rw-r--r-- root/root 2256 2020-12-22 08:12 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root 1284 2020-12-22 08:12 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root 645 2020-12-22 08:12 ./usr/share/man/man1/iva_qc_make_db.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 37064
Build-Time: 154
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1609
Job: iva_1.0.9+ds-11
Machine Architecture: armhf
Package: iva
Package-Time: 1818
Source-Version: 1.0.9+ds-11
Space: 37064
Status: successful
Version: 1.0.9+ds-11
--------------------------------------------------------------------------------
Finished at 2021-01-24T22:44:31Z
Build needed 00:30:18, 37064k disc space