iva →
1.0.9+ds-10 →
armhf → 2020-02-14 05:14:41
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| iva 1.0.9+ds-10 (armhf) Fri, 14 Feb 2020 05:02:57 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.9+ds-10
Source Version: 1.0.9+ds-10
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-a9ee51cc-9278-41d6-a793-0200f8ba0219' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.2 MB in 10s (2538 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 8683 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-10 (dsc) [1913 B]
Get:2 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-10 (tar) [8675 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main iva 1.0.9+ds-10 (diff) [5556 B]
Fetched 8683 kB in 2s (4614 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-4YvTtl/iva-1.0.9+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-4YvTtl' 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-STTZom/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-STTZom/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-STTZom/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-STTZom/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (10.1 kB/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:
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 7 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-STTZom/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12214 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 (= 12), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, 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 (= 12), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, 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-STTZom/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-STTZom/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Sources [604 B]
Get:5 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ Packages [683 B]
Fetched 2620 B in 0s (12.4 kB/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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdmainutils
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
libcroco3 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 libgssapi-krb5-2
libhts3 libicu63 libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnspr4 libnss3
libpcsclite1 libpipeline1 libpng16-16 libpsl5 libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal
libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsub-override-perl libsub-uplevel-perl libtest-deep-perl
libtest-differences-perl libtest-exception-perl libtest-most-perl
libtest-warn-perl libtext-diff-perl libtinfo5 libtool libuchardet0 libx11-6
libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1
libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless
openjdk-11-jre-headless openssl po-debconf python3 python3-attr
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-six python3.7 python3.7-minimal python3.8 python3.8-minimal samtools
sensible-utils smalt ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make default-jre gawk-doc gettext-doc libasprintf-dev
libgettextpo-dev groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl
cups-common krb5-doc krb5-user liblcms2-utils pcscd libssl-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-attr-doc python-networkx-doc python-nose-doc gfortran
python-numpy-doc python3-dev python3-pytest python3-numpy-dbg
python-pyparsing-doc python-setuptools-doc python3.7-venv python3.7-doc
binfmt-support python3.8-venv python3.8-doc
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 krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl python3-gdal python3-matplotlib python3-pydot
python3-pygraphviz python3-scipy python3-yaml cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdmainutils
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
libcroco3 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 libgssapi-krb5-2
libhts3 libicu63 libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnspr4 libnss3
libpcsclite1 libpipeline1 libpng16-16 libpsl5 libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal
libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsub-override-perl libsub-uplevel-perl libtest-deep-perl
libtest-differences-perl libtest-exception-perl libtest-most-perl
libtest-warn-perl libtext-diff-perl libtinfo5 libtool libuchardet0 libx11-6
libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1
libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless
openjdk-11-jre-headless openssl po-debconf python3 python3-attr
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-six python3.7 python3.7-minimal python3.8 python3.8-minimal samtools
sbuild-build-depends-iva-dummy sensible-utils smalt ucf x11-common
0 upgraded, 144 newly installed, 0 to remove and 7 not upgraded.
Need to get 273 MB of archives.
After this operation, 556 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-STTZom/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [972 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gawk armhf 1:5.0.1+dfsg-1 [540 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1+b1 [585 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1+b1 [1525 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1+b1 [1669 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1+b1 [351 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.1-2+b1 [743 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.1-2+b1 [1621 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbio-perl-perl all 1.7.7-1 [2603 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libexception-class-perl all 1.44-1 [32.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libtest-deep-perl all 1.128-1 [48.8 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libalgorithm-diff-perl all 1.19.03-2 [47.9 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libtest-differences-perl all 0.67-1 [18.7 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libsub-uplevel-perl all 0.2800-1 [16.3 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libtest-exception-perl all 0.43-1 [18.7 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libtest-warn-perl all 0.36-1 [16.2 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libtest-most-perl all 0.35-1 [24.5 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf bioperl all 1.7.7-1 [246 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf java-common all 0.72 [14.5 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common-data armhf 0.7-5 [122 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libavahi-common3 armhf 0.7-5 [51.2 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libdbus-1-3 armhf 1.12.16-2+b1 [189 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libavahi-client3 armhf 0.7-5 [54.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcups2 armhf 2.3.1-4 [309 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf liblcms2-2 armhf 2.9-3 [116 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libnspr4 armhf 2:4.24-1 [90.2 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libnss3 armhf 2:3.49.1-1 [979 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libasound2-data all 1.2.1.2-2 [38.2 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libasound2 armhf 1.2.1.2-2 [295 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libpcsclite1 armhf 1.8.26-3 [56.4 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libxi6 armhf 2:1.7.9-1 [77.8 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jre-headless armhf 11.0.6+10-1 [33.1 MB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates-java all 20190909 [15.7 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1+rpi1 [1137 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf openjdk-11-jdk-headless armhf 11.0.6+10-1 [184 MB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf default-jdk-headless armhf 2:1.11-72+b4 [1100 B]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 44.0.0-1 [155 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-1 [78.0 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-2 [327 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.10-3 [477 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf fastaq all 3.17.0-2 [47.8 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.12 [180 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf kmc armhf 2.3+dfsg-7 [422 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libbambamc0 armhf 0.0.50-3 [30.4 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-25+rpi1 [231 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.1-2+b1 [1598 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1d-2 [1570 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf mummer armhf 3.23+dfsg-4+b1 [767 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 19.3.0-1 [43.1 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf python3-decorator all 4.3.0-1.1 [14.5 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf python3-networkx all 2.4-3 [873 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf python3-nose all 1.3.7-4 [132 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.1-2+b1 [406 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.17.4-5+b1 [4484 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.6-1 [109 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.14.0-2 [16.7 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 19.1-2 [23.9 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf python3-pysam armhf 0.15.4+ds-1 [2363 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 44.0.0-1 [313 kB]
Get:144 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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Unpacking libnspr4:armhf (2:4.24-1) ...
Selecting previously unselected package libnss3:armhf.
Preparing to unpack .../051-libnss3_2%3a3.49.1-1_armhf.deb ...
Unpacking libnss3:armhf (2:3.49.1-1) ...
Selecting previously unselected package libasound2-data.
Preparing to unpack .../052-libasound2-data_1.2.1.2-2_all.deb ...
Unpacking libasound2-data (1.2.1.2-2) ...
Selecting previously unselected package libasound2:armhf.
Preparing to unpack .../053-libasound2_1.2.1.2-2_armhf.deb ...
Unpacking libasound2:armhf (1.2.1.2-2) ...
Selecting previously unselected package libpcsclite1:armhf.
Preparing to unpack .../054-libpcsclite1_1.8.26-3_armhf.deb ...
Unpacking libpcsclite1:armhf (1.8.26-3) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../055-libxau6_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../056-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../057-libxcb1_1.13.1-2_armhf.deb ...
Unpacking libxcb1:armhf (1.13.1-2) ...
Selecting previously unselected package libx11-data.
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Unpacking libx11-data (2:1.6.8-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../059-libx11-6_2%3a1.6.8-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.8-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../060-libxext6_2%3a1.3.3-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../061-libxi6_2%3a1.7.9-1_armhf.deb ...
Unpacking libxi6:armhf (2:1.7.9-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../062-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../063-x11-common_1%3a7.7+20_all.deb ...
Unpacking x11-common (1:7.7+20) ...
Selecting previously unselected package libxtst6:armhf.
Preparing to unpack .../064-libxtst6_2%3a1.2.3-1_armhf.deb ...
Unpacking libxtst6:armhf (2:1.2.3-1) ...
Selecting previously unselected package openjdk-11-jre-headless:armhf.
Preparing to unpack .../065-openjdk-11-jre-headless_11.0.6+10-1_armhf.deb ...
Unpacking openjdk-11-jre-headless:armhf (11.0.6+10-1) ...
Selecting previously unselected package default-jre-headless.
Preparing to unpack .../066-default-jre-headless_2%3a1.11-72+b4_armhf.deb ...
Unpacking default-jre-headless (2:1.11-72+b4) ...
Selecting previously unselected package ca-certificates-java.
Preparing to unpack .../067-ca-certificates-java_20190909_all.deb ...
Unpacking ca-certificates-java (20190909) ...
Selecting previously unselected package libtool.
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Unpacking libtool (2.4.6-11) ...
Selecting previously unselected package dh-autoreconf.
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Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../070-libdebhelper-perl_12.9_all.deb ...
Unpacking libdebhelper-perl (12.9) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../071-libarchive-zip-perl_1.67-1_all.deb ...
Unpacking libarchive-zip-perl (1.67-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../072-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../073-libfile-stripnondeterminism-perl_1.6.3-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.6.3-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
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Unpacking dh-strip-nondeterminism (1.6.3-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../075-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../076-dwz_0.13-5_armhf.deb ...
Unpacking dwz (0.13-5) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../077-libglib2.0-0_2.62.4-1+rpi1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.62.4-1+rpi1) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../078-libicu63_63.2-2_armhf.deb ...
Unpacking libicu63:armhf (63.2-2) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../079-libxml2_2.9.4+dfsg1-8_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-8) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../080-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../081-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
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Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../083-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
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Unpacking debhelper (12.9) ...
Selecting previously unselected package openjdk-11-jdk-headless:armhf.
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Unpacking openjdk-11-jdk-headless:armhf (11.0.6+10-1) ...
Selecting previously unselected package default-jdk-headless.
Preparing to unpack .../086-default-jdk-headless_2%3a1.11-72+b4_armhf.deb ...
Unpacking default-jdk-headless (2:1.11-72+b4) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../087-python3-lib2to3_3.8.0-1_all.deb ...
Unpacking python3-lib2to3 (3.8.0-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../088-python3-distutils_3.8.0-1_all.deb ...
Unpacking python3-distutils (3.8.0-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../089-dh-python_4.20191017_all.deb ...
Unpacking dh-python (4.20191017) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../090-python3-pkg-resources_44.0.0-1_all.deb ...
Unpacking python3-pkg-resources (44.0.0-1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../091-libbrotli1_1.0.7-6_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.7-6) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../092-libnghttp2-14_1.40.0-1+b2_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.40.0-1+b2) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../093-libpsl5_0.20.2-2_armhf.deb ...
Unpacking libpsl5:armhf (0.20.2-2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../094-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../095-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../096-libcurl3-gnutls_7.67.0-2_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.67.0-2) ...
Selecting previously unselected package libdeflate0.
Preparing to unpack .../097-libdeflate0_1.5-1_armhf.deb ...
Unpacking libdeflate0 (1.5-1) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../098-libhts3_1.10.2-2_armhf.deb ...
Unpacking libhts3:armhf (1.10.2-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../099-libncurses6_6.1+20191019-1_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20191019-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../100-samtools_1.10-3_armhf.deb ...
Unpacking samtools (1.10-3) ...
Selecting previously unselected package fastaq.
Preparing to unpack .../101-fastaq_3.17.0-2_all.deb ...
Unpacking fastaq (3.17.0-2) ...
Selecting previously unselected package help2man.
Preparing to unpack .../102-help2man_1.47.12_armhf.deb ...
Unpacking help2man (1.47.12) ...
Selecting previously unselected package kmc.
Preparing to unpack .../103-kmc_2.3+dfsg-7_armhf.deb ...
Unpacking kmc (2.3+dfsg-7) ...
Selecting previously unselected package libbambamc0.
Preparing to unpack .../104-libbambamc0_0.0.50-3_armhf.deb ...
Unpacking libbambamc0 (0.0.50-3) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../105-libblas3_3.9.0-1_armhf.deb ...
Unpacking libblas3:armhf (3.9.0-1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../106-libgfortran5_9.2.1-25+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (9.2.1-25+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../107-liblapack3_3.9.0-1_armhf.deb ...
Unpacking liblapack3:armhf (3.9.0-1) ...
Selecting previously unselected package libpython3.8-stdlib:armhf.
Preparing to unpack .../108-libpython3.8-stdlib_3.8.1-2+b1_armhf.deb ...
Unpacking libpython3.8-stdlib:armhf (3.8.1-2+b1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../109-libssl-dev_1.1.1d-2_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1d-2) ...
Selecting previously unselected package mummer.
Preparing to unpack .../110-mummer_3.23+dfsg-4+b1_armhf.deb ...
Unpacking mummer (3.23+dfsg-4+b1) ...
Selecting previously unselected package python3-attr.
Preparing to unpack .../111-python3-attr_19.3.0-1_all.deb ...
Unpacking python3-attr (19.3.0-1) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../112-python3-decorator_4.3.0-1.1_all.deb ...
Unpacking python3-decorator (4.3.0-1.1) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../113-python3-networkx_2.4-3_all.deb ...
Unpacking python3-networkx (2.4-3) ...
Selecting previously unselected package python3-nose.
Preparing to unpack .../114-python3-nose_1.3.7-4_all.deb ...
Unpacking python3-nose (1.3.7-4) ...
Selecting previously unselected package python3.8.
Preparing to unpack .../115-python3.8_3.8.1-2+b1_armhf.deb ...
Unpacking python3.8 (3.8.1-2+b1) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../116-python3-numpy_1%3a1.17.4-5+b1_armhf.deb ...
Unpacking python3-numpy (1:1.17.4-5+b1) ...
Selecting previously unselected package python3-pyparsing.
Preparing to unpack .../117-python3-pyparsing_2.4.6-1_all.deb ...
Unpacking python3-pyparsing (2.4.6-1) ...
Selecting previously unselected package python3-six.
Preparing to unpack .../118-python3-six_1.14.0-2_all.deb ...
Unpacking python3-six (1.14.0-2) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../119-python3-packaging_19.1-2_all.deb ...
Unpacking python3-packaging (19.1-2) ...
Selecting previously unselected package python3-pysam.
Preparing to unpack .../120-python3-pysam_0.15.4+ds-1_armhf.deb ...
Unpacking python3-pysam (0.15.4+ds-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../121-python3-setuptools_44.0.0-1_all.deb ...
Unpacking python3-setuptools (44.0.0-1) ...
Selecting previously unselected package smalt.
Preparing to unpack .../122-smalt_0.7.6-9_armhf.deb ...
Unpacking smalt (0.7.6-9) ...
Selecting previously unselected package sbuild-build-depends-iva-dummy.
Preparing to unpack .../123-sbuild-build-depends-iva-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-iva-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up liblcms2-2:armhf (2.9-3) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libpython3.8-minimal:armhf (3.8.1-2+b1) ...
Setting up mime-support (3.64) ...
Setting up java-common (0.72) ...
Setting up libtest-deep-perl (1.128-1) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up gawk (1:5.0.1+dfsg-1) ...
Setting up libalgorithm-diff-perl (1.19.03-2) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-1+rpi1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.9) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up x11-common (1:7.7+20) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up libdeflate0 (1.5-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up m4 (1.4.18-4) ...
Setting up file (1:5.38-4) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up libasound2-data (1.2.1.2-2) ...
Setting up libio-string-perl (1.08-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-1) ...
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
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libnspr4:armhf (2:4.24-1) ...
Setting up libtext-diff-perl (1.45-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libavahi-common-data:armhf (0.7-5) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libdbus-1-3:armhf (1.12.16-2+b1) ...
Setting up libbambamc0 (0.0.50-3) ...
Setting up libssl-dev:armhf (1.1.1d-2) ...
Setting up libpng16-16:armhf (1.6.37-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpcsclite1:armhf (1.8.26-3) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libgfortran5:armhf (9.2.1-25+rpi1) ...
Setting up autoconf (2.69-11.1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libdata-stag-perl (0.14-2) ...
Setting up python3.8-minimal (3.8.1-2+b1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libasound2:armhf (1.2.1.2-2) ...
Setting up mummer (3.23+dfsg-4+b1) ...
Setting up libsub-uplevel-perl (0.2800-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libdevel-stacktrace-perl (2.0400-1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbio-perl-perl (1.7.7-1) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libpython3.8-stdlib:armhf (3.8.1-2+b1) ...
Setting up python3.8 (3.8.1-2+b1) ...
Setting up openssl (1.1.1d-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up kmc (2.3+dfsg-7) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up smalt (0.7.6-9) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1+b1) ...
Setting up liblapack3:armhf (3.9.0-1) ...
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 (1.13.1-2) ...
Setting up libtool (2.4.6-11) ...
Setting up libtest-warn-perl (0.36-1) ...
Setting up libavahi-common3:armhf (0.7-5) ...
Setting up libtest-differences-perl (0.67-1) ...
Setting up libnss3:armhf (2:3.49.1-1) ...
Setting up libexception-class-perl (1.44-1) ...
Setting up help2man (1.47.12) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libtest-exception-perl (0.43-1) ...
Setting up libfreetype6:armhf (2.10.1-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libavahi-client3:armhf (0.7-5) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up python3.7 (3.7.6-1+b1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libtest-most-perl (0.35-1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libcurl3-gnutls:armhf (7.67.0-2) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-six (1.14.0-2) ...
Setting up python3-decorator (4.3.0-1.1) ...
Setting up python3-pyparsing (2.4.6-1) ...
Setting up libcups2:armhf (2.3.1-4) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python3-pkg-resources (44.0.0-1) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up dh-python (4.20191017) ...
Setting up bioperl (1.7.7-1) ...
Setting up python3-attr (19.3.0-1) ...
Setting up libhts3:armhf (1.10.2-2) ...
Setting up python3-pysam (0.15.4+ds-1) ...
Setting up python3-setuptools (44.0.0-1) ...
Setting up libxi6:armhf (2:1.7.9-1) ...
Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3-networkx (2.4-3) ...
/usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="?
assert H.nodes['n1']['special'] is 0
/usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="?
assert H.edges['n0','n1',1]['special'] is 0
Setting up python3-nose (1.3.7-4) ...
Setting up samtools (1.10-3) ...
Setting up python3-packaging (19.1-2) ...
Setting up python3-numpy (1:1.17.4-5+b1) ...
Setting up fastaq (3.17.0-2) ...
Setting up dh-autoreconf (19) ...
Setting up default-jre-headless (2:1.11-72+b4) ...
Setting up openjdk-11-jre-headless:armhf (11.0.6+10-1) ...
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/java to provide /usr/bin/java (java) 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/jjs to provide /usr/bin/jjs (jjs) 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/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/bin/jfr to provide /usr/bin/jfr (jfr) 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 (12.9) ...
Setting up openjdk-11-jdk-headless:armhf (11.0.6+10-1) ...
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:AddTrust_External_Root.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:Certinomis_-_Root_CA.pem
Adding debian:Certplus_Class_2_Primary_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:Deutsche_Telekom_Root_CA_2.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:EE_Certification_Centre_Root_CA.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:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:GeoTrust_Universal_CA_2.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: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:LuxTrust_Global_Root_2.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GA_CA.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_-_G2.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:Taiwan_GRCA.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:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
done.
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
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 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+rpi1 bioperl_1.7.7-1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 ca-certificates-java_20190909 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 default-jdk-headless_2:1.11-72+b4 default-jre-headless_2:1.11-72+b4 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fastaq_3.17.0-2 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gawk_1:5.0.1+dfsg-1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3 help2man_1.47.12 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 java-common_0.72 kmc_2.3+dfsg-7 libacl1_2.2.53-5 libalgorithm-diff-perl_1.19.03-2 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-25+rpi1 libasound2_1.2.1.2-2 libasound2-data_1.2.1.2-2 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libavahi-client3_0.7-5 libavahi-common-data_0.7-5 libavahi-common3_0.7-5 libbambamc0_0.0.50-3 libbinutils_2.33.90.20200122-2+rpi1 libbio-perl-perl_1.7.7-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcapture-tiny-perl_0.48-1 libcc1-0_9.2.1-25+rpi1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libcups2_2.3.1-4 libcurl3-gnutls_7.67.0-2 libdata-stag-perl_0.14-2 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.16-2+b1 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdeflate0_1.5-1 libdevel-stacktrace-perl_2.0400-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexception-class-perl_1.44-1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-25+rpi1 libglib2.0-0_2.62.4-1+rpi1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl22_0.22-2 libjpeg62-turbo_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack3_3.9.0-1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libnspr4_2:4.24-1 libnss3_2:3.49.1-1 libp11-kit0_0.23.18.1-2+b1 libpam-cap_1:2.27-1 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_10.34-7 libpcre3_2:8.39-12 libpcsclite1_1.8.26-3 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpng16-16_1.6.37-2 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libpython3.8-minimal_3.8.1-2+b1 libpython3.8-stdlib_3.8.1-2+b1 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsub-uplevel-perl_0.2800-1 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libtest-deep-perl_1.128-1 libtest-differences-perl_0.67-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-diff-perl_1.45-1 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-8 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mime-support_3.64 mount_2.34-0.1 mummer_3.23+dfsg-4+b1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 openjdk-11-jdk-headless_11.0.6+10-1 openjdk-11-jre-headless_11.0.6+10-1 openssl_1.1.1d-2 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.7.5-3 python3-attr_19.3.0-1 python3-decorator_4.3.0-1.1 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3-networkx_2.4-3 python3-nose_1.3.7-4 python3-numpy_1:1.17.4-5+b1 python3-packaging_19.1-2 python3-pkg-resources_44.0.0-1 python3-pyparsing_2.4.6-1 python3-pysam_0.15.4+ds-1 python3-setuptools_44.0.0-1 python3-six_1.14.0-2 python3.7_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 python3.8_3.8.1-2+b1 python3.8-minimal_3.8.1-2+b1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.10-3 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_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 x11-common_1:7.7+20 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Feb 9 08:55:46 2020 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-10.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-10.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 disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-a9ee51cc-9278-41d6-a793-0200f8ba0219
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.9+ds-10
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 build-arch
dh build-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:217: python3.7 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 135ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.java]]
[parsing completed 10ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 7ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.java]]
[parsing completed 38ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 98ms]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/jdk.scripting.nashorn/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/java.base/module-info.class]
[loading /modules/jdk.pack/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.rmic/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/java.management/module-info.class]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/jdk.scripting.nashorn.shell/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/java.desktop/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/java.compiler/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 3389ms]
dh_auto_build --
I: pybuild base:217: /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_3.7_iva/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.7
copying and adjusting scripts/iva -> build/scripts-3.7
copying and adjusting scripts/iva_qc -> build/scripts-3.7
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.7
changing mode of build/scripts-3.7/iva from 644 to 755
changing mode of build/scripts-3.7/iva_qc from 644 to 755
changing mode of build/scripts-3.7/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.o1rs__86/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.7_4dglci/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 16.247s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:217: /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/python3.7
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/__init__.py to __init__.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/assembly.py to assembly.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/common.py to common.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/contig.py to contig.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/contig_trim.py to contig_trim.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/edge.py to edge.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/egg_extract.py to egg_extract.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/external_progs.py to external_progs.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/graph.py to graph.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kcount.py to kcount.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kmers.py to kmers.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kraken.py to kraken.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/mummer.py to mummer.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/qc.py to qc.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/qc_external.py to qc_external.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim.py to read_trim.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/seed.py to seed.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/seed_processor.py to seed_processor.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/mapping.py to mapping.cpython-37.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/python3.7/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-3.7/iva -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.7/iva_qc -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.7/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_installinit -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 -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -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-10_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../iva_1.0.9+ds-10_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 2020-02-14T05:14:37Z
Finished
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I: Built successfully
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| Changes |
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iva_1.0.9+ds-10_armhf.changes:
------------------------------
Format: 1.8
Date: Sun, 09 Feb 2020 09:51:06 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.9+ds-10
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
iva - iterative virus sequence assembler
Changes:
iva (1.0.9+ds-10) unstable; urgency=medium
.
* Disable tests that run KMC to circumvent failing builds on low-RAM
machines.
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Checksums-Sha256:
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Files:
2c63707181c549ac4edfccafec1a726b 8096 science optional iva_1.0.9+ds-10_armhf.buildinfo
9fba9f501fe86468324db5594147a106 8578428 science optional iva_1.0.9+ds-10_armhf.deb
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iva_1.0.9+ds-10_armhf.deb
-------------------------
new Debian package, version 2.0.
size 8578428 bytes: control archive=3012 bytes.
941 bytes, 21 lines control
5477 bytes, 64 lines md5sums
232 bytes, 12 lines * postinst #!/bin/sh
381 bytes, 12 lines * prerm #!/bin/sh
Package: iva
Version: 1.0.9+ds-10
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 2020-02-09 08:51 ./
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/bin/
-rwxr-xr-x root/root 17240 2020-02-09 08:51 ./usr/bin/iva
-rwxr-xr-x root/root 6228 2020-02-09 08:51 ./usr/bin/iva_qc
-rwxr-xr-x root/root 2406 2020-02-09 08:51 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root 483 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root 4 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root 0 2020-02-09 08:51 ./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 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root 508 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root 10192 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root 14839 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root 3689 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root 3611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root 2898 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root 2229 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root 640 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root 4583 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root 1244 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root 5920 2020-02-09 08:51 ./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 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root 13703 2020-02-09 08:51 ./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 2020-02-09 08:51 ./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 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root 1008 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root 1045 2020-02-09 08:51 ./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 2020-02-09 08:51 ./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 2020-02-09 08:51 ./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 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root 4661713 2020-02-09 08:51 ./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 2020-02-09 08:51 ./usr/share/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/doc/iva/
-rw-r--r-- root/root 1229 2020-02-09 08:51 ./usr/share/doc/iva/changelog.Debian.gz
-rw-r--r-- root/root 1488 2020-01-03 11:30 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/man/man1/
-rw-r--r-- root/root 2258 2020-02-09 08:51 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root 1284 2020-02-09 08:51 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root 646 2020-02-09 08:51 ./usr/share/man/man1/iva_qc_make_db.1.gz
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 37060
Build-Time: 51
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 630
Job: iva_1.0.9+ds-10
Machine Architecture: armhf
Package: iva
Package-Time: 700
Source-Version: 1.0.9+ds-10
Space: 37060
Status: successful
Version: 1.0.9+ds-10
--------------------------------------------------------------------------------
Finished at 2020-02-14T05:14:37Z
Build needed 00:11:40, 37060k disk space