iva →
1.0.8+ds-1 →
armhf → 2017-01-31 23:44:34
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| iva 1.0.8+ds-1 (armhf) Tue, 31 Jan 2017 23:27:01 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.8+ds-1
Source Version: 1.0.8+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a6fa89d3-2568-416a-8e7e-580c1385ea85' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9728 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 23s (915 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://anonscm.debian.org/git/debian-med/iva.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/iva.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8682 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main iva 1.0.8+ds-1 (dsc) [2219 B]
Get:2 http://172.17.0.1/private stretch-staging/main iva 1.0.8+ds-1 (tar) [8674 kB]
Get:3 http://172.17.0.1/private stretch-staging/main iva 1.0.8+ds-1 (diff) [5876 B]
Fetched 8682 kB in 1s (7752 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-AftXSC/iva-1.0.8+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-AftXSC' 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-joD7K1/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-joD7K1/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-joD7K1/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3516 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
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 83 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13928 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 (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
Filtered Build-Depends: debhelper (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, 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-joD7K1/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-joD7K1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Sources [584 B]
Get:5 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ Packages [662 B]
Fetched 2579 B in 0s (3999 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install iva build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev binutils bioperl bsdmainutils
ca-certificates ca-certificates-java cpp-6 debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism fastaq
file fontconfig-config fonts-dejavu-core g++-6 gawk gcc-6 gcc-6-base gettext
gettext-base groff-base help2man intltool-debian java-common kmc
libarchive-zip-perl libasan3 libatomic1 libavahi-client3
libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl
libblas-common libblas3 libbsd0 libcc1-0 libcroco3 libcups2 libcurl3-gnutls
libdata-stag-perl libexpat1 libffi6 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgcc-6-dev libgcc1 libgfortran3 libglib2.0-0
libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed4 libhts1 libicu57 libidn2-0
libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common
liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnettle6
libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpcsclite1 libpipeline1
libpng16-16 libpsl5 libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libstdc++-6-dev libstdc++6
libtasn1-6 libtool libubsan0 libunistring0 libx11-6 libx11-data libxau6
libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db
mime-support mummer openjdk-8-jdk-headless openjdk-8-jre-headless openssl
po-debconf python3 python3-decorator python3-minimal python3-networkx
python3-nose python3-numpy python3-pkg-resources python3-pysam
python3-setuptools python3.5 python3.5-minimal samtools smalt ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican
| wordlist whois vacation gcc-6-locales dh-make default-jre gcc-6-doc
libstdc++6-6-dbg gawk-doc libgcc1-dbg libgomp1-dbg libitm1-dbg
libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg
libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gettext-doc libasprintf-dev
libgettextpo-dev groff libxml-sax-expatxs-perl cups-common gnutls-bin
krb5-doc krb5-user liblcms2-utils pcscd libstdc++-6-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc less www-browser openjdk-8-demo
openjdk-8-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic
libmail-box-perl python3-doc python3-tk python3-venv python-networkx-doc
python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg
python-setuptools-doc python3.5-venv python3.5-doc binfmt-support
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-cur 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 libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales
publicsuffix libsasl2-modules libssl-doc libltdl-dev xml-core
libmail-sendmail-perl python3-scipy python3-yaml python
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 fastaq
file fontconfig-config fonts-dejavu-core gawk gettext gettext-base
groff-base help2man intltool-debian java-common kmc libarchive-zip-perl
libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0
libbio-perl-perl libblas-common libblas3 libbsd0 libcroco3 libcups2
libcurl3-gnutls libdata-stag-perl libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu57
libidn2-0 libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common
liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnettle6
libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpcsclite1 libpipeline1
libpng16-16 libpsl5 libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libreadline6 librtmp1 libsasl2-2 libsasl2-modules-db
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libtasn1-6 libtool libunistring0
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2
libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-8-jdk-headless
openjdk-8-jre-headless openssl po-debconf python3 python3-decorator
python3-minimal python3-networkx python3-nose python3-numpy
python3-pkg-resources python3-pysam python3-setuptools python3.5
python3.5-minimal samtools sbuild-build-depends-iva-dummy smalt ucf
x11-common
The following packages will be upgraded:
binutils cpp-6 g++-6 gcc-6 gcc-6-base libasan3 libatomic1 libcc1-0
libgcc-6-dev libgcc1 libgomp1 libstdc++-6-dev libstdc++6 libubsan0
14 upgraded, 123 newly installed, 0 to remove and 69 not upgraded.
Need to get 103 MB/104 MB of archives.
After this operation, 299 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-joD7K1/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b1 [18.3 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libgomp1 armhf 6.3.0-5+rpi1 [63.9 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf gcc-6-base armhf 6.3.0-5+rpi1 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libgcc1 armhf 1:6.3.0-5+rpi1 [38.3 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libcc1-0 armhf 6.3.0-5+rpi1 [24.9 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf binutils armhf 2.27.90.20170124-2 [3605 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libatomic1 armhf 6.3.0-5+rpi1 [6838 B]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libasan3 armhf 6.3.0-5+rpi1 [268 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libubsan0 armhf 6.3.0-5+rpi1 [91.6 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf g++-6 armhf 6.3.0-5+rpi1 [5543 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libstdc++-6-dev armhf 6.3.0-5+rpi1 [1442 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libgcc-6-dev armhf 6.3.0-5+rpi1 [512 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf gcc-6 armhf 6.3.0-5+rpi1 [5380 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf cpp-6 armhf 6.3.0-5+rpi1 [5137 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libstdc++6 armhf 6.3.0-5+rpi1 [334 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf gawk armhf 1:4.1.3+dfsg-0.1 [509 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.4-2 [290 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.4-2 [681 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0c-2 [1101 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.1.0c-2 [703 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20161130 [203 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf java-common all 0.58 [13.5 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf default-jre-headless armhf 2:1.8-58+b2 [10.3 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libnspr4 armhf 2:4.12-6 [94.8 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libnss3 armhf 2:3.26.2-1 [944 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf ca-certificates-java all 20161107 [14.5 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libavahi-common-data armhf 0.6.32-1 [118 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libavahi-common3 armhf 0.6.32-1 [48.6 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libavahi-client3 armhf 0.6.32-1 [51.2 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.10-1 [45.3 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.8-1 [823 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libcups2 armhf 2.2.1-6 [272 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.8-4 [118 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-2 [62.2 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.28-1 [263 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.7 [271 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.7 [313 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libpcsclite1 armhf 1.8.20-1 [54.2 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libxi6 armhf 2:1.7.8-2 [77.8 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+18 [251 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf openjdk-8-jre-headless armhf 8u121-b13-2 [25.3 MB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.3~rc1-1 [566 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.3~rc1-1 [1439 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-4 [35.3 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.3~rc1-1 [2091 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.3~rc1-1 [229 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-4 [18.6 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20160818 [83.0 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-4 [21.7 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-2 [66.8 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-2 [98.0 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-3 [84.5 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-3 [194 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libbio-perl-perl all 1.7.1-2 [4605 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf bioperl all 1.7.1-2 [422 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 13 [15.8 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.029-2 [15.3 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.029-2 [9330 B]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.3 [829 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf openjdk-8-jdk-headless armhf 8u121-b13-2 [6213 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf default-jdk-headless armhf 2:1.8-58+b2 [994 B]
Get:108 http://172.17.0.1/private stretch-staging/main armhf python3-pkg-resources all 33.1.1-1 [137 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libidn2-0 armhf 0.16-1 [59.3 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.18.1-1 [68.0 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf libpsl5 armhf 0.16.1-1 [41.2 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.52.1-1 [258 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-2+rpi1 [215 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-3 [220 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf fastaq all 3.14.0-1 [46.6 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf kmc armhf 2.3+dfsg-5 [459 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.7.0-1 [14.0 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.3.0-5+rpi1 [166 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.7.0-1 [107 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.7.0-1 [1503 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf libssl-dev armhf 1.1.0c-2 [1365 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf mummer armhf 3.23+dfsg-2 [765 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf python3-decorator all 4.0.10-1 [13.3 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf python3-networkx all 1.11-2 [624 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf python3-nose all 1.3.7-2 [132 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf python3-numpy armhf 1:1.12.0-2 [1692 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf python3-pysam armhf 0.9.1.4+ds-1+rpi1 [989 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf python3-setuptools all 33.1.1-1 [215 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf smalt armhf 0.7.6-6 [96.6 kB]
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Setting up libgomp1:armhf (6.3.0-5+rpi1) ...
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Setting up libssh2-1:armhf (1.7.0-1) ...
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Processing triggers for systemd (232-6) ...
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Setting up cpp-6 (6.3.0-5+rpi1) ...
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Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12) ...
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 x11-common (1:7.7+18) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
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Setting up ca-certificates (20161130) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
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No schema files found: doing nothing.
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Not building database; man-db/auto-update is not 'true'.
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-3) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libavahi-client3:armhf (0.6.32-1) ...
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Setting up libxi6:armhf (2:1.7.8-2) ...
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Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up libhts1:armhf (1.3.2-2+rpi1) ...
Setting up samtools (1.3.1-3) ...
Setting up openjdk-8-jre-headless:armhf (8u121-b13-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up ca-certificates-java (20161107) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:AC_Raíz_Certicámara_S.A..pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:AddTrust_Qualified_Certificates_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:ApplicationCA_-_Japanese_Government.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_CA_1.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CA_WoSign_ECC_Root.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Certification_Authority_of_WoSign_G2.pem
Adding debian:Certigna.pem
Adding debian:Certinomis_-_Autorité_Racine.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Certplus_Root_CA_G1.pem
Adding debian:Certplus_Root_CA_G2.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:ComSign_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:Comodo_Trusted_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_ACES_CA_X6.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:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.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:Equifax_Secure_CA.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:GeoTrust_Global_CA_2.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: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:IGC_A.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:Juur-SK.pem
Adding debian:Microsec_e-Szigno_Root_CA.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:OpenTrust_Root_CA_G1.pem
Adding debian:OpenTrust_Root_CA_G2.pem
Adding debian:OpenTrust_Root_CA_G3.pem
Adding debian:PSCProcert.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:RSA_Security_2048_v3.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
Adding debian:S-TRUST_Universal_Root_CA.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_EV_RootCA1.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:StartCom_Certification_Authority.pem
Adding debian:StartCom_Certification_Authority_2.pem
Adding debian:StartCom_Certification_Authority_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Platinum_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.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:Trustis_FPS_Root_CA.pem
Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.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_1_Public_Primary_Certification_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
Adding debian:WoSign.pem
Adding debian:WoSign_China.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 dh-autoreconf (13) ...
Setting up python3 (3.5.1-4) ...
Setting up openjdk-8-jdk-headless:armhf (8u121-b13-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
Setting up python3-numpy (1:1.12.0-2) ...
Setting up python3-pkg-resources (33.1.1-1) ...
Setting up fastaq (3.14.0-1) ...
Setting up dh-strip-nondeterminism (0.029-2) ...
Setting up python3-pysam (0.9.1.4+ds-1+rpi1) ...
Setting up python3-nose (1.3.7-2) ...
Setting up python3-setuptools (33.1.1-1) ...
Setting up dh-python (2.20160818) ...
Setting up python3-decorator (4.0.10-1) ...
Setting up default-jre-headless (2:1.8-58+b2) ...
Setting up default-jdk-headless (2:1.8-58+b2) ...
Setting up debhelper (10.2.3) ...
Setting up python3-networkx (1.11-2) ...
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Processing triggers for systemd (232-6) ...
Processing triggers for ca-certificates (20161130) ...
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 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.90.20170124-2 dpkg-dev_1.18.15 g++-6_6.3.0-5+rpi1 gcc-6_6.3.0-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-5+rpi1 libstdc++6_6.3.0-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.90.20170124-2 bioperl_1.7.1-2 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20161130 ca-certificates-java_20161107 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.3.0-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.3 debianutils_4.8.1 default-jdk-headless_2:1.8-58+b2 default-jre-headless_2:1.8-58+b2 dh-autoreconf_13 dh-python_2.20160818 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 fastaq_3.14.0-1 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.3.0-5+rpi1 gawk_1:4.1.3+dfsg-0.1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.3.0-5+rpi1 gcc-6-base_6.3.0-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 java-common_0.58 klibc-utils_2.0.4-9+rpi1 kmc_2.3+dfsg-5 kmod_23-1 libacl1_2.2.52-3 libapparmor1_2.10.95-6 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.3.0-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libavahi-client3_0.6.32-1 libavahi-common-data_0.6.32-1 libavahi-common3_0.6.32-1 libbambamc0_0.0.50-1 libbio-perl-perl_1.7.1-2 libblas-common_3.7.0-1 libblas3_3.7.0-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libcups2_2.2.1-6 libcurl3-gnutls_7.52.1-1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-2 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.029-2 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-5+rpi1 libgcc1_1:6.3.0-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.3.0-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.8-1 libgomp1_6.3.0-5+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15-1 libhogweed4_3.3-1 libhts1_1.3.2-2+rpi1 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.16-1 libio-string-perl_1.08-3 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjpeg62-turbo_1:1.5.1-2 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 liblapack3_3.7.0-1 liblcms2-2_2.8-4 libldap-2.4-2_2.4.44+dfsg-3 libldap-common_2.4.44+dfsg-3 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.18.1-1 libnpth0_1.3-1 libnspr4_2:4.12-6 libnss3_2:3.26.2-1 libp11-kit0_0.23.3-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libpcsclite1_1.8.20-1 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libpng16-16_1.6.28-1 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libpsl5_0.16.1-1 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.3~rc1-1 libpython3.5-stdlib_3.5.3~rc1-1 libreadline6_6.3-9 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl-dev_1.1.0c-2 libssl1.1_1.1.0c-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-5+rpi1 libstdc++6_6.3.0-5+rpi1 libsystemd0_232-6 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.3.0-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libx11-6_2:1.6.4-2 libx11-data_2:1.6.4-2 libxau6_1:1.0.8-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxi6_2:1.7.8-2 libxml2_2.9.4+dfsg1-2.1 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 mummer_3.23+dfsg-2 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 openjdk-8-jdk-headless_8u121-b13-2 openjdk-8-jre-headless_8u121-b13-2 openssl_1.1.0c-2 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 python3_3.5.1-4 python3-decorator_4.0.10-1 python3-minimal_3.5.1-4 python3-networkx_1.11-2 python3-nose_1.3.7-2 python3-numpy_1:1.12.0-2 python3-pkg-resources_33.1.1-1 python3-pysam_0.9.1.4+ds-1+rpi1 python3-setuptools_33.1.1-1 python3.5_3.5.3~rc1-1 python3.5-minimal_3.5.3~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 samtools_1.3.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 smalt_0.7.6-6 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 ucf_3.0036 udev_232-6 util-linux_2.29-1 x11-common_1:7.7+18 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Jan 12 15:16:26 2017 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./iva_1.0.8+ds-1.dsc
dpkg-source: info: extracting iva in /<<BUILDDIR>>/iva-1.0.8+ds
dpkg-source: info: unpacking iva_1.0.8+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.8+ds-1.debian.tar.xz
dpkg-source: info: applying disable-multithreaded-test.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a6fa89d3-2568-416a-8e7e-580c1385ea85
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.8+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build iva-1.0.8+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.8+ds'
rm -rf .pybuild
rm -f iva/gage/*.class
rm -rf /<<BUILDDIR>>/iva-1.0.8+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.8+ds'
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python3 --buildsystem=pybuild
dh_testdir -a -O--buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python3.5 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-1.0.8+ds'
chmod a-x /<<BUILDDIR>>/iva-1.0.8+ds/iva/read_trim/adapters.fasta
chmod a+x /<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /<<BUILDDIR>>/iva-1.0.8+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/*.java
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/GetFastaStats.java]]
[parsing completed 740ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/SizeFasta.java]]
[parsing completed 96ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 60ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/Utils.java]]
[parsing completed 271ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 537ms]
[search path for source files: .]
[search path for class files: /usr/lib/jvm/java-8-openjdk-armhf/jre/lib/resources.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/rt.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/sunrsasign.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/jsse.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/jce.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/charsets.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/jfr.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/classes,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/cldrdata.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/dnsns.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/icedtea-sound.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/jaccess.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/localedata.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/nashorn.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/sunec.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/sunjce_provider.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/sunpkcs11.jar,/usr/lib/jvm/java-8-openjdk-armhf/jre/lib/ext/zipfs.jar,.]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/BufferedReader.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileInputStream.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStreamReader.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/text/DecimalFormat.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/text/NumberFormat.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/ArrayList.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Arrays.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/HashMap.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/String.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Integer.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Exception.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuffer.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/management/ManagementFactory.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/management/MemoryMXBean.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/File.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileReader.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Boolean.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Enum.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Comparable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/Serializable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Collections.class)]]
[checking GetFastaStats]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AutoCloseable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Byte.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Character.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Short.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Long.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Float.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Double.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Void.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Map.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Throwable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CharSequence.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/Reader.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Readable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/Closeable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Number.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Cloneable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractMap.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AbstractStringBuilder.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Appendable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileDescriptor.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/System.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/PrintStream.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/FilterOutputStream.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/OutputStream.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/Flushable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Set.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Iterable.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Collection.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Math.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/List.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/RandomAccess.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractList.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/AbstractCollection.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Comparator.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/text/Format.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Error.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/RuntimeException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/IOException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/NumberFormatException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/IllegalArgumentException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/FileNotFoundException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/util/Iterator.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/GetFastaStats$ContigAt.class]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuilder.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStream.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/GetFastaStats.class]]
[checking SizeFasta]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/SizeFasta.class]]
[checking SplitFastaByLetter]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/SplitFastaByLetter.class]]
[checking Utils]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CloneNotSupportedException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Class.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/net/URI.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Process.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Runtime.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/GenericDeclaration.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/AnnotatedElement.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/Type.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AssertionError.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/Utils$Pair.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/Utils$Translate.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/Utils$ToProtein.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/Utils.class]]
[checking getScaffoldStats]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/getScaffoldStats$Scaffold.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/getScaffoldStats$1.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.8+ds/iva/gage/getScaffoldStats.class]]
[total 39496ms]
dh_auto_build --
I: pybuild base:184: /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-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva
creating /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats$1.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.5
copying and adjusting scripts/iva -> build/scripts-3.5
copying and adjusting scripts/iva_qc -> build/scripts-3.5
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.5
changing mode of build/scripts-3.5/iva from 664 to 775
changing mode of build/scripts-3.5/iva_qc from 664 to 775
changing mode of build/scripts-3.5/iva_qc_make_db from 664 to 775
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.8+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.8+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
running egg_info
creating iva.egg-info
writing top-level names to iva.egg-info/top_level.txt
writing dependency_links to iva.egg-info/dependency_links.txt
writing iva.egg-info/PKG-INFO
writing requirements to iva.egg-info/requires.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
test_add_new_seed_contig (assembly_test.TestAssembly)
Test add_new_seed_contig ... ok
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 ... 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 ... ok
test_get_ref_length_sam_pair (assembly_test.TestAssembly)
Test _get_ref_length_sam_pair ... ok
test_get_unmapped_pairs (assembly_test.TestAssembly)
Test _get_unmapped_pairs ... 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 ... ok
test_merge_overlapping_contigs (assembly_test.TestAssembly)
Test _merge_overlapping_contigs ... ok
test_read_pair_extend (assembly_test.TestAssembly)
Test read_pair_extend ... 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_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_in_path (external_progs_test.TestExternalProgs)
Test kmc in path ... ok
test_nucmer_in_path (external_progs_test.TestExternalProgs)
Test nucmer in path ... ok
test_samtools_in_path (external_progs_test.TestExternalProgs)
Test samtools in path ... 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_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_get_most_common_kmers (kcount_test.TestKcount)
Test get_most_common_kmers ... 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_run_kmc (kcount_test.TestKcount)
Test test_run_kmc ... ok
test_run_kmc_two_threads (kcount_test.TestKcount)
Test test_run_kmc with two threads ... 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 ... 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 ... 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 ... ok
test_get_ref_name (mapping_test.TestMapping)
Test get_ref_name ... ok
test_map_reads (mapping_test.TestMapping)
Test mapping reads ... 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 ... ok
test_remove_indels (mapping_test.TestMapping)
Test _remove_indels ... ok
test_sam_to_fasta (mapping_test.TestMapping)
Test sam_to_fasta ... 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 ... 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 ... 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 155 tests in 31.986s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.8+ds'
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:184: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/iva-1.0.8+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-1.0.8+ds/debian/iva/usr
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats$1.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/gage
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.8+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_run_data
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/__init__.py to __init__.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/assembly.py to assembly.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/common.py to common.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/contig.py to contig.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/contig_trim.py to contig_trim.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/edge.py to edge.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/egg_extract.py to egg_extract.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/external_progs.py to external_progs.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/graph.py to graph.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kcount.py to kcount.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kmers.py to kmers.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/kraken.py to kraken.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/mapping.py to mapping.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/mummer.py to mummer.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/qc.py to qc.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/qc_external.py to qc_external.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/read_trim.py to read_trim.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/seed.py to seed.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/seed_processor.py to seed_processor.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-35.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-1.0.8+ds/debian/iva/usr/lib/python3.5/dist-packages/iva-1.0.8.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin
copying build/scripts-3.5/iva -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin
copying build/scripts-3.5/iva_qc -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin
copying build/scripts-3.5/iva_qc_make_db -> /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin
changing mode of /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin/iva to 775
changing mode of /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin/iva_qc to 775
changing mode of /<<BUILDDIR>>/iva-1.0.8+ds/debian/iva/usr/bin/iva_qc_make_db to 775
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.8+ds'
mkdir -p /<<BUILDDIR>>/iva-1.0.8+ds/debian/man
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.8+ds/debian/man/iva.1 \
-n 'iterative virus assembler' \
--no-discard-stderr ./scripts/iva
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.8+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-1.0.8+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-1.0.8+ds'
dh_python3 -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_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
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package iva: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'iva' in '../iva_1.0.8+ds-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../iva_1.0.8+ds-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build iva-1.0.8+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-01-31T23:44:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
iva_1.0.8+ds-1_armhf.changes:
-----------------------------
Format: 1.8
Date: Thu, 12 Jan 2017 16:10:08 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.8+ds-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
iva - iterative virus sequence assembler
Changes:
iva (1.0.8+ds-1) unstable; urgency=medium
.
* New upstream release.
* Drop patches applied by upstream.
Checksums-Sha1:
3fac79498f0efd3c376f842643a943a79e62712a 6894 iva_1.0.8+ds-1_armhf.buildinfo
4237e32f2967deef4dae8fcbbbe610ff08f47817 8577340 iva_1.0.8+ds-1_armhf.deb
Checksums-Sha256:
72a425cf9a0d67aa8b21d71d51fdbb8fd87b9f966e94db8985516ab9ac3f3132 6894 iva_1.0.8+ds-1_armhf.buildinfo
b9a19a19dc277cc9955290c92ead440cf01b4db204a117967ff81486f7f8ddef 8577340 iva_1.0.8+ds-1_armhf.deb
Files:
1da590e5f821ef10dbe1489c1748e778 6894 science optional iva_1.0.8+ds-1_armhf.buildinfo
dbc7f50924c37309b9fc4cff0ea95779 8577340 science optional iva_1.0.8+ds-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
iva_1.0.8+ds-1_armhf.deb
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new debian package, version 2.0.
size 8577340 bytes: control archive=3099 bytes.
944 bytes, 21 lines control
5575 bytes, 65 lines md5sums
162 bytes, 9 lines * postinst #!/bin/sh
381 bytes, 12 lines * prerm #!/bin/sh
Package: iva
Version: 1.0.8+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8766
Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any (>= 3.3.2-2~), 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 2017-01-12 15:10 ./
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/bin/
-rwxr-xr-x root/root 17240 2017-01-12 15:10 ./usr/bin/iva
-rwxr-xr-x root/root 6228 2017-01-12 15:10 ./usr/bin/iva_qc
-rwxr-xr-x root/root 2406 2017-01-12 15:10 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva-1.0.8.egg-info/
-rw-r--r-- root/root 483 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva-1.0.8.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva-1.0.8.egg-info/dependency_links.txt
-rw-r--r-- root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva-1.0.8.egg-info/requires.txt
-rw-r--r-- root/root 4 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva-1.0.8.egg-info/top_level.txt
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/
-rw-r--r-- root/root 1033 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/__init__.py
-rw-r--r-- root/root 28055 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/assembly.py
-rw-r--r-- root/root 1856 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/common.py
-rw-r--r-- root/root 1960 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/contig.py
-rw-r--r-- root/root 4391 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/contig_trim.py
-rw-r--r-- root/root 4903 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/edge.py
-rw-r--r-- root/root 3077 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/egg_extract.py
-rw-r--r-- root/root 4110 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/external_progs.py
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root 489 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root 10178 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root 14839 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root 3408 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root 3611 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root 2621 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root 2229 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root 621 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root 4564 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root 1225 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root 5575 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/Utils.class
-rw-r--r-- root/root 9230 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/Utils.java
-rwxr-xr-x root/root 80 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl
-rwxr-xr-x root/root 1773 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh
-rwxr-xr-x root/root 1430 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh
-rw-r--r-- root/root 196 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$1.class
-rw-r--r-- root/root 1229 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root 13434 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class
-rw-r--r-- root/root 19111 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java
-rw-r--r-- root/root 7133 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/graph.py
-rw-r--r-- root/root 9487 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/kcount.py
-rw-r--r-- root/root 3466 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/kmers.py
-rw-r--r-- root/root 16961 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/kraken.py
-rw-r--r-- root/root 13238 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/mapping.py
-rw-r--r-- root/root 8365 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/mummer.py
-rw-r--r-- root/root 36646 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/qc.py
-rw-r--r-- root/root 8190 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/qc_external.py
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root 1012 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root 1049 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl
-rwxr-xr-x root/root 41988 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl
-rw-r--r-- root/root 90 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config
-rw-r--r-- root/root 90 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv
-rw-r--r-- root/root 57611 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm
-rwxr-xr-x root/root 13201 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh
-rw-r--r-- root/root 1428 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/read_trim.py
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/read_trim/
-rw-r--r-- root/root 3143 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta
-rw-r--r-- root/root 6056 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/seed.py
-rw-r--r-- root/root 5586 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/seed_processor.py
-rw-r--r-- root/root 2443 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/test_data_runner.py
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/test_run_data/
-rw-r--r-- root/root 672 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa
-rw-r--r-- root/root 9981 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta
-rw-r--r-- root/root 9200 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta
-rw-r--r-- root/root 3813239 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root 4661713 2017-01-12 15:10 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz
-rw-r--r-- root/root 9217 2017-01-12 14:38 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/share/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/share/doc/iva/
-rw-r--r-- root/root 408 2017-01-12 15:10 ./usr/share/doc/iva/changelog.Debian.gz
-rw-r--r-- root/root 1487 2017-01-12 15:08 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/share/man/
drwxr-xr-x root/root 0 2017-01-12 15:10 ./usr/share/man/man1/
-rw-r--r-- root/root 2256 2017-01-12 15:10 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root 1283 2017-01-12 15:10 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root 645 2017-01-12 15:10 ./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: 37080
Build-Time: 168
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 824
Job: iva_1.0.8+ds-1
Machine Architecture: armhf
Package: iva
Package-Time: 1038
Source-Version: 1.0.8+ds-1
Space: 37080
Status: successful
Version: 1.0.8+ds-1
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Finished at 2017-01-31T23:44:19Z
Build needed 00:17:18, 37080k disc space