Build log for iva (1.0.9+ds-2) on armhf

iva → 1.0.9+ds-2 → armhf → 2018-02-15 04:55:13

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| iva 1.0.9+ds-2 (armhf)                       Thu, 15 Feb 2018 04:45:24 +0000 |
+==============================================================================+

Package: iva
Version: 1.0.9+ds-2
Source Version: 1.0.9+ds-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-c120f40f-6b27-4772-a20d-074b5b5f71f4' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.6 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.3 MB]
Fetched 22.9 MB in 9s (2510 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 8681 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main iva 1.0.9+ds-2 (dsc) [2220 B]
Get:2 http://172.17.0.1/private buster-staging/main iva 1.0.9+ds-2 (tar) [8675 kB]
Get:3 http://172.17.0.1/private buster-staging/main iva 1.0.9+ds-2 (diff) [3888 B]
Fetched 8681 kB in 1s (6675 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-QHyh4m/iva-1.0.9+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-QHyh4m' 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-cptv5T/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-cptv5T/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-cptv5T/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Packages [435 B]
Fetched 2111 B in 1s (3624 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:
  ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 25 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (33.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15333 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 (>= 10), 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 (>= 10), 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-cptv5T/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-cptv5T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Sources [581 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ Packages [669 B]
Fetched 2583 B in 1s (4989 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:
  e2fsprogs-l10n libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bioperl bsdmainutils
  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 libalgorithm-diff-perl
  libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3
  libbambamc0 libbio-perl-perl libblas3 libbsd0 libcapture-tiny-perl
  libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls
  libdata-stag-perl libdevel-stacktrace-perl libexception-class-perl libexpat1
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran4
  libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libio-string-perl
  libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblapack3 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1
  libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5
  libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librtmp1
  libsigsegv2 libssh2-1 libssl-dev libsub-uplevel-perl libtest-deep-perl
  libtest-differences-perl libtest-exception-perl libtest-most-perl
  libtest-warn-perl libtext-diff-perl libtimedate-perl libtool 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 po-debconf python3 python3-decorator
  python3-distutils python3-lib2to3 python3-minimal python3-networkx
  python3-nose python3-numpy python3-pkg-resources python3-pysam
  python3-setuptools python3.6 python3.6-minimal samtools smalt ucf x11-common
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make dwz default-jre gawk-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff libxml-sax-expatxs-perl cups-common krb5-doc
  krb5-user liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler
  gcj-jdk m4-doc less www-browser apparmor openjdk-8-demo openjdk-8-source
  libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
  fonts-wqy-microhei fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc
  python3-tk python3-venv python-networkx-doc python-nose-doc gfortran
  python-numpy-doc python3-dev python3-numpy-dbg python-setuptools-doc
  python3.6-venv python3.6-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 libalgorithm-diff-xs-perl 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 libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales publicsuffix libssl-doc libltdl-dev
  libmail-sendmail-perl python3-scipy python3-yaml python cwltool
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bioperl bsdmainutils
  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 libalgorithm-diff-perl
  libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3
  libbambamc0 libbio-perl-perl libblas3 libbsd0 libcapture-tiny-perl
  libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls
  libdata-stag-perl libdevel-stacktrace-perl libexception-class-perl libexpat1
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran4
  libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libio-string-perl
  libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblapack3 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1
  libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5
  libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librtmp1
  libsigsegv2 libssh2-1 libssl-dev libsub-uplevel-perl libtest-deep-perl
  libtest-differences-perl libtest-exception-perl libtest-most-perl
  libtest-warn-perl libtext-diff-perl libtimedate-perl libtool 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 po-debconf python3 python3-decorator
  python3-distutils python3-lib2to3 python3-minimal python3-networkx
  python3-nose python3-numpy python3-pkg-resources python3-pysam
  python3-setuptools python3.6 python3.6-minimal samtools
  sbuild-build-depends-iva-dummy smalt ucf x11-common
0 upgraded, 120 newly installed, 0 to remove and 25 not upgraded.
Need to get 72.8 MB/76.9 MB of archives.
After this operation, 292 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cptv5T/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [956 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-4 [1012 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf gawk armhf 1:4.1.4+dfsg-1+b1 [506 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf java-common all 0.59 [13.6 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf default-jre-headless armhf 2:1.8-59+b6 [10.4 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.18-1 [94.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.35-2 [930 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf ca-certificates-java all 20170930 [14.9 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libavahi-common-data armhf 0.7-3 [122 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libavahi-common3 armhf 0.7-3 [50.6 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libavahi-client3 armhf 0.7-3 [53.4 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libcups2 armhf 2.2.6-4 [282 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.9-1 [117 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-1 [402 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.12.6-0.1 [304 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.12.6-0.1 [351 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libpcsclite1 armhf 1.8.23-1 [55.0 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.4-3 [290 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.4-3 [683 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libxi6 armhf 2:1.7.9-1 [77.8 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf openjdk-8-jre-headless armhf 8u141-b15-3 [25.4 MB]
Get:43 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.4-2 [78.4 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.4-2 [147 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.4-3 [223 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.4-1 [19.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.4-1 [22.3 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20171216.1 [75.9 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libbio-perl-perl all 1.7.2-2 [4560 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libclass-data-inheritable-perl all 0.08-2 [9296 B]
Get:58 http://172.17.0.1/private buster-staging/main armhf libdevel-stacktrace-perl all 2.0300-1 [28.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libexception-class-perl all 1.44-1 [32.3 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libtest-deep-perl all 1.127-1 [48.5 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libcapture-tiny-perl all 0.46-1 [25.7 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libalgorithm-diff-perl all 1.19.03-1 [48.7 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libtest-differences-perl all 0.64-1 [18.0 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libsub-uplevel-perl all 0.2800-1 [16.3 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libtest-exception-perl all 0.43-1 [18.7 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libtest-warn-perl all 0.32-1 [15.1 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libtest-most-perl all 0.35-1 [24.5 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf bioperl all 1.7.2-2 [418 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.3-2 [2651 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.4 [1005 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf openjdk-8-jdk-headless armhf 8u141-b15-3 [6220 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf default-jdk-headless armhf 2:1.8-59+b6 [1080 B]
Get:86 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 38.4.0-1 [142 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.29.0-1 [70.5 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.19.1-4 [43.2 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.58.0-2 [275 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.6-4 [249 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.6-4 [231 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf fastaq all 3.16.0-1 [47.3 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.5 [162 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf kmc armhf 2.3+dfsg-5 [459 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-19+b1 [191 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-4 [103 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-4 [1508 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0g-2 [1371 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf mummer armhf 3.23+dfsg-2+b1 [766 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf python3-decorator all 4.1.2-1 [13.7 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf python3-networkx all 1.11-2 [624 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf python3-nose all 1.3.7-3 [132 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf python3-numpy armhf 1:1.13.3-2 [1732 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf python3-pysam armhf 0.12.0.1+ds-4+rpi1 [1323 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 38.4.0-1 [229 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf smalt armhf 0.7.6-6 [96.6 kB]
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Preparing to unpack .../46-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../47-libcurl3-gnutls_7.58.0-2_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.58.0-2) ...
Selecting previously unselected package libhts2:armhf.
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Unpacking libhts2:armhf (1.6-4) ...
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Unpacking samtools (1.6-4) ...
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Unpacking fastaq (3.16.0-1) ...
Selecting previously unselected package help2man.
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Unpacking help2man (1.47.5) ...
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Unpacking kmc (2.3+dfsg-5) ...
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Unpacking libbambamc0 (0.0.50-1) ...
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Unpacking libgfortran4:armhf (7.2.0-19+b1) ...
Selecting previously unselected package libblas3:armhf.
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Unpacking libblas3:armhf (3.7.1-4) ...
Selecting previously unselected package liblapack3:armhf.
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Unpacking liblapack3:armhf (3.7.1-4) ...
Selecting previously unselected package libssl-dev:armhf.
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Unpacking libssl-dev:armhf (1.1.0g-2) ...
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Unpacking mummer (3.23+dfsg-2+b1) ...
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Unpacking python3-decorator (4.1.2-1) ...
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Unpacking python3-networkx (1.11-2) ...
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Unpacking python3-nose (1.3.7-3) ...
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Unpacking python3-numpy (1:1.13.3-2) ...
Selecting previously unselected package python3-pysam.
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Unpacking python3-pysam (0.12.0.1+ds-4+rpi1) ...
Selecting previously unselected package python3-setuptools.
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Unpacking python3-setuptools (38.4.0-1) ...
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Unpacking smalt (0.7.6-6) ...
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Unpacking sbuild-build-depends-iva-dummy (0.invalid.0) ...
Setting up libtest-deep-perl (1.127-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libclass-data-inheritable-perl (0.08-2) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.29.0-1) ...
Setting up mime-support (3.60) ...
Setting up libgfortran4:armhf (7.2.0-19+b1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up liblcms2-2:armhf (2.9-1) ...
Setting up libpcsclite1:armhf (1.8.23-1) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpsl5:armhf (0.19.1-4) ...
Setting up libdevel-stacktrace-perl (2.0300-1) ...
Setting up libssl-dev:armhf (1.1.0g-2) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.3-2) ...
No schema files found: doing nothing.
Setting up libcapture-tiny-perl (0.46-1) ...
Setting up java-common (0.59) ...
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up kmc (2.3+dfsg-5) ...
Setting up m4 (1.4.18-1) ...
Setting up gawk (1:4.1.4+dfsg-1+b1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libnspr4:armhf (2:4.18-1) ...
Setting up ucf (3.0036) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libfreetype6:armhf (2.8.1-1) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libblas3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
Setting up autotools-dev (20171216.1) ...
Processing triggers for systemd (236-2) ...
Setting up libio-string-perl (1.08-3) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
Setting up libbambamc0 (0.0.50-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libsub-uplevel-perl (0.2800-1) ...
Setting up x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Processing triggers for ca-certificates (20170717) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Setting up libx11-data (2:1.6.4-3) ...
Setting up libdata-stag-perl (0.14-2) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up libavahi-common-data:armhf (0.7-3) ...
Setting up libtest-warn-perl (0.32-1) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up libpython3.6-stdlib:armhf (3.6.4-3) ...
Setting up fontconfig-config (2.12.6-0.1) ...
Setting up libbio-perl-perl (1.7.2-2) ...
Setting up libexception-class-perl (1.44-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up mummer (3.23+dfsg-2+b1) ...
Setting up liblapack3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libtext-diff-perl (1.45-1) ...
Setting up libtest-exception-perl (0.43-1) ...
Setting up libnss3:armhf (2:3.35-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up smalt (0.7.6-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.5) ...
Setting up man-db (2.7.6.1-4) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libavahi-common3:armhf (0.7-3) ...
Setting up libxcb1:armhf (1.12-1) ...
Setting up libtool (2.4.6-2) ...
Setting up libpython3-stdlib:armhf (3.6.4-1) ...
Setting up libfontconfig1:armhf (2.12.6-0.1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libtest-differences-perl (0.64-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libx11-6:armhf (2:1.6.4-3) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libavahi-client3:armhf (0.7-3) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libtest-most-perl (0.35-1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up bioperl (1.7.2-2) ...
Setting up libcups2:armhf (2.2.6-4) ...
Setting up libxi6:armhf (2:1.7.9-1) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up libxtst6:armhf (2:1.2.3-1) ...
Setting up libhts2:armhf (1.6-4) ...
Setting up samtools (1.6-4) ...
Setting up openjdk-8-jre-headless:armhf (8u141-b15-3) ...
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 (20170930) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:ACEDICOM_Root.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:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:CA_Disig_Root_R2.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: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: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: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: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:ISRG_Root_X1.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian: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: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:SwissSign_Gold_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: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:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.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_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Visa_eCommerce_Root.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
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:LuxTrust_Global_Root_2.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
done.
Setting up dh-autoreconf (16) ...
Setting up python3 (3.6.4-1) ...
Setting up openjdk-8-jdk-headless:armhf (8u141-b15-3) ...
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-pkg-resources (38.4.0-1) ...
Setting up fastaq (3.16.0-1) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up python3-pysam (0.12.0.1+ds-4+rpi1) ...
Setting up python3-nose (1.3.7-3) ...
Setting up python3-lib2to3 (3.6.4-2) ...
Setting up dh-python (2.20170125) ...
Setting up python3-decorator (4.1.2-1) ...
Setting up python3-distutils (3.6.4-2) ...
Setting up default-jre-headless (2:1.8-59+b6) ...
Setting up default-jdk-headless (2:1.8-59+b6) ...
Setting up debhelper (11.1.4) ...
Setting up python3.6 (3.6.4-3) ...
Setting up python3-numpy (1:1.13.3-2) ...
Setting up python3-networkx (1.11-2) ...
Setting up python3-setuptools (38.4.0-1) ...
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
Processing triggers for systemd (236-2) ...
Processing triggers for ca-certificates (20170717) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...

done.
done.
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-13+rpi1 dpkg-dev_1.19.0.5 g++-7_7.2.0-19+b1 gcc-7_7.2.0-19+b1 libc6-dev_2.26-4+rpi1 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha6 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20171216.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-13+rpi1 binutils-arm-linux-gnueabihf_2.29.1-13+rpi1 binutils-common_2.29.1-13+rpi1 bioperl_1.7.2-2 bsdmainutils_11.1.2 bsdutils_1:2.30.2-0.3 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 ca-certificates-java_20170930 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-19+b1 dash_0.5.8-2.10 debconf_1.5.65 debhelper_11.1.4 debianutils_4.8.4 default-jdk-headless_2:1.8-59+b6 default-jre-headless_2:1.8-59+b6 dh-autoreconf_16 dh-python_2.20170125 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.4-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.43.8-2 e2fsprogs_1.43.8-2 e2fsprogs-l10n_1.43.8-2 fakeroot_1.22-2 fastaq_3.16.0-1 fdisk_2.30.2-0.3 file_1:5.32-1 findutils_4.6.0+git+20170828-2 fontconfig-config_2.12.6-0.1 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.2.0-19+b1 gawk_1:4.1.4+dfsg-1+b1 gcc_4:7.2.0-1d1 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-5-base_5.4.1-4 gcc-7_7.2.0-19+b1 gcc-7-base_7.2.0-19+b1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.4-1 gnupg-agent_2.2.4-1 gnupg-l10n_2.2.4-1 gnupg-utils_2.2.4-1 gpg_2.2.4-1 gpg-agent_2.2.4-1 gpg-wks-client_2.2.4-1 gpg-wks-server_2.2.4-1 gpgconf_2.2.4-1 gpgsm_2.2.4-1 gpgv_2.2.4-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.5 hostname_3.20 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 java-common_0.59 klibc-utils_2.0.4-11+rpi1 kmc_2.3+dfsg-5 kmod_25-1 libacl1_2.2.52-3 libalgorithm-diff-perl_1.19.03-1 libapparmor1_2.12-2 libapt-pkg5.0_1.6~alpha6 libarchive-zip-perl_1.60-1 libasan4_7.2.0-19+b1 libassuan0_2.5.1-1 libatomic1_7.2.0-19+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libavahi-client3_0.7-3 libavahi-common-data_0.7-3 libavahi-common3_0.7-3 libbambamc0_0.0.50-1 libbinutils_2.29.1-13+rpi1 libbio-perl-perl_1.7.2-2 libblas3_3.7.1-4 libblkid1_2.30.2-0.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-4+rpi1 libc-dev-bin_2.26-4+rpi1 libc6_2.26-4+rpi1 libc6-dev_2.26-4+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcapture-tiny-perl_0.46-1 libcc1-0_7.2.0-19+b1 libcilkrts5_7.2.0-19+b1 libclass-data-inheritable-perl_0.08-2 libcomerr2_1.43.8-2 libcroco3_0.6.12-2 libcryptsetup4_2:1.7.5-1 libcups2_2.2.6-4 libcurl3-gnutls_7.58.0-2 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.239 libdevel-stacktrace-perl_2.0300-1 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.89-1+rpi1 libdrm2_2.4.89-1+rpi1 libexception-class-perl_1.44-1 libexpat1_2.2.5-3 libfakeroot_1.22-2 libfdisk1_2.30.2-0.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libfontconfig1_2.12.6-0.1 libfreetype6_2.8.1-1 libgcc-7-dev_7.2.0-19+b1 libgcc1_1:7.2.0-19+b1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libgfortran4_7.2.0-19+b1 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.17-1 libgomp1_7.2.0-19+b1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhts2_1.6-4 libicu57_57.1-8 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libio-string-perl_1.08-3 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libjpeg62-turbo_1:1.5.2-2+b1 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack3_3.7.1-4 liblcms2-2_2.9-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.3 libmpc3_1.1.0-1 libmpdec2_2.4.2-1 libmpfr6_4.0.0-7 libncurses5_6.0+20171125-1 libncursesw5_6.0+20171125-1 libnettle6_3.4-1 libnghttp2-14_1.29.0-1 libnpth0_1.5-3 libnspr4_2:4.18-1 libnss3_2:3.35-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-8 libpcsclite1_1.8.23-1 libperl5.24_5.24.1-7 libperl5.26_5.26.1-4 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.19.1-4 libpython3-stdlib_3.6.4-1 libpython3.6-minimal_3.6.4-3 libpython3.6-stdlib_3.6.4-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.30.2-0.3 libsqlite3-0_3.22.0-1 libss2_1.43.8-2 libssh2-1_1.8.0-1 libssl-dev_1.1.0g-2 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 libsub-uplevel-perl_0.2800-1 libsystemd0_236-2 libtasn1-6_4.13-2 libtest-deep-perl_1.127-1 libtest-differences-perl_0.64-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.32-1 libtext-diff-perl_1.45-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20171125-1 libtool_2.4.6-2 libubsan0_7.2.0-19+b1 libudev1_236-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.3 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1+b2 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-6.1 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-4 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.3 multiarch-support_2.26-4+rpi1 mummer_3.23+dfsg-2+b1 nano_2.9.2-1 ncurses-base_6.0+20171125-1 ncurses-bin_6.0+20171125-1 openjdk-8-jdk-headless_8u141-b15-3 openjdk-8-jre-headless_8u141-b15-3 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-4 perl-base_5.26.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-4 pinentry-curses_1.0.0-3 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-3 python3_3.6.4-1 python3-decorator_4.1.2-1 python3-distutils_3.6.4-2 python3-lib2to3_3.6.4-2 python3-minimal_3.6.4-1 python3-networkx_1.11-2 python3-nose_1.3.7-3 python3-numpy_1:1.13.3-2 python3-pkg-resources_38.4.0-1 python3-pysam_0.12.0.1+ds-4+rpi1 python3-setuptools_38.4.0-1 python3.6_3.6.4-3 python3.6-minimal_3.6.4-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.6-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 smalt_0.7.6-6 systemd_236-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 ucf_3.0036 udev_236-2 util-linux_2.30.2-0.3 x11-common_1:7.7+19 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Feb 10 11:07:40 2018 UTC
gpgv:                using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-2.dsc
dpkg-source: info: extracting iva in /<<BUILDDIR>>/iva-1.0.9+ds
dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.9+ds-2.debian.tar.xz
dpkg-source: info: applying disable-multithreaded-test.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c120f40f-6b27-4772-a20d-074b5b5f71f4
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.9+ds-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build iva-1.0.9+ds
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
rm -rf .pybuild
rm -f iva/gage/*.class
rm -rf /<<BUILDDIR>>/iva-1.0.9+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python3.6 setup.py config 
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
chmod a-x /<<BUILDDIR>>/iva-1.0.9+ds/iva/read_trim/adapters.fasta
chmod a+x /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /<<BUILDDIR>>/iva-1.0.9+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/*.java
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/GetFastaStats.java]]
[parsing completed 257ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.java]]
[parsing completed 34ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 21ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.java]]
[parsing completed 100ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 193ms]
[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-1.0.9+ds/iva/gage/GetFastaStats$ContigAt.class]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuilder.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStream.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/GetFastaStats.class]]
[checking SizeFasta]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.class]]
[checking SplitFastaByLetter]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class]]
[checking Utils]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CloneNotSupportedException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Class.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/net/URI.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Process.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Runtime.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/GenericDeclaration.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/AnnotatedElement.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/Type.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AssertionError.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$Pair.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$Translate.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.class]]
[checking getScaffoldStats]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats$1.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.class]]
[total 13938ms]
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-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getScaffoldStats$1.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.6
copying and adjusting scripts/iva_qc -> build/scripts-3.6
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.6
copying and adjusting scripts/iva -> build/scripts-3.6
changing mode of build/scripts-3.6/iva_qc from 664 to 775
changing mode of build/scripts-3.6/iva_qc_make_db from 664 to 775
changing mode of build/scripts-3.6/iva from 664 to 775
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.9+ds'
python3 setup.py test
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running test
running egg_info
creating iva.egg-info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
writing manifest file 'iva.egg-info/SOURCES.txt'
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
running build_ext
/usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/<<BUILDDIR>>/iva-1.0.9+ds/iva/mapping.py:157: DeprecationWarning: invalid escape sequence \^
  s = re.sub('\^.', '', s)
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \(
  'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \(
  'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \(
  'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \(
  'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d
  'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
/<<BUILDDIR>>/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \.
  self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
/<<BUILDDIR>>/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W
  return re.sub('\W', '_', s).strip('_')
test_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_blastn_version (external_progs_test.TestExternalProgs)
Test blastn version ... ok
test_delta_filter_in_path (external_progs_test.TestExternalProgs)
Test delta-filter in path ... ok
test_kmc_dump_in_path (external_progs_test.TestExternalProgs)
Test kmc_dump in path ... ok
test_kmc_dump_version (external_progs_test.TestExternalProgs)
Test kmc_dump version ... ok
test_kmc_in_path (external_progs_test.TestExternalProgs)
Test kmc in path ... ok
test_kmc_version (external_progs_test.TestExternalProgs)
Test kmc version ... ok
test_makeblastdb_version (external_progs_test.TestExternalProgs)
Test makeblastdb version ... ok
test_nucmer_in_path (external_progs_test.TestExternalProgs)
Test nucmer in path ... ok
test_nucmer_version (external_progs_test.TestExternalProgs)
Test nucmer version ... ok
test_r_version (external_progs_test.TestExternalProgs)
Test R versions ... ok
test_samtools_in_path (external_progs_test.TestExternalProgs)
Test samtools in path ... ok
test_samtools_original_version (external_progs_test.TestExternalProgs)
Test samtools original version ... ok
test_samtools_version (external_progs_test.TestExternalProgs)
Test samtools version ... ok
test_show_coords_in_path (external_progs_test.TestExternalProgs)
Test show-coords in path ... ok
test_smalt_in_path (external_progs_test.TestExternalProgs)
Test smalt in path ... ok
test_smalt_version (external_progs_test.TestExternalProgs)
Test smalt version ... ok
test_add_and_get_edges (graph_test.TestGraph)
test adding and getting edges ... ok
test_connected_components (graph_test.TestGraph)
test connected_components ... ok
test_degree (graph_test.TestGraph)
test degree ... ok
test_edges_are_consistent (graph_test.TestGraph)
test edges_are_consistent ... ok
test_find_simple_path (graph_test.TestGraph)
test find_simple_path ... ok
test_get_nodes (graph_test.TestGraph)
test get_nodes ... ok
test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph)
test merged_coords_from_simple_nonredundant_path ... ok
test_node_to_coords (graph_test.TestGraph)
test _node_to_coords ... ok
test_remove_middle_node (graph_test.TestGraph)
test remove_middle_node ... ok
test_remove_node (graph_test.TestGraph)
test remove_node ... ok
test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph)
test remove_redundant_nodes_from_simple_path ... ok
test_simple_path_is_consistent (graph_test.TestGraph)
test simple_path_is_consistent ... ok
test_counts_file_to_fasta (kcount_test.TestKcount)
Test _counts_file_to_fasta ... ok
test_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 164 tests in 14.381s

OK
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
   dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva 
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running install
running build
running build_py
running build_scripts
running install_lib
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getScaffoldStats$1.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kmers.py to kmers.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/external_progs.py to external_progs.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/assembly.py to assembly.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kcount.py to kcount.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/common.py to common.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kraken.py to kraken.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/mapping.py to mapping.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/graph.py to graph.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/seed_processor.py to seed_processor.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/seed.py to seed.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/qc.py to qc.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/contig.py to contig.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/qc_external.py to qc_external.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/egg_extract.py to egg_extract.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/__init__.py to __init__.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/edge.py to edge.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim.py to read_trim.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/contig_trim.py to contig_trim.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/mummer.py to mummer.cpython-36.pyc
running install_egg_info
running egg_info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
Copying iva.egg-info to /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva-1.0.9.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.6/iva_qc -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.6/iva_qc_make_db -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
copying build/scripts-3.6/iva -> /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 775
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 775
changing mode of /<<BUILDDIR>>/iva-1.0.9+ds/debian/iva/usr/bin/iva 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-1.0.9+ds'
mkdir -p /<<BUILDDIR>>/iva-1.0.9+ds/debian/man
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva.1 \
          -n 'iterative virus assembler' \
          --no-discard-stderr  ./scripts/iva
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva_qc.1 \
          -n 'compare an assembly to a reference' \
          --no-discard-stderr ./scripts/iva_qc
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.9+ds/debian/man/iva_qc_make_db.1 \
          -n 'make a database as input for iva_qc' \
          --no-discard-stderr  ./scripts/iva_qc_make_db
dh_installman --
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
   dh_python3 -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
   dh_fixperms -a -O--buildsystem=pybuild
   dh_missing -a -O--buildsystem=pybuild
   dh_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: 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_1.0.9+ds-2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../iva_1.0.9+ds-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build iva-1.0.9+ds
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-02-15T04:55:10Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


iva_1.0.9+ds-2_armhf.changes:
-----------------------------

Format: 1.8
Date: Sat, 10 Feb 2018 11:27:13 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.9+ds-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
 iva        - iterative virus sequence assembler
Changes:
 iva (1.0.9+ds-2) unstable; urgency=medium
 .
   * Fix watchfile to not report non-release tags (with '-X' suffix).
   * Respect nocheck option in tests.
   * Update debhelper compat level to 10.
Checksums-Sha1:
 974b602d1dc15e445e78a6accaf42930110de64f 7366 iva_1.0.9+ds-2_armhf.buildinfo
 6bab5d7a5b7305379f5824216d34a85a3efd49d9 8577500 iva_1.0.9+ds-2_armhf.deb
Checksums-Sha256:
 c0353157302bd556c1bdb97ca54d7bebfeb49ff337b2a6a93dc075ed0c8f18c9 7366 iva_1.0.9+ds-2_armhf.buildinfo
 463f7c79d70c53d3cf0eb8416a667c5530742ef04d560762c4292cb2a21b2aec 8577500 iva_1.0.9+ds-2_armhf.deb
Files:
 34e13b1b2ea60196c3f677505b184249 7366 science optional iva_1.0.9+ds-2_armhf.buildinfo
 52c4280df7ff71951c5693ed1e486567 8577500 science optional iva_1.0.9+ds-2_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


iva_1.0.9+ds-2_armhf.deb
------------------------

 new Debian package, version 2.0.
 size 8577500 bytes: control archive=3024 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: 1.0.9+ds-2
 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 2018-02-10 10:27 ./
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/bin/
-rwxr-xr-x root/root     17240 2018-02-10 10:27 ./usr/bin/iva
-rwxr-xr-x root/root      6228 2018-02-10 10:27 ./usr/bin/iva_qc
-rwxr-xr-x root/root      2406 2018-02-10 10:27 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root       517 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root         4 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/
-rw-r--r-- root/root      1033 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/__init__.py
-rw-r--r-- root/root     28055 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/assembly.py
-rw-r--r-- root/root      1856 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/common.py
-rw-r--r-- root/root      1960 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig.py
-rw-r--r-- root/root      4391 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig_trim.py
-rw-r--r-- root/root      4903 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/edge.py
-rw-r--r-- root/root      3077 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/egg_extract.py
-rw-r--r-- root/root      4110 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/external_progs.py
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root       489 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root     10178 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root     14839 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root      3408 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root      3611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root      2621 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root      2229 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root       621 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root      4564 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root      1225 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root      5575 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/Utils.class
-rw-r--r-- root/root      9230 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/Utils.java
-rwxr-xr-x root/root        80 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl
-rwxr-xr-x root/root      1773 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh
-rwxr-xr-x root/root      1430 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh
-rw-r--r-- root/root       196 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$1.class
-rw-r--r-- root/root      1229 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root     13434 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class
-rw-r--r-- root/root     19111 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java
-rw-r--r-- root/root      7133 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/graph.py
-rw-r--r-- root/root      9487 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kcount.py
-rw-r--r-- root/root      3466 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kmers.py
-rw-r--r-- root/root     16961 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kraken.py
-rw-r--r-- root/root     13238 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/mapping.py
-rw-r--r-- root/root      8365 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/mummer.py
-rw-r--r-- root/root     36646 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc.py
-rw-r--r-- root/root      8190 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc_external.py
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root      1012 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root      1049 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl
-rwxr-xr-x root/root     41988 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl
-rw-r--r-- root/root        90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config
-rw-r--r-- root/root        90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv
-rw-r--r-- root/root     57611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm
-rwxr-xr-x root/root     13201 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh
-rw-r--r-- root/root      1428 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim.py
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/read_trim/
-rw-r--r-- root/root      3143 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta
-rw-r--r-- root/root      6056 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed.py
-rw-r--r-- root/root      5586 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed_processor.py
-rw-r--r-- root/root      2443 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_data_runner.py
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/test_run_data/
-rw-r--r-- root/root       672 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa
-rw-r--r-- root/root      9981 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta
-rw-r--r-- root/root      9200 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta
-rw-r--r-- root/root   3813239 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root   4661713 2018-02-10 10:27 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz
-rw-r--r-- root/root      9217 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/share/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/share/doc/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/share/doc/iva/
-rw-r--r-- root/root       621 2018-02-10 10:27 ./usr/share/doc/iva/changelog.Debian.gz
-rw-r--r-- root/root      1488 2018-02-10 10:27 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/share/man/
drwxr-xr-x root/root         0 2018-02-10 10:27 ./usr/share/man/man1/
-rw-r--r-- root/root      2255 2018-02-10 10:27 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root      1282 2018-02-10 10:27 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root       644 2018-02-10 10:27 ./usr/share/man/man1/iva_qc_make_db.1.gz


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| Post Build                                                                   |
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| Cleanup                                                                      |
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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: 37292
Build-Time: 68
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 500
Job: iva_1.0.9+ds-2
Machine Architecture: armhf
Package: iva
Package-Time: 586
Source-Version: 1.0.9+ds-2
Space: 37292
Status: successful
Version: 1.0.9+ds-2
--------------------------------------------------------------------------------
Finished at 2018-02-15T04:55:10Z
Build needed 00:09:46, 37292k disk space
Raspbian Package Auto-Building

Build log for iva (1.0.9+ds-2) on armhf
