iva →
1.0.9+ds-1 →
armhf → 2018-02-05 05:17:45
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| iva 1.0.9+ds-1 (armhf) Mon, 05 Feb 2018 04:49:54 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.9+ds-1
Source Version: 1.0.9+ds-1
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-fbe5d561-3e53-4c46-b478-64d923c907ae' 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 28s (822 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-1 (dsc) [2219 B]
Get:2 http://172.17.0.1/private buster-staging/main iva 1.0.9+ds-1 (tar) [8675 kB]
Get:3 http://172.17.0.1/private buster-staging/main iva 1.0.9+ds-1 (diff) [3768 B]
Fetched 8681 kB in 2s (3689 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-sT3Ch2/iva-1.0.9+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-sT3Ch2' 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-QBiBzj/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-QBiBzj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QBiBzj/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2998 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 36 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (21.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15339 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
Filtered Build-Depends: debhelper (>= 9), libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<<BUILDDIR>>/resolver-QBiBzj/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-QBiBzj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Sources [584 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QBiBzj/apt_archive ./ Packages [663 B]
Fetched 2580 B in 1s (3653 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 36 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-QBiBzj/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 2.11-1 [29.3 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf gawk armhf 1:4.1.4+dfsg-1 [508 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+b4 [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 11.1.3 [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+b4 [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 [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 [765 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]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 72.8 MB in 26s (2789 kB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 15339 files and directories currently installed.)
Preparing to unpack .../0-liblocale-gettext-perl_1.07-3+b2_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-3+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../2-libbsd0_0.8.7-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.7-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../3-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../4-libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../5-man-db_2.7.6.1-4_armhf.deb ...
Unpacking man-db (2.7.6.1-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../6-libsigsegv2_2.11-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.11-1) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Selecting previously unselected package gawk.
(Reading database ... 15931 files and directories currently installed.)
Preparing to unpack .../00-gawk_1%3a4.1.4+dfsg-1_armhf.deb ...
Unpacking gawk (1:4.1.4+dfsg-1) ...
Selecting previously unselected package java-common.
Preparing to unpack .../01-java-common_0.59_all.deb ...
Unpacking java-common (0.59) ...
Selecting previously unselected package default-jre-headless.
Preparing to unpack .../02-default-jre-headless_2%3a1.8-59+b4_armhf.deb ...
Unpacking default-jre-headless (2:1.8-59+b4) ...
Selecting previously unselected package libnspr4:armhf.
Preparing to unpack .../03-libnspr4_2%3a4.18-1_armhf.deb ...
Unpacking libnspr4:armhf (2:4.18-1) ...
Selecting previously unselected package libnss3:armhf.
Preparing to unpack .../04-libnss3_2%3a3.35-2_armhf.deb ...
Unpacking libnss3:armhf (2:3.35-2) ...
Selecting previously unselected package ca-certificates-java.
Preparing to unpack .../05-ca-certificates-java_20170930_all.deb ...
Unpacking ca-certificates-java (20170930) ...
Selecting previously unselected package libavahi-common-data:armhf.
Preparing to unpack .../06-libavahi-common-data_0.7-3_armhf.deb ...
Unpacking libavahi-common-data:armhf (0.7-3) ...
Selecting previously unselected package libavahi-common3:armhf.
Preparing to unpack .../07-libavahi-common3_0.7-3_armhf.deb ...
Unpacking libavahi-common3:armhf (0.7-3) ...
Selecting previously unselected package libavahi-client3:armhf.
Preparing to unpack .../08-libavahi-client3_0.7-3_armhf.deb ...
Unpacking libavahi-client3:armhf (0.7-3) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../09-libkeyutils1_1.5.9-9.2_armhf.deb ...
Unpacking libkeyutils1:armhf (1.5.9-9.2) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../10-libkrb5support0_1.16-2_armhf.deb ...
Unpacking libkrb5support0:armhf (1.16-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../11-libk5crypto3_1.16-2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.16-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../12-libkrb5-3_1.16-2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.16-2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../13-libgssapi-krb5-2_1.16-2_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.16-2) ...
Selecting previously unselected package libcups2:armhf.
Preparing to unpack .../14-libcups2_2.2.6-4_armhf.deb ...
Unpacking libcups2:armhf (2.2.6-4) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../15-liblcms2-2_2.9-1_armhf.deb ...
Unpacking liblcms2-2:armhf (2.9-1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../16-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../17-libexpat1_2.2.5-3_armhf.deb ...
Unpacking libexpat1:armhf (2.2.5-3) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../18-libfreetype6_2.8.1-1_armhf.deb ...
Unpacking libfreetype6:armhf (2.8.1-1) ...
Selecting previously unselected package ucf.
Preparing to unpack .../19-ucf_3.0036_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0036) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../20-fonts-dejavu-core_2.37-1_all.deb ...
Unpacking fonts-dejavu-core (2.37-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../21-fontconfig-config_2.12.6-0.1_all.deb ...
Unpacking fontconfig-config (2.12.6-0.1) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../22-libfontconfig1_2.12.6-0.1_armhf.deb ...
Unpacking libfontconfig1:armhf (2.12.6-0.1) ...
Selecting previously unselected package libpcsclite1:armhf.
Preparing to unpack .../23-libpcsclite1_1.8.23-1_armhf.deb ...
Unpacking libpcsclite1:armhf (1.8.23-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../24-libxau6_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../25-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../26-libxcb1_1.12-1_armhf.deb ...
Unpacking libxcb1:armhf (1.12-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../27-libx11-data_2%3a1.6.4-3_all.deb ...
Unpacking libx11-data (2:1.6.4-3) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../28-libx11-6_2%3a1.6.4-3_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.4-3) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../29-libxext6_2%3a1.3.3-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../30-libxi6_2%3a1.7.9-1_armhf.deb ...
Unpacking libxi6:armhf (2:1.7.9-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../31-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../32-x11-common_1%3a7.7+19_all.deb ...
Unpacking x11-common (1:7.7+19) ...
Selecting previously unselected package libxtst6:armhf.
Preparing to unpack .../33-libxtst6_2%3a1.2.3-1_armhf.deb ...
Unpacking libxtst6:armhf (2:1.2.3-1) ...
Selecting previously unselected package openjdk-8-jre-headless:armhf.
Preparing to unpack .../34-openjdk-8-jre-headless_8u141-b15-3_armhf.deb ...
Unpacking openjdk-8-jre-headless:armhf (8u141-b15-3) ...
Selecting previously unselected package libpython3.6-minimal:armhf.
Preparing to unpack .../35-libpython3.6-minimal_3.6.4-3_armhf.deb ...
Unpacking libpython3.6-minimal:armhf (3.6.4-3) ...
Selecting previously unselected package python3.6-minimal.
Preparing to unpack .../36-python3.6-minimal_3.6.4-3_armhf.deb ...
Unpacking python3.6-minimal (3.6.4-3) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../37-python3-minimal_3.6.4-1_armhf.deb ...
Unpacking python3-minimal (3.6.4-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../38-mime-support_3.60_all.deb ...
Unpacking mime-support (3.60) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../39-libmpdec2_2.4.2-1_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.2-1) ...
Selecting previously unselected package libpython3.6-stdlib:armhf.
Preparing to unpack .../40-libpython3.6-stdlib_3.6.4-3_armhf.deb ...
Unpacking libpython3.6-stdlib:armhf (3.6.4-3) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../41-python3-lib2to3_3.6.4-2_all.deb ...
Unpacking python3-lib2to3 (3.6.4-2) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../42-python3-distutils_3.6.4-2_all.deb ...
Unpacking python3-distutils (3.6.4-2) ...
Selecting previously unselected package python3.6.
Preparing to unpack .../43-python3.6_3.6.4-3_armhf.deb ...
Unpacking python3.6 (3.6.4-3) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../44-libpython3-stdlib_3.6.4-1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.6.4-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../45-dh-python_2.20170125_all.deb ...
Unpacking dh-python (2.20170125) ...
Setting up libpython3.6-minimal:armhf (3.6.4-3) ...
Setting up libexpat1:armhf (2.2.5-3) ...
Setting up python3.6-minimal (3.6.4-3) ...
Setting up python3-minimal (3.6.4-1) ...
Selecting previously unselected package python3.
(Reading database ... 17993 files and directories currently installed.)
Preparing to unpack .../00-python3_3.6.4-1_armhf.deb ...
Unpacking python3 (3.6.4-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.32-1_armhf.deb ...
Unpacking libmagic-mgc (1:5.32-1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.32-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.32-1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.32-1_armhf.deb ...
Unpacking file (1:5.32-1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.19.8.1-4_armhf.deb ...
Unpacking gettext-base (0.19.8.1-4) ...
Selecting previously unselected package m4.
Preparing to unpack .../05-m4_1.4.18-1_armhf.deb ...
Unpacking m4 (1.4.18-1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../06-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../07-autotools-dev_20171216.1_all.deb ...
Unpacking autotools-dev (20171216.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../08-automake_1%3a1.15.1-3_all.deb ...
Unpacking automake (1:1.15.1-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../09-autopoint_0.19.8.1-4_all.deb ...
Unpacking autopoint (0.19.8.1-4) ...
Selecting previously unselected package libio-string-perl.
Preparing to unpack .../10-libio-string-perl_1.08-3_all.deb ...
Unpacking libio-string-perl (1.08-3) ...
Selecting previously unselected package libdata-stag-perl.
Preparing to unpack .../11-libdata-stag-perl_0.14-2_all.deb ...
Unpacking libdata-stag-perl (0.14-2) ...
Selecting previously unselected package libbio-perl-perl.
Preparing to unpack .../12-libbio-perl-perl_1.7.2-2_all.deb ...
Unpacking libbio-perl-perl (1.7.2-2) ...
Selecting previously unselected package libclass-data-inheritable-perl.
Preparing to unpack .../13-libclass-data-inheritable-perl_0.08-2_all.deb ...
Unpacking libclass-data-inheritable-perl (0.08-2) ...
Selecting previously unselected package libdevel-stacktrace-perl.
Preparing to unpack .../14-libdevel-stacktrace-perl_2.0300-1_all.deb ...
Unpacking libdevel-stacktrace-perl (2.0300-1) ...
Selecting previously unselected package libexception-class-perl.
Preparing to unpack .../15-libexception-class-perl_1.44-1_all.deb ...
Unpacking libexception-class-perl (1.44-1) ...
Selecting previously unselected package libtest-deep-perl.
Preparing to unpack .../16-libtest-deep-perl_1.127-1_all.deb ...
Unpacking libtest-deep-perl (1.127-1) ...
Selecting previously unselected package libcapture-tiny-perl.
Preparing to unpack .../17-libcapture-tiny-perl_0.46-1_all.deb ...
Unpacking libcapture-tiny-perl (0.46-1) ...
Selecting previously unselected package libalgorithm-diff-perl.
Preparing to unpack .../18-libalgorithm-diff-perl_1.19.03-1_all.deb ...
Unpacking libalgorithm-diff-perl (1.19.03-1) ...
Selecting previously unselected package libtext-diff-perl.
Preparing to unpack .../19-libtext-diff-perl_1.45-1_all.deb ...
Unpacking libtext-diff-perl (1.45-1) ...
Selecting previously unselected package libtest-differences-perl.
Preparing to unpack .../20-libtest-differences-perl_0.64-1_all.deb ...
Unpacking libtest-differences-perl (0.64-1) ...
Selecting previously unselected package libsub-uplevel-perl.
Preparing to unpack .../21-libsub-uplevel-perl_0.2800-1_all.deb ...
Unpacking libsub-uplevel-perl (0.2800-1) ...
Selecting previously unselected package libtest-exception-perl.
Preparing to unpack .../22-libtest-exception-perl_0.43-1_all.deb ...
Unpacking libtest-exception-perl (0.43-1) ...
Selecting previously unselected package libtest-warn-perl.
Preparing to unpack .../23-libtest-warn-perl_0.32-1_all.deb ...
Unpacking libtest-warn-perl (0.32-1) ...
Selecting previously unselected package libtest-most-perl.
Preparing to unpack .../24-libtest-most-perl_0.35-1_all.deb ...
Unpacking libtest-most-perl (0.35-1) ...
Selecting previously unselected package bioperl.
Preparing to unpack .../25-bioperl_1.7.2-2_all.deb ...
Unpacking bioperl (1.7.2-2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../26-libtool_2.4.6-2_all.deb ...
Unpacking libtool (2.4.6-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../27-dh-autoreconf_16_all.deb ...
Unpacking dh-autoreconf (16) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../28-libarchive-zip-perl_1.60-1_all.deb ...
Unpacking libarchive-zip-perl (1.60-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../29-libfile-stripnondeterminism-perl_0.040-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.040-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../30-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../31-dh-strip-nondeterminism_0.040-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.040-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../32-libglib2.0-0_2.54.3-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.54.3-2) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../33-libicu57_57.1-8_armhf.deb ...
Unpacking libicu57:armhf (57.1-8) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../34-libxml2_2.9.4+dfsg1-6.1_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-6.1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../35-libcroco3_0.6.12-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../36-gettext_0.19.8.1-4_armhf.deb ...
Unpacking gettext (0.19.8.1-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../37-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../38-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../39-debhelper_11.1.3_all.deb ...
Unpacking debhelper (11.1.3) ...
Selecting previously unselected package openjdk-8-jdk-headless:armhf.
Preparing to unpack .../40-openjdk-8-jdk-headless_8u141-b15-3_armhf.deb ...
Unpacking openjdk-8-jdk-headless:armhf (8u141-b15-3) ...
Selecting previously unselected package default-jdk-headless.
Preparing to unpack .../41-default-jdk-headless_2%3a1.8-59+b4_armhf.deb ...
Unpacking default-jdk-headless (2:1.8-59+b4) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../42-python3-pkg-resources_38.4.0-1_all.deb ...
Unpacking python3-pkg-resources (38.4.0-1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../43-libnghttp2-14_1.29.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.29.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../44-libpsl5_0.19.1-4_armhf.deb ...
Unpacking libpsl5:armhf (0.19.1-4) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
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.
Preparing to unpack .../48-libhts2_1.6-4_armhf.deb ...
Unpacking libhts2:armhf (1.6-4) ...
Selecting previously unselected package samtools.
Preparing to unpack .../49-samtools_1.6-4_armhf.deb ...
Unpacking samtools (1.6-4) ...
Selecting previously unselected package fastaq.
Preparing to unpack .../50-fastaq_3.16.0-1_all.deb ...
Unpacking fastaq (3.16.0-1) ...
Selecting previously unselected package help2man.
Preparing to unpack .../51-help2man_1.47.5_armhf.deb ...
Unpacking help2man (1.47.5) ...
Selecting previously unselected package kmc.
Preparing to unpack .../52-kmc_2.3+dfsg-5_armhf.deb ...
Unpacking kmc (2.3+dfsg-5) ...
Selecting previously unselected package libbambamc0.
Preparing to unpack .../53-libbambamc0_0.0.50-1_armhf.deb ...
Unpacking libbambamc0 (0.0.50-1) ...
Selecting previously unselected package libgfortran4:armhf.
Preparing to unpack .../54-libgfortran4_7.2.0-19_armhf.deb ...
Unpacking libgfortran4:armhf (7.2.0-19) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../55-libblas3_3.7.1-4_armhf.deb ...
Unpacking libblas3:armhf (3.7.1-4) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../56-liblapack3_3.7.1-4_armhf.deb ...
Unpacking liblapack3:armhf (3.7.1-4) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../57-libssl-dev_1.1.0g-2_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.0g-2) ...
Selecting previously unselected package mummer.
Preparing to unpack .../58-mummer_3.23+dfsg-2_armhf.deb ...
Unpacking mummer (3.23+dfsg-2) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../59-python3-decorator_4.1.2-1_all.deb ...
Unpacking python3-decorator (4.1.2-1) ...
Selecting previously unselected package python3-networkx.
Preparing to unpack .../60-python3-networkx_1.11-2_all.deb ...
Unpacking python3-networkx (1.11-2) ...
Selecting previously unselected package python3-nose.
Preparing to unpack .../61-python3-nose_1.3.7-3_all.deb ...
Unpacking python3-nose (1.3.7-3) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../62-python3-numpy_1%3a1.13.3-2_armhf.deb ...
Unpacking python3-numpy (1:1.13.3-2) ...
Selecting previously unselected package python3-pysam.
Preparing to unpack .../63-python3-pysam_0.12.0.1+ds-4+rpi1_armhf.deb ...
Unpacking python3-pysam (0.12.0.1+ds-4+rpi1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../64-python3-setuptools_38.4.0-1_all.deb ...
Unpacking python3-setuptools (38.4.0-1) ...
Selecting previously unselected package smalt.
Preparing to unpack .../65-smalt_0.7.6-6_armhf.deb ...
Unpacking smalt (0.7.6-6) ...
Selecting previously unselected package sbuild-build-depends-iva-dummy.
Preparing to unpack .../66-sbuild-build-depends-iva-dummy_0.invalid.0_armhf.deb ...
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) ...
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) ...
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 (2.26-2+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) ...
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+b4) ...
Setting up default-jdk-headless (2:1.8-59+b4) ...
Setting up debhelper (11.1.3) ...
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 (2.26-2+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 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-13+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-19 gcc-7_7.2.0-19 libc6-dev_2.26-2+rpi1 libstdc++-7-dev_7.2.0-19 libstdc++6_7.2.0-19 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+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_1:2.30.2-0.1 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 dash_0.5.8-2.5 debconf_1.5.65 debhelper_11.1.3 debianutils_4.8.4 default-jdk-headless_2:1.8-59+b4 default-jre-headless_2:1.8-59+b4 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_1.19.0.4 dpkg-dev_1.19.0.4 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_2.30.2-0.1 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 gawk_1:4.1.4+dfsg-1 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 gcc-7-base_7.2.0-19 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_3.18 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_24-1 libacl1_2.2.52-3 libalgorithm-diff-perl_1.19.03-1 libapparmor1_2.11.1-4 libapt-pkg5.0_1.6~alpha6 libarchive-zip-perl_1.60-1 libasan4_7.2.0-19 libassuan0_2.5.1-1 libatomic1_7.2.0-19 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_2.30.2-0.1 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-2+rpi1 libc-dev-bin_2.26-2+rpi1 libc6_2.26-2+rpi1 libc6-dev_2.26-2+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 libcilkrts5_7.2.0-19 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_0.237 libdevel-stacktrace-perl_2.0300-1 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.4 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_2.30.2-0.1 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 libgcc1_1:7.2.0-19 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libgfortran4_7.2.0-19 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-19 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_24-1 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_2.30.2-0.1 libmpc3_1.0.3-2 libmpdec2_2.4.2-1 libmpfr4_3.1.6-1 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_5.26.1-3 libpipeline1_1.5.0-1 libplymouth4_0.9.3-1 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_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.21.0-1 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 libstdc++6_7.2.0-19 libsub-uplevel-perl_0.2800-1 libsystemd0_236-2 libtasn1-6_4.12-3 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-charwidth-perl_0.04-7.1 libtext-diff-perl_1.45-1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20171125-1 libtool_2.4.6-2 libubsan0_7.2.0-19 libudev1_236-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 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_2.30.2-0.1 multiarch-support_2.26-2+rpi1 mummer_3.23+dfsg-2 nano_2.9.1-1 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_5.26.1-3 perl-base_5.26.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-3 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 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_4.4-1 sensible-utils_0.0.11 smalt_0.7.6-6 systemd_236-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 ucf_3.0036 udev_236-2 util-linux_2.30.2-0.1 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 Wed Jan 31 13:11:33 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-1.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-1.debian.tar.xz
dpkg-source: info: applying disable-multithreaded-test.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-fbe5d561-3e53-4c46-b478-64d923c907ae
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.9+ds-1
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_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 755ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SizeFasta.java]]
[parsing completed 98ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 61ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/Utils.java]]
[parsing completed 275ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 541ms]
[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 40377ms]
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/__init__.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/common.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/contig_trim.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/egg_extract.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/graph.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/kmers.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/mummer.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/qc_external.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/seed.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/test_data_runner.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/GetFastaStats.java -> /<<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.java -> /<<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/colsum.pl -> /<<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/getMummerStats.sh -> /<<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/GetFastaStats.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/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.9+ds/.pybuild/pythonX.Y_3.6/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<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/getScaffoldStats.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/embl2gff.pl -> /<<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/ratt.config -> /<<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/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/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/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/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/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/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 -> 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
changing mode of build/scripts-3.6/iva from 664 to 775
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
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 ... The following command failed with exit code 134
bash run_kmc.sh
The output was:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run_kmc.sh: line 2: 23276 Aborted kmc -fa -m4 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.common_kmers.43x0feap/reads.fa kmc_out $PWD
ERROR
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 ... The following command failed with exit code 134
bash run_kmc.sh
The output was:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run_kmc.sh: line 2: 23480 Aborted kmc -fa -m4 -k10 -sf1 -ci2 -cs4 -cx4 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.run_kmc.o_5r6uzf/tmp.common_kmers.cz9i1ewy/reads.fa kmc_out $PWD > /dev/null
ERROR
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 ... The following command failed with exit code 134
bash run_kmc.sh
The output was:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run_kmc.sh: line 2: 23486 Aborted kmc -fa -m4 -k10 -sf1 -ci2 -cs4 -cx4 /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/kcount_test.run_kmc.fa kmc_out $PWD > /dev/null
ERROR
test_run_kmc_two_threads (kcount_test.TestKcount)
Test test_run_kmc with two threads ... The following command failed with exit code 134
bash run_kmc.sh
The output was:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
run_kmc.sh: line 2: 23492 Aborted kmc -fa -m4 -k10 -sf2 -ci2 -cs4 -cx4 /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/kcount_test.run_kmc.fa kmc_out $PWD > /dev/null
ERROR
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
======================================================================
ERROR: test_add_new_seed_contig (assembly_test.TestAssembly)
Test add_new_seed_contig
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/assembly_test.py", line 166, in test_add_new_seed_contig
new_contig_name = a.add_new_seed_contig(reads1, reads2)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/assembly.py", line 601, in add_new_seed_contig
s = seed.Seed(reads1=seed_reads1, reads2=seed_reads2, extend_length=self.seed_ext_max_bases, seed_length=self.seed_start_length, seed_min_count=self.seed_min_kmer_count, seed_max_count=self.seed_max_kmer_count, ext_min_cov=self.seed_min_cov, ext_min_ratio=self.seed_min_ratio, verbose=self.verbose, kmc_threads=self.kmc_threads, map_threads=self.threads, sequences_to_ignore=self.used_seeds, contigs_to_check=self.contigs)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/seed.py", line 41, in __init__
kmer_counts = kcount.get_most_common_kmers(reads1, reads2, most_common=1, min_count=seed_min_count, max_count=seed_max_count, kmer_length=seed_length, verbose=self.verbose, ignore_seqs=sequences_to_ignore, contigs_to_check=contigs_to_check, kmc_threads=self.kmc_threads, map_threads=self.map_threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 234, in get_most_common_kmers
counts_file = _run_kmc(reads, os.path.join(tmpdir, 'out'), kmer_length, min_count, max_count, verbose=verbose, threads=kmc_threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc
ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script
return common.syscall('bash ' + script, allow_fail=allow_fail)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/common.py", line 44, in syscall
sys.exit(1)
SystemExit: 1
-------------------- >> begin captured stdout << ---------------------
map reads /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_1.fa /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_2.fa
map reads. Index: smalt index -k 15 -s 3 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.make_seed.fmdqy2oh/out.map_index /<<BUILDDIR>>/iva-1.0.9+ds/tmp.make_seed.fmdqy2oh/out.ref.fa
map reads. Mapping: smalt map -i 800 -y 0.5 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.make_seed.fmdqy2oh/out.map_index /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_1.fa /<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_2.fa | samtools view -f 12 -bS -T /<<BUILDDIR>>/iva-1.0.9+ds/tmp.make_seed.fmdqy2oh/out.ref.fa - > /<<BUILDDIR>>/iva-1.0.9+ds/tmp.make_seed.fmdqy2oh/out.bam
run kmc: /<<BUILDDIR>>/iva-1.0.9+ds/tmp.run_kmc.o_5r6uzf kmc -fa -m32 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.common_kmers.43x0feap/reads.fa kmc_out $PWD
First try of running kmc failed. Trying again with -m4 instead of -m32...
run kmc: /<<BUILDDIR>>/iva-1.0.9+ds/tmp.run_kmc.o_5r6uzf kmc -fa -m4 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<<BUILDDIR>>/iva-1.0.9+ds/tmp.common_kmers.43x0feap/reads.fa kmc_out $PWD
--------------------- >> end captured stdout << ----------------------
======================================================================
ERROR: test_get_most_common_kmers (kcount_test.TestKcount)
Test get_most_common_kmers
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 88, in test_get_most_common_kmers
counts = kcount.get_most_common_kmers(reads1, reads2, kmer_length=10, head=100000, min_count=2, max_count=4, most_common=100, method='kmc')
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 234, in get_most_common_kmers
counts_file = _run_kmc(reads, os.path.join(tmpdir, 'out'), kmer_length, min_count, max_count, verbose=verbose, threads=kmc_threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc
ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script
return common.syscall('bash ' + script, allow_fail=allow_fail)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/common.py", line 44, in syscall
sys.exit(1)
SystemExit: 1
======================================================================
ERROR: test_run_kmc (kcount_test.TestKcount)
Test test_run_kmc
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 54, in test_run_kmc
counts_file = kcount._run_kmc(reads, 'tmp.run_kmc', 10, 2, 4)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc
ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script
return common.syscall('bash ' + script, allow_fail=allow_fail)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/common.py", line 44, in syscall
sys.exit(1)
SystemExit: 1
======================================================================
ERROR: test_run_kmc_two_threads (kcount_test.TestKcount)
Test test_run_kmc with two threads
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 62, in test_run_kmc_two_threads
counts_file = kcount._run_kmc(reads, 'tmp.run_kmc', 10, 2, 4, threads=2)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc
ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script
return common.syscall('bash ' + script, allow_fail=allow_fail)
File "/<<BUILDDIR>>/iva-1.0.9+ds/iva/common.py", line 44, in syscall
sys.exit(1)
SystemExit: 1
----------------------------------------------------------------------
Ran 164 tests in 31.925s
FAILED (errors=4)
Test failed: <unittest.runner.TextTestResult run=164 errors=4 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=164 errors=4 failures=0>
debian/rules:43: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.9+ds'
debian/rules:13: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-02-05T05:17:08Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 97
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1482
Job: iva_1.0.9+ds-1
Machine Architecture: armhf
Package: iva
Package-Time: 1634
Source-Version: 1.0.9+ds-1
Space: 0
Status: failed
Version: 1.0.9+ds-1
--------------------------------------------------------------------------------
Finished at 2018-02-05T05:17:08Z
Build needed 00:00:00, 0k disc space