iva →
1.0.6+ds-1 →
armhf → 2016-08-18 06:42:46
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| iva 1.0.6+ds-1 (armhf) 17 Aug 2016 05:25 |
+==============================================================================+
Package: iva
Version: 1.0.6+ds-1
Source Version: 1.0.6+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/iva-dOeq1z/iva-1.0.6+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-dOeq1z' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-a1399ae5-c02a-48c3-9722-e64a05c2298d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9226 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
Fetched 20.4 MB in 36s (553 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...
Need to get 8681 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main iva 1.0.6+ds-1 (dsc) [2101 B]
Get:2 http://172.17.0.1/private stretch-staging/main iva 1.0.6+ds-1 (tar) [8674 kB]
Get:3 http://172.17.0.1/private stretch-staging/main iva 1.0.6+ds-1 (diff) [5592 B]
Fetched 8681 kB in 12s (722 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-SDDxYD/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-SDDxYD/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-SDDxYD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13715 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.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
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-lzsCp1/apt_archive/sbuild-build-depends-iva-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Sources [305 B]
Get:5 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ Packages [626 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-lzsCp1/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install iva build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdmainutils
ca-certificates ca-certificates-java debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism fastaq
file fontconfig-config fonts-dejavu-core gawk gettext gettext-base
groff-base help2man intltool-debian java-common kmc libarchive-zip-perl
libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0
libbio-perl-perl libblas-common libblas3 libbsd0 libcroco3 libcups2
libcurl3-gnutls libdata-stag-perl libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu57
libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14 libnspr4 libnss3
libp11-kit0 libpcsclite1 libpipeline1 libpng16-16 libpython3-stdlib
libpython3.5-minimal libpython3.5-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl-dev
libssl1.0.2 libtasn1-6 libtool libunistring0 libx11-6 libx11-data libxau6
libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db
mime-support mummer openjdk-8-jdk-headless openjdk-8-jre-headless openssl
po-debconf python3 python3-decorator python3-minimal python3-networkx
python3-nose python3-numpy python3-pkg-resources python3-pysam
python3-setuptools python3.5 python3.5-minimal samtools smalt ucf x11-common
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make default-jre gawk-doc gettext-doc libasprintf-dev
libgettextpo-dev groff libxml-sax-expatxs-perl cups-common gnutls-bin
krb5-doc krb5-user liblcms2-utils pcscd libtool-doc gfortran
| fortran95-compiler gcj-jdk less www-browser openjdk-8-demo
openjdk-8-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic
libmail-box-perl python3-doc python3-tk python3-venv python-networkx-doc
python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg
python-setuptools-doc python3.5-venv python3.5-doc binfmt-support
Recommended packages:
bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl
libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl
liburi-perl libxml-simple-perl libyaml-perl libace-perl
liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget
| lynx-cur bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl
libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
libsort-naturally-perl libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl
libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk
libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl
libxml-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales
libsasl2-modules libssl-doc libltdl-dev xml-core openjdk-8-jre-jamvm
libmail-sendmail-perl python3-scipy python3-yaml python
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdmainutils
ca-certificates ca-certificates-java debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism fastaq
file fontconfig-config fonts-dejavu-core gawk gettext gettext-base
groff-base help2man intltool-debian java-common kmc libarchive-zip-perl
libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0
libbio-perl-perl libblas-common libblas3 libbsd0 libcroco3 libcups2
libcurl3-gnutls libdata-stag-perl libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu57
libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 liblocale-gettext-perl
libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14 libnspr4 libnss3
libp11-kit0 libpcsclite1 libpipeline1 libpng16-16 libpython3-stdlib
libpython3.5-minimal libpython3.5-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl-dev
libssl1.0.2 libtasn1-6 libtool libunistring0 libx11-6 libx11-data libxau6
libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db
mime-support mummer openjdk-8-jdk-headless openjdk-8-jre-headless openssl
po-debconf python3 python3-decorator python3-minimal python3-networkx
python3-nose python3-numpy python3-pkg-resources python3-pysam
python3-setuptools python3.5 python3.5-minimal samtools
sbuild-build-depends-iva-dummy smalt ucf x11-common zlib1g-dev
0 upgraded, 121 newly installed, 0 to remove and 1 not upgraded.
Need to get 79.4 MB/79.4 MB of archives.
After this operation, 296 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-lzsCp1/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [864 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3 [18.0 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf gawk armhf 1:4.1.3+dfsg-0.1 [509 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1.1 [41.3 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libxi6 armhf 2:1.7.6-1 [75.9 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libxtst6 armhf 2:1.2.2-1+b1 [25.5 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2h-1 [667 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf java-common all 0.57 [13.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf default-jre-headless armhf 2:1.8-57+b2 [10.3 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libnspr4 armhf 2:4.12-2 [94.1 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.13.0-1 [479 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libnss3 armhf 2:3.25-1 [943 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf ca-certificates-java all 20160321 [14.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libavahi-common-data armhf 0.6.32-1 [118 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libavahi-common3 armhf 0.6.32-1 [48.6 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libavahi-client3 armhf 0.6.32-1 [51.2 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.2-1 [202 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.2-1 [126 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-4 [93.2 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.8-1 [44.1 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.2-2 [721 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-1 [57.4 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-1 [111 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-1 [263 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-1 [131 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libcups2 armhf 2.1.4-4 [268 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.7-1 [116 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.0-1 [109 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.23-1 [260 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.36-1 [1068 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.5 [271 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.5 [313 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libpcsclite1 armhf 1.8.18-1 [54.0 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf openjdk-8-jre-headless armhf 8u102-b14.1-2 [24.8 MB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.2-3 [564 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.2-3 [1433 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-4 [35.3 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.2-3 [2080 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.2-3 [214 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-4 [18.6 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20160721 [82.2 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-4 [21.7 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [65.6 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [96.7 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-2 [7404 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libio-string-perl all 1.08-3 [12.3 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libdata-stag-perl all 0.14-2 [448 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libbio-perl-perl all 1.6.924-5 [4746 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf bioperl all 1.6.924-5 [418 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-2 [2546 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.58-1 [95.5 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.022-1 [13.1 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.022-1 [7902 B]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160709 [799 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf openjdk-8-jdk-headless armhf 8u102-b14.1-2 [6151 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf default-jdk-headless armhf 2:1.8-57+b2 [940 B]
Get:96 http://172.17.0.1/private stretch-staging/main armhf python3-pkg-resources all 20.10.1-1.1 [112 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.13.0-1 [68.7 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-2+rpi1 [215 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-2 [219 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf fastaq all 3.12.1-1 [46.0 kB]
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Get:105 http://172.17.0.1/private stretch-staging/main armhf kmc armhf 2.3+dfsg-5 [459 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf libssl-dev armhf 1.0.2h-1 [1146 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf mummer armhf 3.23+dfsg-1 [787 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf python3-decorator all 4.0.6-1 [12.8 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf python3-networkx all 1.11-2 [624 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf python3-nose all 1.3.7-2 [132 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf python3-numpy armhf 1:1.11.1~rc1-1 [1598 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf python3-pysam armhf 0.9.0+ds-1 [936 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf python3-setuptools all 20.10.1-1.1 [122 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf smalt armhf 0.7.6-6 [96.6 kB]
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Processing triggers for libc-bin (2.23-4) ...
Setting up libnettle6:armhf (3.2-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.0-1) ...
Setting up libarchive-zip-perl (1.58-1) ...
Setting up libnghttp2-14:armhf (1.13.0-1) ...
Setting up mime-support (3.60) ...
Setting up libpng16-16:armhf (1.6.23-1) ...
Setting up liblcms2-2:armhf (2.7-1) ...
Setting up libpcsclite1:armhf (1.8.18-1) ...
Setting up fonts-dejavu-core (2.36-1) ...
Setting up libblas-common (3.6.1-2) ...
Setting up libgfortran3:armhf (6.1.1-11+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-15) ...
Setting up java-common (0.57) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-15) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up kmc (2.3+dfsg-5) ...
Setting up m4 (1.4.17-5) ...
Setting up gawk (1:4.1.3+dfsg-0.1) ...
Setting up libicu57:armhf (57.1-2) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libnspr4:armhf (2:4.12-2) ...
Setting up ucf (3.0036) ...
Setting up libxml2:armhf (2.9.4+dfsg1-1+b1) ...
Setting up libfreetype6:armhf (2.6.3-3+b1) ...
Setting up libtasn1-6:armhf (4.8-1) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libhogweed4:armhf (3.2-1) ...
Setting up libblas3 (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.7.0-1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up openssl (1.0.2h-1) ...
Setting up libsqlite3-0:armhf (3.13.0-1) ...
Setting up libio-string-perl (1.08-3) ...
Setting up liblocale-gettext-perl (1.07-3) ...
Setting up libbambamc0 (0.0.50-1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up x11-common (1:7.7+16) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up ca-certificates (20160104) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libdata-stag-perl (0.14-2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up libavahi-common-data:armhf (0.6.32-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.022-1) ...
Setting up fontconfig-config (2.11.0-6.5) ...
Setting up libbio-perl-perl (1.6.924-5) ...
Setting up libssl-dev:armhf (1.0.2h-1) ...
Setting up mummer (3.23+dfsg-1) ...
Setting up liblapack3 (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libglib2.0-0:armhf (2.48.1-2) ...
No schema files found: doing nothing.
Setting up libpython3.5-stdlib:armhf (3.5.2-3) ...
Setting up libnss3:armhf (2:3.25-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-1) ...
Setting up smalt (0.7.6-6) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libp11-kit0:armhf (0.23.2-4) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.4) ...
Setting up bioperl (1.6.924-5) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libavahi-common3:armhf (0.6.32-1) ...
Setting up libxcb1:armhf (1.11.1-1.1) ...
Setting up libtool (2.4.6-0.1) ...
Setting up python3.5 (3.5.2-3) ...
Setting up libpython3-stdlib:armhf (3.5.1-4) ...
Setting up libfontconfig1:armhf (2.11.0-6.5) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libgnutls30:armhf (3.5.2-2) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libavahi-client3:armhf (0.6.32-1) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.19) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-1) ...
Setting up libcups2:armhf (2.1.4-4) ...
Setting up libxi6:armhf (2:1.7.6-1) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up libxtst6:armhf (2:1.2.2-1+b1) ...
Setting up libhts1:armhf (1.3.1-2+rpi1) ...
Setting up samtools (1.3.1-2) ...
Setting up openjdk-8-jre-headless:armhf (8u102-b14.1-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up ca-certificates-java (20160321) ...
done.
Setting up python3 (3.5.1-4) ...
Setting up openjdk-8-jdk-headless:armhf (8u102-b14.1-2) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
Setting up python3-numpy (1:1.11.1~rc1-1) ...
Setting up python3-pkg-resources (20.10.1-1.1) ...
Setting up fastaq (3.12.1-1) ...
Setting up dh-strip-nondeterminism (0.022-1) ...
Setting up python3-pysam (0.9.0+ds-1) ...
Setting up python3-nose (1.3.7-2) ...
Setting up python3-setuptools (20.10.1-1.1) ...
Setting up dh-python (2.20160721) ...
Setting up python3-decorator (4.0.6-1) ...
Setting up default-jre-headless (2:1.8-57+b2) ...
Setting up default-jdk-headless (2:1.8-57+b2) ...
Setting up debhelper (9.20160709) ...
Setting up dh-autoreconf (12) ...
Setting up python3-networkx (1.11-2) ...
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-4) ...
Processing triggers for systemd (230-7+b1) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
Adding debian:ACCVRAIZ1.pem
Adding debian:ACEDICOM_Root.pem
Adding debian:AC_Raíz_Certicámara_S.A..pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AddTrust_External_Root.pem
Adding debian:AddTrust_Low-Value_Services_Root.pem
Adding debian:AddTrust_Public_Services_Root.pem
Adding debian:AddTrust_Qualified_Certificates_Root.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:ApplicationCA_-_Japanese_Government.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_CA_1.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig.pem
Adding debian:CA_Disig_Root_R1.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CA_WoSign_ECC_Root.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:CNNIC_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem
Adding debian:Camerfirma_Global_Chambersign_Root.pem
Adding debian:Certification_Authority_of_WoSign_G2.pem
Adding debian:Certigna.pem
Adding debian:Certinomis_-_Autorité_Racine.pem
Adding debian:Certinomis_-_Root_CA.pem
Adding debian:Certplus_Class_2_Primary_CA.pem
Adding debian:Certum_Root_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Chambers_of_Commerce_Root_-_2008.pem
Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem
Adding debian:ComSign_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Comodo_Secure_Services_root.pem
Adding debian:Comodo_Trusted_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DST_ACES_CA_X6.pem
Adding debian:DST_Root_CA_X3.pem
Adding debian:Deutsche_Telekom_Root_CA_2.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem
Adding debian:EC-ACC.pem
Adding debian:EE_Certification_Centre_Root_CA.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Equifax_Secure_CA.pem
Adding debian:Equifax_Secure_Global_eBusiness_CA.pem
Adding debian:Equifax_Secure_eBusiness_CA_1.pem
Adding debian:GeoTrust_Global_CA.pem
Adding debian:GeoTrust_Global_CA_2.pem
Adding debian:GeoTrust_Primary_Certification_Authority.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem
Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem
Adding debian:GeoTrust_Universal_CA.pem
Adding debian:GeoTrust_Universal_CA_2.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:Global_Chambersign_Root_-_2008.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:IGC_A.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Juur-SK.pem
Adding debian:Microsec_e-Szigno_Root_CA.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:NetLock_Business_=Class_B=_Root.pem
Adding debian:NetLock_Express_=Class_C=_Root.pem
Adding debian:NetLock_Notary_=Class_A=_Root.pem
Adding debian:NetLock_Qualified_=Class_QA=_Root.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:PSCProcert.pem
Adding debian:QuoVadis_Root_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:RSA_Security_2048_v3.pem
Adding debian:Root_CA_Generalitat_Valenciana.pem
Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem
Adding debian:S-TRUST_Universal_Root_CA.pem
Adding debian: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_1_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.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem
Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:StartCom_Certification_Authority.pem
Adding debian:StartCom_Certification_Authority_2.pem
Adding debian:StartCom_Certification_Authority_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Platinum_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:Swisscom_Root_CA_1.pem
Adding debian:Swisscom_Root_CA_2.pem
Adding debian:Swisscom_Root_EV_CA_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TC_TrustCenter_Class_3_CA_II.pem
Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Taiwan_GRCA.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Trustis_FPS_Root_CA.pem
Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem
Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:UTN_USERFirst_Email_Root_CA.pem
Adding debian:UTN_USERFirst_Hardware_Root_CA.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem
Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem
Adding debian:VeriSign_Universal_Root_Certification_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem
Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem
Adding debian:Visa_eCommerce_Root.pem
Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem
Adding debian:WoSign.pem
Adding debian:WoSign_China.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:thawte_Primary_Root_CA.pem
Adding debian:thawte_Primary_Root_CA_-_G2.pem
Adding debian:thawte_Primary_Root_CA_-_G3.pem
done.
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bioperl_1.6.924-5 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 ca-certificates-java_20160321 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160709 debianutils_4.8 default-jdk-headless_2:1.8-57+b2 default-jre-headless_2:1.8-57+b2 dh-autoreconf_12 dh-python_2.20160721 dh-strip-nondeterminism_0.022-1 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 fastaq_3.12.1-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fontconfig-config_2.11.0-6.5 fonts-dejavu-core_2.36-1 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gawk_1:4.1.3+dfsg-0.1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 java-common_0.57 klibc-utils_2.0.4-9+rpi1 kmc_2.3+dfsg-5 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.58-1 libasan1_4.9.3-14 libasan3_6.1.1-11+rpi1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libavahi-client3_0.6.32-1 libavahi-common-data_0.6.32-1 libavahi-common3_0.6.32-1 libbambamc0_0.0.50-1 libbio-perl-perl_1.6.924-5 libblas-common_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcups2_2.1.4-4 libcurl3-gnutls_7.50.1-1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libexpat1_2.2.0-1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.022-1 libfontconfig1_2.11.0-6.5 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.48.1-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.2-2 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-1 libhogweed4_3.2-1 libhts1_1.3.1-2+rpi1 libicu57_57.1-2 libidn11_1.33-1 libio-string-perl_1.08-3 libisl15_0.17.1-1 libjpeg62-turbo_1:1.5.0-1 libk5crypto3_1.14.3+dfsg-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-1 libkrb5support0_1.14.3+dfsg-1 liblapack3_3.6.1-2 liblcms2-2_2.7-1 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libnettle6_3.2-1 libnghttp2-14_1.13.0-1 libnspr4_2:4.12-2 libnss3_2:3.25-1 libp11-kit0_0.23.2-4 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-1 libpcsclite1_1.8.18-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libpng16-16_1.6.23-1 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-2 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.2-3 libpython3.5-stdlib_3.5.2-3 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-3 libsmartcols1_2.28-6 libsqlite3-0_3.13.0-1 libss2_1.43.1-1 libssh2-1_1.7.0-1 libssl-dev_1.0.2h-1 libssl1.0.2_1.0.2h-1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-0.1 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb1_1.11.1-1.1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxi6_2:1.7.6-1 libxml2_2.9.4+dfsg1-1+b1 libxrender1_1:0.9.9-2 libxtst6_2:1.2.2-1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-6 multiarch-support_2.23-4 mummer_3.23+dfsg-1 nano_2.6.2-1 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 openjdk-8-jdk-headless_8u102-b14.1-2 openjdk-8-jre-headless_8u102-b14.1-2 openssl_1.0.2h-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 po-debconf_1.0.19 procps_2:3.3.12-2 python3_3.5.1-4 python3-decorator_4.0.6-1 python3-minimal_3.5.1-4 python3-networkx_1.11-2 python3-nose_1.3.7-2 python3-numpy_1:1.11.1~rc1-1 python3-pkg-resources_20.10.1-1.1 python3-pysam_0.9.0+ds-1 python3-setuptools_20.10.1-1.1 python3.5_3.5.2-3 python3.5-minimal_3.5.2-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 smalt_0.7.6-6 startpar_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 ucf_3.0036 udev_230-7+b1 util-linux_2.28-6 x11-common_1:7.7+16 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu May 12 10:02:15 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./iva_1.0.6+ds-1.dsc
dpkg-source: info: extracting iva in iva-1.0.6+ds
dpkg-source: info: unpacking iva_1.0.6+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.6+ds-1.debian.tar.xz
dpkg-source: info: applying add-shebang-line-to-getMummerStats
dpkg-source: info: applying adjust_required_pysam_version.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a1399ae5-c02a-48c3-9722-e64a05c2298d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.6+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build iva-1.0.6+ds
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.6+ds'
rm -rf .pybuild
rm -f iva/gage/*.class
rm -rf /<<BUILDDIR>>/iva-1.0.6+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.6+ds'
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python3 --buildsystem=pybuild
dh_testdir -a -O--buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python3.5 setup.py config
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.6+ds'
chmod a-x /<<BUILDDIR>>/iva-1.0.6+ds/iva/read_trim/adapters.fasta
chmod a+x /<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /<<BUILDDIR>>/iva-1.0.6+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/*.java
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/GetFastaStats.java]]
[parsing completed 592ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/SizeFasta.java]]
[parsing completed 70ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 44ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/Utils.java]]
[parsing completed 198ms]
[parsing started RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 383ms]
[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-1.0.6+ds/iva/gage/GetFastaStats$ContigAt.class]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/StringBuilder.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/io/InputStream.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/GetFastaStats.class]]
[checking SizeFasta]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/SizeFasta.class]]
[checking SplitFastaByLetter]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/SplitFastaByLetter.class]]
[checking Utils]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/CloneNotSupportedException.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Class.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/net/URI.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Process.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Runtime.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/GenericDeclaration.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/AnnotatedElement.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/reflect/Type.class)]]
[loading ZipFileIndexFileObject[/usr/lib/jvm/java-8-openjdk-armhf/lib/ct.sym(META-INF/sym/rt.jar/java/lang/AssertionError.class)]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/Utils$Pair.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/Utils$Translate.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/Utils$ToProtein.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/Utils.class]]
[checking getScaffoldStats]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/getScaffoldStats$Scaffold.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/getScaffoldStats$1.class]]
[wrote RegularFileObject[/<<BUILDDIR>>/iva-1.0.6+ds/iva/gage/getScaffoldStats.class]]
[total 28921ms]
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-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva
creating /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats$1.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.6+ds/.pybuild/pythonX.Y_3.5/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.5
copying and adjusting scripts/iva -> build/scripts-3.5
copying and adjusting scripts/iva_qc -> build/scripts-3.5
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.5
changing mode of build/scripts-3.5/iva from 664 to 775
changing mode of build/scripts-3.5/iva_qc from 664 to 775
changing mode of build/scripts-3.5/iva_qc_make_db from 664 to 775
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.6+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.6+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 dependency_links to iva.egg-info/dependency_links.txt
writing top-level names to iva.egg-info/top_level.txt
writing requirements to iva.egg-info/requires.txt
writing iva.egg-info/PKG-INFO
writing manifest file 'iva.egg-info/SOURCES.txt'
reading manifest file 'iva.egg-info/SOURCES.txt'
writing manifest file 'iva.egg-info/SOURCES.txt'
running build_ext
test_add_new_seed_contig (assembly_test.TestAssembly)
Test add_new_seed_contig ... ok
test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly)
Test _contig_contained_in_nucmer_hits ... ok
test_contig_names_size_order (assembly_test.TestAssembly)
Test _contig_names_size_order ... ok
test_contig_worth_extending (assembly_test.TestAssembly)
Test _contig_worth_extending ... ok
test_coords_to_new_contig (assembly_test.TestAssembly)
Test _coords_to_new_contig ... ok
test_extend_contigs_with_bam (assembly_test.TestAssembly)
test _extend_contigs_with_bam ... ok
test_get_contig_order_by_orfs (assembly_test.TestAssembly)
Test get_contig_order_by_orfs ... ok
test_get_ref_length (assembly_test.TestAssembly)
Test _get_ref_length ... ok
test_get_ref_length_sam_pair (assembly_test.TestAssembly)
Test _get_ref_length_sam_pair ... ok
test_get_unmapped_pairs (assembly_test.TestAssembly)
Test _get_unmapped_pairs ... ok
test_good_intervals_from_strand_coverage (assembly_test.TestAssembly)
Test good_intervals_from_strand_coverage ... ok
test_init_and_write (assembly_test.TestAssembly)
test assembly initialise and write to file ... ok
test_map_reads (assembly_test.TestAssembly)
test _map_reads ... ok
test_merge_overlapping_contigs (assembly_test.TestAssembly)
Test _merge_overlapping_contigs ... ok
test_read_pair_extend (assembly_test.TestAssembly)
Test read_pair_extend ... ok
test_remove_contained_contigs (assembly_test.TestAssembly)
Test _remove_contained_contigs ... ok
test_remove_contig (assembly_test.TestAssembly)
Test _remove_contig ... ok
test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly)
Test _remove_contig_from_nucmer_hits ... ok
test_subcontigs_from_strand_bias (assembly_test.TestAssembly)
Test _subcontigs_from_strand_bias ... ok
test_trim_contig_for_strand_bias (assembly_test.TestAssembly)
Test _trim_contig_for_strand_bias ... ok
test_trim_contigs (assembly_test.TestAssembly)
Test trim_contigs ... ok
test_trim_strand_biased_ends (assembly_test.TestAssembly)
Test _trim_strand_biased_ends ... ok
test_worth_extending (assembly_test.TestAssembly)
Test worth_extending ... ok
test_add_left_kmer (contig_test.TestContig)
Test add_left_kmer ... ok
test_add_right_kmer (contig_test.TestContig)
Test add_right_kmer ... ok
test_extend (contig_test.TestContig)
Test extend ... ok
test_init (contig_test.TestContig)
Test init ... ok
test_len (contig_test.TestContig)
Test len ... ok
test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim)
Test _coverage_to_trimmed_coords ... ok
test_trim_ends (contig_trim_test.TestContigTrim)
Test _trim_ends ... ok
test_trim_primers_and_adapters (contig_trim_test.TestContigTrim)
Test trim_primers_and_adapters ... ok
test_change_hit_coords_with_intersection (edge_test.TestEdge)
test test_change_hit_coords_with_intersection ... ok
test_make_contig_first (edge_test.TestEdge)
test make_contig_first ... ok
test_make_contig_forwards (edge_test.TestEdge)
test make_contig_forwards ... ok
test_merge_into (edge_test.TestEdge)
test merge_into ... ok
test_open_end (edge_test.TestEdge)
test open_end ... ok
test_reverse (edge_test.TestEdge)
test reverse ... ok
test_copy_dir (egg_extract_test.TestEggExtract)
test copy_dir ... ok
test_copy_dir_unzipped (egg_extract_test.TestEggExtract)
test copy_dir_unzipped ... ok
test_copy_dir_zipped (egg_extract_test.TestEggExtract)
test copy_dir_zipped ... ok
test_copy_file (egg_extract_test.TestEggExtract)
test copy_file ... ok
test_copy_file_unzipped (egg_extract_test.TestEggExtract)
test _copy_file_unzipped ... ok
test_copy_file_zipped (egg_extract_test.TestEggExtract)
test _copy_file_zipped ... ok
test_init_and_write (egg_extract_test.TestEggExtract)
test __init__ ... ok
test_delta_filter_in_path (external_progs_test.TestExternalProgs)
Test delta-filter in path ... ok
test_kmc_dump_in_path (external_progs_test.TestExternalProgs)
Test kmc_dump in path ... ok
test_kmc_in_path (external_progs_test.TestExternalProgs)
Test kmc in path ... ok
test_nucmer_in_path (external_progs_test.TestExternalProgs)
Test nucmer in path ... ok
test_samtools_in_path (external_progs_test.TestExternalProgs)
Test samtools in path ... ok
test_show_coords_in_path (external_progs_test.TestExternalProgs)
Test show-coords in path ... ok
test_smalt_in_path (external_progs_test.TestExternalProgs)
Test smalt in path ... ok
test_add_and_get_edges (graph_test.TestGraph)
test adding and getting edges ... ok
test_connected_components (graph_test.TestGraph)
test connected_components ... ok
test_degree (graph_test.TestGraph)
test degree ... ok
test_edges_are_consistent (graph_test.TestGraph)
test edges_are_consistent ... ok
test_find_simple_path (graph_test.TestGraph)
test find_simple_path ... ok
test_get_nodes (graph_test.TestGraph)
test get_nodes ... ok
test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph)
test merged_coords_from_simple_nonredundant_path ... ok
test_node_to_coords (graph_test.TestGraph)
test _node_to_coords ... ok
test_remove_middle_node (graph_test.TestGraph)
test remove_middle_node ... ok
test_remove_node (graph_test.TestGraph)
test remove_node ... ok
test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph)
test remove_redundant_nodes_from_simple_path ... ok
test_simple_path_is_consistent (graph_test.TestGraph)
test simple_path_is_consistent ... ok
test_counts_file_to_fasta (kcount_test.TestKcount)
Test _counts_file_to_fasta ... ok
test_get_most_common_kmers (kcount_test.TestKcount)
Test get_most_common_kmers ... ok
test_head_fastaq_fa (kcount_test.TestKcount)
Test head_fastaq with FASTA input ... ok
test_head_fastaq_fq (kcount_test.TestKcount)
Test head_fastaq with FASTQ input ... ok
test_kmc_to_kmer_counts (kcount_test.TestKcount)
Test _kmc_to_kmer_counts ... ok
test_median (kcount_test.TestKcount)
Test _median() ... ok
test_run_kmc (kcount_test.TestKcount)
Test test_run_kmc ... ok
test_run_kmc_two_threads (kcount_test.TestKcount)
Test test_run_kmc with two threads ... ok
test_append (kmers_test.TestKmers)
Test append ... ok
test_commonest_kmers (kmers_test.TestKmers) ... ok
test_extend (kmers_test.TestKmers)
Test extend ... ok
test_extension (kmers_test.TestKmers)
Test extension ... ok
test_init (kmers_test.TestKmers)
Test __init__ ... ok
test_kmer_dict (kmers_test.TestKmers)
Test kmer_dict ... ok
test_append_to_file (kraken_test.TestKraken)
test _append_to_file ... ok
test_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_process_seeds (seed_processor_test.TestSeedProcessor)
Test process_seeds ... 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: 16765 Aborted kmc -fa -m4 -k60 -sf1 -ci10 -cs100000000 -cx100000000 /<<BUILDDIR>>/iva-1.0.6+ds/tmp.common_kmers.aq8vzh1a/reads.fa kmc_out $PWD
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: 16772 Aborted kmc -fa -m4 -k60 -sf1 -ci10 -cs100000000 -cx100000000 /<<BUILDDIR>>/iva-1.0.6+ds/tmp.common_kmers.rd4ohm69/reads.fa kmc_out $PWD
E: Caught signal ‘Terminated’: terminating immediately
debian/rules:13: recipe for target 'build-arch' failed
make: *** [build-arch] Terminated
debian/rules:43: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Terminated
Build killed with signal TERM after 1500 minutes of inactivity
--------------------------------------------------------------------------------
Build finished at 20160818-0639
Finished
--------
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 20240
Build-Time: 90083
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 663
Job: iva_1.0.6+ds-1
Machine Architecture: armhf
Package: iva
Package-Time: 90818
Source-Version: 1.0.6+ds-1
Space: 20240
Status: attempted
Version: 1.0.6+ds-1
--------------------------------------------------------------------------------
Finished at 20160818-0639
Build needed 25:13:38, 20240k disc space