iva →
1.0.11+ds-2 →
armhf → 2022-10-14 05:25:17
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| iva 1.0.11+ds-2 (armhf) Fri, 14 Oct 2022 05:16:09 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.11+ds-2
Source Version: 1.0.11+ds-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-09ba38df-29ec-4721-813a-966208471458' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 11s (2584 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'iva' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/iva.git
Please use:
git clone https://salsa.debian.org/med-team/iva.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8689 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main iva 1.0.11+ds-2 (dsc) [2261 B]
Get:2 http://172.17.4.1/private bookworm-staging/main iva 1.0.11+ds-2 (tar) [8681 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main iva 1.0.11+ds-2 (diff) [5828 B]
Fetched 8689 kB in 1s (8290 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-o3qPIU/iva-1.0.11+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-o3qPIU' 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-dUSjUE/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-dUSjUE/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-dUSjUE/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (4287 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:
krb5-locales libpam-cap netbase sensible-utils
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 28 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-dUSjUE/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 (61.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12808 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq, kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
Filtered Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq, kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless
dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<<BUILDDIR>>/resolver-dUSjUE/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-dUSjUE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Sources [603 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ Packages [686 B]
Fetched 2622 B in 0s (8479 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:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdextrautils bsdutils
ca-certificates ca-certificates-java debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz
fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base
groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl
libarchive-zip-perl libasound2 libasound2-data libavahi-client3
libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3
libblkid1 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl
libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl
libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl
libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2
libicu71 libio-string-perl libjpeg62-turbo liblapack3 liblcms2-2
liblocale-gettext-perl libmagic-mgc libmagic1 libmount1 libmpdec3
libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1
libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsigsegv2 libsmartcols1 libssh2-1 libssl-dev
libsub-override-perl libsub-uplevel-perl libtest-deep-perl
libtest-differences-perl libtest-exception-perl libtest-most-perl
libtest-warn-perl libtext-diff-perl libtool libuchardet0 libuuid1 libxml2 m4
man-db media-types mount mummer openjdk-11-jdk-headless
openjdk-11-jre-headless openssl po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy
python3-packaging python3-pkg-resources python3-pyparsing python3-pysam
python3-setuptools python3.10 python3.10-minimal samtools smalt ucf
util-linux util-linux-extra
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make default-jre flit
python3-build python3-tomli python3-installer gawk-doc gettext-doc
libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils
libxml-sax-expatxs-perl cups-common liblcms2-utils cryptsetup-bin pcscd
libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
less www-browser nfs-common openjdk-11-demo openjdk-11-source libnss-mdns
fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl
python3-doc python3-tk python3-venv python-networkx-doc python-nose-doc
gfortran python-numpy-doc python3-dev python3-pytest python-pyparsing-doc
python-setuptools-doc python3.10-venv python3.10-doc binfmt-support cwltool
dosfstools kbd util-linux-locales
Recommended packages:
bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl
libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl
liburi-perl libxml-simple-perl libyaml-perl libace-perl
liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget
| lynx libalgorithm-diff-xs-perl alsa-ucm-conf alsa-topology-conf
bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl
libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl
libsort-naturally-perl libspreadsheet-parseexcel-perl
libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl
libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl
libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk
libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl
libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 publicsuffix libltdl-dev uuid-runtime
libmail-sendmail-perl python3-gdal python3-matplotlib python3-pydot
python3-pygraphviz python3-scipy python3-yaml
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bioperl bsdextrautils
ca-certificates ca-certificates-java debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz
fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base
groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl
libarchive-zip-perl libasound2 libasound2-data libavahi-client3
libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3
libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcups2
libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0
libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5
libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libicu71
libio-string-perl libjpeg62-turbo liblapack3 liblcms2-2
liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncurses6
libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libpsl5
libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libsub-override-perl libsub-uplevel-perl
libtest-deep-perl libtest-differences-perl libtest-exception-perl
libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0
libxml2 m4 man-db media-types mummer openjdk-11-jdk-headless
openjdk-11-jre-headless openssl po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy
python3-packaging python3-pkg-resources python3-pyparsing python3-pysam
python3-setuptools python3.10 python3.10-minimal samtools
sbuild-build-depends-iva-dummy smalt ucf
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
util-linux-extra
8 upgraded, 120 newly installed, 0 to remove and 20 not upgraded.
Need to get 260 MB of archives.
After this operation, 531 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dUSjUE/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-1.1 [82.5 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-1.1 [90.6 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-1.1 [97.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-1.1 [1063 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf liblocale-gettext-perl armhf 1.07-4+b2 [18.3 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-1.1 [125 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf gawk armhf 1:5.1.0-1 [533 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.7-1 [813 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.7-1 [1518 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-1.1 [25.9 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.7-1 [1598 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.7-1 [547 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-1.1 [130 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-1.1 [142 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-3 [1364 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.5-2 [1372 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libio-string-perl all 1.08-3.1 [11.8 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libdata-stag-perl all 0.14-3 [448 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libexception-class-perl all 1.45-1 [34.6 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libtest-deep-perl all 1.130-2 [49.4 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libtest-differences-perl all 0.69-1 [18.9 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libsub-uplevel-perl all 0.2800-2 [16.6 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libtest-exception-perl all 0.43-2 [19.1 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libtest-warn-perl all 0.37-1 [16.5 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libtest-most-perl all 0.38-1 [25.1 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf bioperl all 1.7.8-1 [246 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates-java all 20220719 [16.1 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10 [79.8 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10 [940 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf java-common all 0.72 [14.5 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-6+b1 [124 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-6+b1 [55.8 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.14.4-1 [211 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-6+b1 [58.5 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.4.2-1+b1 [311 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libnspr4 armhf 2:4.35-1 [90.9 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libnss3 armhf 2:3.83-1 [1106 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libasound2-data all 1.2.7.2-1 [39.1 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libasound2 armhf 1.2.7.2-1 [322 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.0-2 [1265 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2 [1835 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libpcsclite1 armhf 1.9.9-1 [58.1 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf openjdk-11-jre-headless armhf 11.0.16+8-1 [32.9 MB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf default-jre-headless armhf 2:1.11-72+b4 [11.2 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf openjdk-11-jdk-headless armhf 11.0.16+8-1 [173 MB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf default-jdk-headless armhf 2:1.11-72+b4 [1100 B]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.7-1 [79.9 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.7-1 [141 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 59.6.0-1.2 [196 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.85.0-1 [320 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-2 [371 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf fastaq all 3.17.0-5 [48.2 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf help2man armhf 1.49.2 [202 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf kmc armhf 3.2.1+dfsg-1 [776 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libbambamc0 armhf 0.0.50-6 [31.0 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-3+rpi1 [238 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.5-2 [2116 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf mummer armhf 3.23+dfsg-7 [618 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf python3-networkx all 2.6.3-1 [943 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf python3-nose all 1.3.7-8 [133 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.21.5-1+b2 [3423 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.7-2 [140 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf python3-pysam armhf 0.17.0+ds-2+b1 [1834 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 59.6.0-1.2 [401 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf smalt armhf 0.7.6-12 [94.0 kB]
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
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Setting up libhtscodecs2:armhf (1.3.0-4) ...
Setting up media-types (8.0.0) ...
Setting up libpipeline1:armhf (1.5.6-3) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.13.1-1) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.38.1-1.1) ...
Setting up java-common (0.72) ...
Setting up libtest-deep-perl (1.130-2) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up gawk (1:5.1.0-1) ...
Setting up libalgorithm-diff-perl (1.201-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.74.0-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.10) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up libnghttp2-14:armhf (1.50.0-1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libdeflate0:armhf (1.14-1) ...
Setting up gettext-base (0.21-9) ...
Setting up m4 (1.4.19-1) ...
Setting up file (1:5.41-4) ...
Setting up libasound2-data (1.2.7.2-1) ...
Setting up libio-string-perl (1.08-3.1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up libnspr4:armhf (2:4.35-1) ...
Setting up libtext-diff-perl (1.45-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libavahi-common-data:armhf (0.8-6+b1) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up libdbus-1-3:armhf (1.14.4-1) ...
Setting up libbambamc0:armhf (0.0.50-6) ...
Setting up libssl-dev:armhf (3.0.5-2) ...
Setting up libpng16-16:armhf (1.6.38-2) ...
Setting up autopoint (0.21-9) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libpcsclite1:armhf (1.9.9-1) ...
Setting up ucf (3.0043) ...
Setting up libgfortran5:armhf (12.2.0-3+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up mount (2.38.1-1.1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libasound2:armhf (1.2.7.2-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up mummer (3.23+dfsg-7) ...
Setting up libsub-uplevel-perl (0.2800-2) ...
Setting up libsub-override-perl (0.09-3) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up libdevel-stacktrace-perl (2.0400-1) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up openssl (3.0.5-2) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up kmc (3.2.1+dfsg-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up liblocale-gettext-perl (1.07-4+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up smalt (0.7.6-12) ...
Setting up liblapack3:armhf (3.10.1-2) ...
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 gettext (0.21-9) ...
Setting up libtool (2.4.7-4) ...
Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libtest-warn-perl (0.37-1) ...
Setting up libavahi-common3:armhf (0.8-6+b1) ...
Setting up libtest-differences-perl (0.69-1) ...
Setting up libcurl3-gnutls:armhf (7.85.0-1) ...
Setting up libnss3:armhf (2:3.83-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up help2man (1.49.2) ...
Setting up libpython3.10-stdlib:armhf (3.10.7-1) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libtest-exception-perl (0.43-2) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-8) ...
Setting up libharfbuzz0b:armhf (5.2.0-2) ...
Setting up ca-certificates-java (20220719) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:Cybertrust_Global_Root.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian: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: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:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R2.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.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:Hongkong_Post_Root_CA_3.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:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:Network_Solutions_Certificate_Authority.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
done.
Setting up libavahi-client3:armhf (0.8-6+b1) ...
Setting up libpython3-stdlib:armhf (3.10.6-1) ...
Setting up libhts3:armhf (1.16+ds-2) ...
Setting up python3.10 (3.10.7-1) ...
Setting up libtest-most-perl (0.38-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.10.6-1) ...
Setting up man-db (2.10.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.16.1-1) ...
Setting up python3-pyparsing (3.0.7-2) ...
Setting up libcups2:armhf (2.4.2-1+b1) ...
Setting up python3-lib2to3 (3.10.7-1) ...
Setting up python3-pkg-resources (59.6.0-1.2) ...
Setting up python3-distutils (3.10.7-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up bioperl (1.7.8-1) ...
Setting up python3-pysam (0.17.0+ds-2+b1) ...
Setting up python3-setuptools (59.6.0-1.2) ...
Setting up fastaq (3.17.0-5) ...
Setting up debhelper (13.10) ...
Setting up python3-networkx (2.6.3-1) ...
Setting up python3-nose (1.3.7-8) ...
Setting up python3-packaging (21.3-1.1) ...
Setting up python3-numpy (1:1.21.5-1+b2) ...
Processing triggers for sgml-base (1.30) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Processing triggers for libc-bin (2.35-1+rpi2) ...
Setting up openjdk-11-jre-headless:armhf (11.0.16+8-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up openjdk-11-jdk-headless:armhf (11.0.16+8-1) ...
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.11-72+b4) ...
Setting up default-jdk-headless (2:1.11-72+b4) ...
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20220719) ...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-1+rpi2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bioperl_1.7.8-1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 ca-certificates-java_20220719 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10 debianutils_5.7-0.3 default-jdk-headless_2:1.11-72+b4 default-jre-headless_2:1.11-72+b4 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 fastaq_3.17.0-5 file_1:5.41-4 findutils_4.9.0-3 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gawk_1:5.1.0-1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 java-common_0.72 kmc_3.2.1+dfsg-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libasound2_1.2.7.2-1 libasound2-data_1.2.7.2-1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libavahi-client3_0.8-6+b1 libavahi-common-data_0.8-6+b1 libavahi-common3_0.8-6+b1 libbambamc0_0.0.50-6 libbinutils_2.39-6+rpi1 libbio-perl-perl_1.7.8-1 libblas3_3.10.1-2 libblkid1_2.38.1-1.1 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-1+rpi2 libc-dev-bin_2.35-1+rpi2 libc6_2.35-1+rpi2 libc6-dev_2.35-1+rpi2 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcapture-tiny-perl_0.48-1 libcc1-0_12.2.0-3+rpi1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcups2_2.4.2-1+b1 libcurl3-gnutls_7.85.0-1 libdata-stag-perl_0.14-3 libdb5.3_5.3.28+dfsg1-0.10 libdbus-1-3_1.14.4-1 libdebconfclient0_0.264 libdebhelper-perl_13.10 libdeflate0_1.14-1 libdevel-stacktrace-perl_2.0400-1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexception-class-perl_1.45-1 libexpat1_2.4.9-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-2 libgdbm6_1.23-2 libgfortran5_12.2.0-3+rpi1 libglib2.0-0_2.74.0-2 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libharfbuzz0b_5.2.0-2 libhogweed6_3.8.1-2 libhts3_1.16+ds-2 libhtscodecs2_1.3.0-4 libicu71_71.1-3 libidn2-0_2.3.3-1 libio-string-perl_1.08-3.1 libisl23_0.25-1 libjpeg62-turbo_1:2.1.2-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack3_3.10.1-2 liblcms2-2_2.13.1-1 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblocale-gettext-perl_1.07-4+b2 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnspr4_2:4.35-1 libnss3_2:3.83-1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libpcsclite1_1.9.9-1 libperl5.34_5.34.0-5 libpipeline1_1.5.6-3 libpng16-16_1.6.38-2 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.7-1 libpython3.10-stdlib_3.10.7-1 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsigsegv2_2.14-1 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.5-2 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-3 libsub-uplevel-perl_0.2800-2 libsystemd0_251.4-3+rpi1 libtasn1-6_4.19.0-2 libtest-deep-perl_1.130-2 libtest-differences-perl_0.69-1 libtest-exception-perl_0.43-2 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-1 libtext-diff-perl_1.45-1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.4-3+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1.1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-3 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1.1 mummer_3.23+dfsg-7 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 openjdk-11-jdk-headless_11.0.16+8-1 openjdk-11-jre-headless_11.0.16+8-1 openssl_3.0.5-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-distutils_3.10.7-1 python3-lib2to3_3.10.7-1 python3-minimal_3.10.6-1 python3-networkx_2.6.3-1 python3-nose_1.3.7-8 python3-numpy_1:1.21.5-1+b2 python3-packaging_21.3-1.1 python3-pkg-resources_59.6.0-1.2 python3-pyparsing_3.0.7-2 python3-pysam_0.17.0+ds-2+b1 python3-setuptools_59.6.0-1.2 python3.10_3.10.7-1 python3.10-minimal_3.10.7-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 samtools_1.16.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 smalt_0.7.6-12 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.LnHrzA7f/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct 8 17:02:29 2022 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./iva_1.0.11+ds-2.dsc
dpkg-source: info: extracting iva in /<<BUILDDIR>>/iva-1.0.11+ds
dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.11+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-multithreaded-test.patch
dpkg-source: info: applying perl-shebang.patch
dpkg-source: info: applying samtools1.10
dpkg-source: info: applying disable-ram-test.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-09ba38df-29ec-4721-813a-966208471458
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.11+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.11+ds'
rm -rf .pybuild
rm -f iva/gage/*.class
rm -rf /<<BUILDDIR>>/iva-1.0.11+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.11+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:240: python3.10 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-1.0.11+ds'
chmod a-x /<<BUILDDIR>>/iva-1.0.11+ds/iva/read_trim/adapters.fasta
chmod a+x /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /<<BUILDDIR>>/iva-1.0.11+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/*.java
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/GetFastaStats.java]]
[parsing completed 154ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SizeFasta.java]]
[parsing completed 12ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 8ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils.java]]
[parsing completed 44ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 115ms]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/java.compiler/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/jdk.pack/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/jdk.rmic/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/java.management/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/java.desktop/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.scripting.nashorn.shell/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/java.base/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/jdk.scripting.nashorn/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.naming.ldap/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[search path for source files: .]
[search path for class files: /usr/lib/jvm/java-11-openjdk-armhf/lib/modules,.]
[loading /modules/java.base/java/io/BufferedReader.class]
[loading /modules/java.base/java/io/FileInputStream.class]
[loading /modules/java.base/java/io/InputStreamReader.class]
[loading /modules/java.base/java/text/DecimalFormat.class]
[loading /modules/java.base/java/text/NumberFormat.class]
[loading /modules/java.base/java/util/ArrayList.class]
[loading /modules/java.base/java/util/Arrays.class]
[loading /modules/java.base/java/util/HashMap.class]
[loading /modules/java.base/java/lang/Object.class]
[loading /modules/java.base/java/lang/String.class]
[loading /modules/java.base/java/lang/Integer.class]
[loading /modules/java.base/java/lang/Exception.class]
[loading /modules/java.base/java/lang/StringBuffer.class]
[loading /modules/java.management/java/lang/management/ManagementFactory.class]
[loading /modules/java.management/java/lang/management/MemoryMXBean.class]
[loading /modules/java.base/java/io/File.class]
[loading /modules/java.base/java/io/FileReader.class]
[loading /modules/java.base/java/lang/Boolean.class]
[loading /modules/java.base/java/lang/Enum.class]
[loading /modules/java.base/java/lang/Comparable.class]
[loading /modules/java.base/java/io/Serializable.class]
[loading /modules/java.base/java/util/Collections.class]
[loading /modules/java.base/java/lang/Deprecated.class]
[loading /modules/java.base/java/lang/annotation/Retention.class]
[loading /modules/java.base/java/lang/annotation/RetentionPolicy.class]
[loading /modules/java.base/java/lang/annotation/Target.class]
[loading /modules/java.base/java/lang/annotation/ElementType.class]
[checking GetFastaStats]
[loading /modules/java.base/java/lang/AutoCloseable.class]
[loading /modules/java.base/java/util/Map.class]
[loading /modules/java.base/java/lang/Throwable.class]
[loading /modules/java.base/java/lang/CharSequence.class]
[loading /modules/java.base/java/io/Reader.class]
[loading /modules/java.base/java/lang/Readable.class]
[loading /modules/java.base/java/io/Closeable.class]
[loading /modules/java.base/java/lang/Number.class]
[loading /modules/java.base/java/lang/Cloneable.class]
[loading /modules/java.base/java/util/AbstractMap.class]
[loading /modules/java.base/java/lang/AbstractStringBuilder.class]
[loading /modules/java.base/java/lang/Appendable.class]
[loading /modules/java.base/java/lang/Byte.class]
[loading /modules/java.base/java/lang/Character.class]
[loading /modules/java.base/java/lang/Short.class]
[loading /modules/java.base/java/lang/Long.class]
[loading /modules/java.base/java/lang/Float.class]
[loading /modules/java.base/java/lang/Double.class]
[loading /modules/java.base/java/lang/Void.class]
[loading /modules/java.base/java/io/FileDescriptor.class]
[loading /modules/java.base/java/lang/System.class]
[loading /modules/java.base/java/io/PrintStream.class]
[loading /modules/java.base/java/io/FilterOutputStream.class]
[loading /modules/java.base/java/io/OutputStream.class]
[loading /modules/java.base/java/io/Flushable.class]
[loading /modules/java.base/java/util/Set.class]
[loading /modules/java.base/java/lang/Iterable.class]
[loading /modules/java.base/java/util/Collection.class]
[loading /modules/java.base/java/lang/Math.class]
[loading /modules/java.base/java/util/List.class]
[loading /modules/java.base/java/util/RandomAccess.class]
[loading /modules/java.base/java/util/AbstractList.class]
[loading /modules/java.base/java/util/AbstractCollection.class]
[loading /modules/java.base/java/util/function/IntFunction.class]
[loading /modules/java.base/java/util/Comparator.class]
[loading /modules/java.base/java/text/Format.class]
[loading /modules/java.base/java/lang/Error.class]
[loading /modules/java.base/java/lang/RuntimeException.class]
[loading /modules/java.base/java/io/IOException.class]
[loading /modules/java.base/java/lang/NumberFormatException.class]
[loading /modules/java.base/java/lang/IllegalArgumentException.class]
[loading /modules/java.base/java/io/FileNotFoundException.class]
[loading /modules/java.base/java/util/Iterator.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/GetFastaStats$ContigAt.class]
[loading /modules/java.base/java/lang/invoke/StringConcatFactory.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class]
[loading /modules/java.base/java/lang/invoke/MethodType.class]
[loading /modules/java.base/java/io/InputStream.class]
[loading /modules/java.base/java/lang/invoke/CallSite.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/GetFastaStats.class]
[checking SizeFasta]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SizeFasta.class]
[checking SplitFastaByLetter]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.class]
[checking Utils]
[loading /modules/java.base/java/lang/CloneNotSupportedException.class]
[loading /modules/java.base/java/lang/Class.class]
[loading /modules/java.base/java/net/URI.class]
[loading /modules/java.base/java/lang/Process.class]
[loading /modules/java.base/java/lang/Runtime.class]
[loading /modules/java.base/java/lang/StringBuilder.class]
[loading /modules/java.base/java/lang/reflect/GenericDeclaration.class]
[loading /modules/java.base/java/lang/reflect/AnnotatedElement.class]
[loading /modules/java.base/java/lang/reflect/Type.class]
[loading /modules/java.base/java/lang/AssertionError.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils$Pair.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils$Translate.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils$ToProtein.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils.class]
[checking getScaffoldStats]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class]
[wrote /<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getScaffoldStats.class]
[total 4286ms]
dh_auto_build --
I: pybuild base:240: /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-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.10
copying and adjusting scripts/iva -> build/scripts-3.10
copying and adjusting scripts/iva_qc -> build/scripts-3.10
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.10
changing mode of build/scripts-3.10/iva from 644 to 755
changing mode of build/scripts-3.10/iva_qc from 644 to 755
changing mode of build/scripts-3.10/iva_qc_make_db from 644 to 755
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.11+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.11+ds'
python3 setup.py test
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
running egg_info
creating iva.egg-info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
writing manifest file 'iva.egg-info/SOURCES.txt'
reading manifest file 'iva.egg-info/SOURCES.txt'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'iva.egg-info/SOURCES.txt'
running build_ext
/<<BUILDDIR>>/iva-1.0.11+ds/iva/mapping.py:161: DeprecationWarning: invalid escape sequence '\^'
s = re.sub('\^.', '', s)
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence '\('
'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence '\('
'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence '\('
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence '\('
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence '\d'
'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
/<<BUILDDIR>>/iva-1.0.11+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence '\.'
self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
/<<BUILDDIR>>/iva-1.0.11+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence '\W'
return re.sub('\W', '_', s).strip('_')
test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly)
Test _contig_contained_in_nucmer_hits ... ok
test_contig_names_size_order (assembly_test.TestAssembly)
Test _contig_names_size_order ... ok
test_contig_worth_extending (assembly_test.TestAssembly)
Test _contig_worth_extending ... ok
test_coords_to_new_contig (assembly_test.TestAssembly)
Test _coords_to_new_contig ... ok
test_extend_contigs_with_bam (assembly_test.TestAssembly)
test _extend_contigs_with_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_get_contig_order_by_orfs (assembly_test.TestAssembly)
Test get_contig_order_by_orfs ... ok
test_get_ref_length (assembly_test.TestAssembly)
Test _get_ref_length ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/assembly_test.mapped.bam'
ok
test_get_ref_length_sam_pair (assembly_test.TestAssembly)
Test _get_ref_length_sam_pair ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/assembly_test.mapped.bam'
ok
test_get_unmapped_pairs (assembly_test.TestAssembly)
Test _get_unmapped_pairs ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.bam'
ok
test_good_intervals_from_strand_coverage (assembly_test.TestAssembly)
Test good_intervals_from_strand_coverage ... ok
test_init_and_write (assembly_test.TestAssembly)
test assembly initialise and write to file ... ok
test_map_reads (assembly_test.TestAssembly)
test _map_reads ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/assembly_test.mapped.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.assembly_test.out.bam'
ok
test_merge_overlapping_contigs (assembly_test.TestAssembly)
Test _merge_overlapping_contigs ... ok
test_read_pair_extend (assembly_test.TestAssembly)
Test read_pair_extend ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.4.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.5.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.4.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.5.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/tmp.filter_reads.owwhc_8_/out.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/tmp.trim_strand_biased_ends.knh1ej64/out.unsorted.bam'
ok
test_remove_contained_contigs (assembly_test.TestAssembly)
Test _remove_contained_contigs ... ok
test_remove_contig (assembly_test.TestAssembly)
Test _remove_contig ... ok
test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly)
Test _remove_contig_from_nucmer_hits ... ok
test_subcontigs_from_strand_bias (assembly_test.TestAssembly)
Test _subcontigs_from_strand_bias ... ok
test_trim_contig_for_strand_bias (assembly_test.TestAssembly)
Test _trim_contig_for_strand_bias ... ok
test_trim_contigs (assembly_test.TestAssembly)
Test trim_contigs ... ok
test_trim_strand_biased_ends (assembly_test.TestAssembly)
Test _trim_strand_biased_ends ... ok
test_worth_extending (assembly_test.TestAssembly)
Test worth_extending ... ok
test_add_left_kmer (contig_test.TestContig)
Test add_left_kmer ... ok
test_add_right_kmer (contig_test.TestContig)
Test add_right_kmer ... ok
test_extend (contig_test.TestContig)
Test extend ... ok
test_init (contig_test.TestContig)
Test init ... ok
test_len (contig_test.TestContig)
Test len ... ok
test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim)
Test _coverage_to_trimmed_coords ... ok
test_trim_ends (contig_trim_test.TestContigTrim)
Test _trim_ends ... ok
test_trim_primers_and_adapters (contig_trim_test.TestContigTrim)
Test trim_primers_and_adapters ... ok
test_change_hit_coords_with_intersection (edge_test.TestEdge)
test test_change_hit_coords_with_intersection ... ok
test_make_contig_first (edge_test.TestEdge)
test make_contig_first ... ok
test_make_contig_forwards (edge_test.TestEdge)
test make_contig_forwards ... ok
test_merge_into (edge_test.TestEdge)
test merge_into ... ok
test_open_end (edge_test.TestEdge)
test open_end ... ok
test_reverse (edge_test.TestEdge)
test reverse ... ok
test_copy_dir (egg_extract_test.TestEggExtract)
test copy_dir ... ok
test_copy_dir_unzipped (egg_extract_test.TestEggExtract)
test copy_dir_unzipped ... ok
test_copy_dir_zipped (egg_extract_test.TestEggExtract)
test copy_dir_zipped ... ok
test_copy_file (egg_extract_test.TestEggExtract)
test copy_file ... ok
test_copy_file_unzipped (egg_extract_test.TestEggExtract)
test _copy_file_unzipped ... ok
test_copy_file_zipped (egg_extract_test.TestEggExtract)
test _copy_file_zipped ... ok
test_init_and_write (egg_extract_test.TestEggExtract)
test __init__ ... ok
test_blastn_version (external_progs_test.TestExternalProgs)
Test blastn version ... ok
test_delta_filter_in_path (external_progs_test.TestExternalProgs)
Test delta-filter in path ... ok
test_kmc_dump_in_path (external_progs_test.TestExternalProgs)
Test kmc_dump in path ... ok
test_kmc_dump_version (external_progs_test.TestExternalProgs)
Test kmc_dump version ... ok
test_kmc_in_path (external_progs_test.TestExternalProgs)
Test kmc in path ... ok
test_kmc_version (external_progs_test.TestExternalProgs)
Test kmc version ... ok
test_makeblastdb_version (external_progs_test.TestExternalProgs)
Test makeblastdb version ... ok
test_nucmer_in_path (external_progs_test.TestExternalProgs)
Test nucmer in path ... ok
test_nucmer_version (external_progs_test.TestExternalProgs)
Test nucmer version ... ok
test_r_version (external_progs_test.TestExternalProgs)
Test R versions ... ok
test_samtools_in_path (external_progs_test.TestExternalProgs)
Test samtools in path ... ok
test_samtools_original_version (external_progs_test.TestExternalProgs)
Test samtools original version ... ok
test_samtools_version (external_progs_test.TestExternalProgs)
Test samtools version ... ok
test_show_coords_in_path (external_progs_test.TestExternalProgs)
Test show-coords in path ... ok
test_smalt_in_path (external_progs_test.TestExternalProgs)
Test smalt in path ... ok
test_smalt_version (external_progs_test.TestExternalProgs)
Test smalt version ... ok
test_add_and_get_edges (graph_test.TestGraph)
test adding and getting edges ... ok
test_connected_components (graph_test.TestGraph)
test connected_components ... ok
test_degree (graph_test.TestGraph)
test degree ... ok
test_edges_are_consistent (graph_test.TestGraph)
test edges_are_consistent ... ok
test_find_simple_path (graph_test.TestGraph)
test find_simple_path ... ok
test_get_nodes (graph_test.TestGraph)
test get_nodes ... ok
test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph)
test merged_coords_from_simple_nonredundant_path ... ok
test_node_to_coords (graph_test.TestGraph)
test _node_to_coords ... ok
test_remove_middle_node (graph_test.TestGraph)
test remove_middle_node ... ok
test_remove_node (graph_test.TestGraph)
test remove_node ... ok
test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph)
test remove_redundant_nodes_from_simple_path ... ok
test_simple_path_is_consistent (graph_test.TestGraph)
test simple_path_is_consistent ... ok
test_counts_file_to_fasta (kcount_test.TestKcount)
Test _counts_file_to_fasta ... ok
test_head_fastaq_fa (kcount_test.TestKcount)
Test head_fastaq with FASTA input ... ok
test_head_fastaq_fq (kcount_test.TestKcount)
Test head_fastaq with FASTQ input ... ok
test_kmc_to_kmer_counts (kcount_test.TestKcount)
Test _kmc_to_kmer_counts ... ok
test_median (kcount_test.TestKcount)
Test _median() ... ok
test_append (kmers_test.TestKmers)
Test append ... ok
test_commonest_kmers (kmers_test.TestKmers) ... ok
test_extend (kmers_test.TestKmers)
Test extend ... ok
test_extension (kmers_test.TestKmers)
Test extension ... ok
test_init (kmers_test.TestKmers)
Test __init__ ... ok
test_kmer_dict (kmers_test.TestKmers)
Test kmer_dict ... ok
test_append_to_file (kraken_test.TestKraken)
test _append_to_file ... ok
test_count_cds_from_embl (kraken_test.TestKraken)
test count_cds_from_embl ... ok
test_genbank_to_taxon_and_gi (kraken_test.TestKraken)
test _genbank_to_taxon_and_gi ... ok
test_get_most_common_species_dir (kraken_test.TestKraken)
Test get_most_common_species ... ok
test_get_parent_taxons (kraken_test.TestKraken)
test _get_parent_taxons ... ok
test_load_extra_ref_info (kraken_test.TestKraken)
test _load_extra_ref_info ... ok
test_replace_fasta_header (kraken_test.TestKraken)
test _replace_fasta_header ... ok
test_species_to_dir (kraken_test.TestKraken)
test species_to_dir ... ok
test_bam_file_to_fasta_pair_files (mapping_test.TestMapping)
Test bam_file_to_fasta_pair_files ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping)
Test bam_file_to_fasta_pair_files with a region ... ok
test_bam_file_to_region_fasta (mapping_test.TestMapping)
Test bam_file_to_region_fasta ... ok
test_bam_to_fasta (mapping_test.TestMapping)
Test bam_to_fasta ... ok
test_can_extend (mapping_test.TestMapping)
Test can_extend ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_consensus_base (mapping_test.TestMapping)
Test consensus_base ... ok
test_consensus_base_both_strands (mapping_test.TestMapping)
Test consensus_base_both_strands ... ok
test_find_incorrect_ref_bases (mapping_test.TestMapping)
Test find_incorrect_ref_bases ... ok
test_get_bam_region_coverage_fwd (mapping_test.TestMapping)
Test get_bam_region_coverage forward strand ... ok
test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping)
Test get_bam_region_coverage both strands ... ok
test_get_bam_region_coverage_rev (mapping_test.TestMapping)
Test get_bam_region_coverage reverse strand ... ok
test_get_pair_type (mapping_test.TestMapping)
Test get_pair_type ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_get_ref_name (mapping_test.TestMapping)
Test get_ref_name ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_map_reads (mapping_test.TestMapping)
Test mapping reads ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam'
ok
test_map_reads_and_sort (mapping_test.TestMapping)
Test mapping reads and sort BAM ... ok
test_map_reads_wth_flag (mapping_test.TestMapping)
Test map_reads with required flag ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.flag12.bam'
[E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam'
ok
test_remove_indels (mapping_test.TestMapping)
Test _remove_indels ... ok
test_sam_to_fasta (mapping_test.TestMapping)
Test sam_to_fasta ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_smalt_in_path (mapping_test.TestMapping)
Test that samtools is in the user's path ... ok
test_soft_clipped (mapping_test.TestMapping)
Test soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.smalt.out.bam'
ok
test_strip_mpileup_coverage_string (mapping_test.TestMapping)
Test strip_mpileup_coverage_string ... ok
test_total_ref_length_from_bam (mapping_test.TestMapping)
Test _total_ref_length_from_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/iva-1.0.11+ds/iva/tests/data/mapping_test.total_ref_length_from_bam.bam'
ok
test_file_read (mummer_test.TestMummer)
test file_read ... ok
test_is_at_ends (mummer_test.TestMummer)
Test is_at_ends ... ok
test_is_self_hit (mummer_test.TestMummer)
Test is_self_hit ... ok
test_on_same_strand (mummer_test.TestMummer)
test on_same_strand ... ok
test_qry_coords (mummer_test.TestMummer)
Test qry_coords ... ok
test_ref_coords (mummer_test.TestMummer)
Test ref_coords ... ok
test_run_nucmer (mummer_test.TestMummer)
test run_nucmer ... ok
test_sort (mummer_test.TestMummer)
test sort ... ok
test_swap (mummer_test.TestMummer)
test swap ... ok
test_to_graph_edge (mummer_test.TestMummer)
Test to_graph_edge ... ok
test_run_gage (qc_external_test.TestQcExternal)
test run_gage ... ok
test_run_ratt (qc_external_test.TestQcExternal)
test run_ratt ... ok
test_calculate_cds_assembly_stats (qc_test.TestQc)
test _calculate_cds_assembly_stats ... ok
test_calculate_contig_placement (qc_test.TestQc)
test calculate_contig_placement ... ok
test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc)
test _calculate_ref_positions_covered_by_contigs ... ok
test_calculate_ref_read_coverage (qc_test.TestQc)
test _calculate_ref_read_coverage ... ok
test_calculate_ref_read_region_coverage (qc_test.TestQc)
test _calculate_ref_read_region_coverage ... ok
test_calculate_refseq_assembly_stats (qc_test.TestQc)
test _calculate_refseq_assembly_stats ... ok
test_calculate_should_have_assembled (qc_test.TestQc)
test _calculate_should_have_assembled ... ok
test_contig_placement_in_reference (qc_test.TestQc)
test _contig_placement_in_reference ... ok
test_contigs_and_bases_that_hit_ref (qc_test.TestQc)
test _contigs_and_bases_that_hit_ref ... ok
test_cov_to_R_string (qc_test.TestQc)
test _cov_to_R_string ... ok
test_coverage_list_to_low_cov_intervals (qc_test.TestQc)
test _coverage_list_to_low_cov_intervals ... ok
test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc)
test _get_R_plot_contig_order_from_contig_placement ... ok
test_get_contig_hits_to_reference (qc_test.TestQc)
test _get_contig_hits_to_reference ... ok
test_get_overlapping_qry_hits (qc_test.TestQc)
test _get_overlapping_qry_hits ... ok
test_get_ref_cds_from_gff (qc_test.TestQc)
test _get_ref_cds_from_gff ... ok
test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc)
test _get_unique_and_repetitive_from_contig_hits ... ok
test_gff_and_fasta_to_cds (qc_test.TestQc)
test _gff_and_fasta_to_cds ... ok
test_has_orf (qc_test.TestQc)
test _has_orf ... ok
test_hash_nucmer_hits_by_ref (qc_test.TestQc)
test _hash_nucmer_hits_by_ref ... ok
test_ids_in_order_from_fai (qc_test.TestQc)
test _ids_in_order_from_fai ... ok
test_invert_list (qc_test.TestQc)
test _invert_list ... ok
test_map_cds_to_assembly (qc_test.TestQc)
test _map_cds_to_assembly ... ok
test_mummer_coords_file_to_dict (qc_test.TestQc)
test _mummer_coords_file_to_dict ... ok
test_write_cds_seqs (qc_test.TestQc)
test _write_cds_seqs ... ok
test_write_fasta_contigs_hit_ref (qc_test.TestQc)
test _write_fasta_contigs_hit_ref ... ok
test_write_fasta_contigs_not_hit_ref (qc_test.TestQc)
test _write_fasta_contigs_not_hit_ref ... ok
test_write_ref_coverage_to_files_for_R (qc_test.TestQc)
test _write_ref_coverage_to_files_for_R ... ok
test_run_trimmomatic (read_trim_test.TestReadTrim)
Test run_trimmomatic ... ok
test_extend (seed_test.TestSeed)
Test extend ... ok
test_extend_with_reads_as_single_end (seed_test.TestSeed)
Test _extend_with_reads_as_single_end ... ok
test_extension_from_read (seed_test.TestSeed)
Test _test_extension_from_read ... ok
test_extensions_from_reads_file (seed_test.TestSeed)
Test _extensions_from_reads_file ... ok
test_init (seed_test.TestSeed)
test init ... ok
test_kmc_in_path (seed_test.TestSeed)
Test that kmc is in the user's path ... ok
test_len (seed_test.TestSeed)
Test len ... ok
test_write_fasta (seed_test.TestSeed)
Test write_fasta ... ok
----------------------------------------------------------------------
Ran 160 tests in 14.663s
OK
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.11+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install --destdir=debian/iva/ -a -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva
Checking dependencies found in path:
OK kmc
OK kmc_dump
OK nucmer
OK delta-filter
OK show-coords
OK samtools
OK smalt
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running build_scripts
running install_lib
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/gage
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/__init__.py to __init__.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/assembly.py to assembly.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/common.py to common.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/contig.py to contig.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/contig_trim.py to contig_trim.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/edge.py to edge.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/egg_extract.py to egg_extract.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/external_progs.py to external_progs.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/graph.py to graph.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/kcount.py to kcount.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/kmers.py to kmers.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/kraken.py to kraken.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/mummer.py to mummer.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/qc.py to qc.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/qc_external.py to qc_external.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim.py to read_trim.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/seed.py to seed.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/seed_processor.py to seed_processor.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-310.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva/mapping.py to mapping.cpython-310.pyc
running install_egg_info
running egg_info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
reading manifest file 'iva.egg-info/SOURCES.txt'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'iva.egg-info/SOURCES.txt'
Copying iva.egg-info to /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.10/dist-packages/iva-1.0.9.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.10/iva -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.10/iva_qc -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.10/iva_qc_make_db -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
changing mode of /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin/iva to 755
changing mode of /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755
changing mode of /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/iva-1.0.11+ds'
mkdir -p /<<BUILDDIR>>/iva-1.0.11+ds/debian/man
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.11+ds/debian/man/iva.1 \
-n 'iterative virus assembler' \
--no-discard-stderr ./scripts/iva
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.11+ds/debian/man/iva_qc.1 \
-n 'compare an assembly to a reference' \
--no-discard-stderr ./scripts/iva_qc
PYTHONPATH=. help2man -N -o /<<BUILDDIR>>/iva-1.0.11+ds/debian/man/iva_qc_make_db.1 \
-n 'make a database as input for iva_qc' \
--no-discard-stderr ./scripts/iva_qc_make_db
dh_installman --
make[1]: Leaving directory '/<<BUILDDIR>>/iva-1.0.11+ds'
dh_python3 -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'iva' in '../iva_1.0.11+ds-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../iva_1.0.11+ds-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-10-14T05:25:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
iva_1.0.11+ds-2_armhf.changes:
------------------------------
Format: 1.8
Date: Sat, 08 Oct 2022 18:53:24 +0200
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.11+ds-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
iva - iterative virus sequence assembler
Changes:
iva (1.0.11+ds-2) unstable; urgency=medium
.
[ Andreas Tille ]
* Enable uscan downloading sensible file name
.
[ Sascha Steinbiss ]
* Fix watchfile.
* Bump Standards-Version.
* Update copyright year.
Checksums-Sha1:
82cc60b64fec302e76e82d583b011e7411d9b601 7750 iva_1.0.11+ds-2_armhf.buildinfo
80c374aa903b30129cff71174b83280831696279 8581292 iva_1.0.11+ds-2_armhf.deb
Checksums-Sha256:
c8d7693d978a1bd9e9256cdaf86b1432d0a0cf75b264ae06312b70c13e67d38c 7750 iva_1.0.11+ds-2_armhf.buildinfo
36effbf0e95fd9809054cf7193dfa33cfef20008fb8e0c1277a92f8d5e922f48 8581292 iva_1.0.11+ds-2_armhf.deb
Files:
c7e0eb6c05785b8d88c515316ddee815 7750 science optional iva_1.0.11+ds-2_armhf.buildinfo
3bb850c5cfadbbc215bc8f3a8dc44ae6 8581292 science optional iva_1.0.11+ds-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
iva_1.0.11+ds-2_armhf.deb
-------------------------
new Debian package, version 2.0.
size 8581292 bytes: control archive=3020 bytes.
951 bytes, 21 lines control
5542 bytes, 65 lines md5sums
253 bytes, 12 lines * postinst #!/bin/sh
366 bytes, 12 lines * prerm #!/bin/sh
Package: iva
Version: 1.0.11+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8769
Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless
Recommends: r-base-core, bioperl, trimmomatic
Section: science
Priority: optional
Homepage: https://github.com/sanger-pathogens/iva
Description: iterative virus sequence assembler
IVA is a de novo assembler designed to assemble
virus genomes that have no repeat sequences,
using Illumina read pairs sequenced from mixed
populations at extremely high depth.
.
IVA's main algorithm works by iteratively extending
contigs using aligned read pairs. Its input can be
just read pairs, or additionally you can provide an
existing set of contigs to be extended. Alternatively,
it can take reads together with a reference sequence.
drwxr-xr-x root/root 0 2022-10-08 16:53 ./
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/bin/
-rwxr-xr-x root/root 17240 2022-10-08 16:53 ./usr/bin/iva
-rwxr-xr-x root/root 6228 2022-10-08 16:53 ./usr/bin/iva_qc
-rwxr-xr-x root/root 2406 2022-10-08 16:53 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root 516 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root 4 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/
-rw-r--r-- root/root 1033 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/__init__.py
-rw-r--r-- root/root 29056 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/assembly.py
-rw-r--r-- root/root 1856 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/common.py
-rw-r--r-- root/root 1960 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig.py
-rw-r--r-- root/root 4391 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig_trim.py
-rw-r--r-- root/root 4903 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/edge.py
-rw-r--r-- root/root 3077 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/egg_extract.py
-rw-r--r-- root/root 4110 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/external_progs.py
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root 508 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root 10192 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root 14839 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root 3689 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root 3611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root 2898 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root 2229 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root 640 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root 4583 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root 1244 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root 5920 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/Utils.class
-rw-r--r-- root/root 9230 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/Utils.java
-rwxr-xr-x root/root 80 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl
-rwxr-xr-x root/root 1773 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh
-rwxr-xr-x root/root 1430 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh
-rw-r--r-- root/root 814 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root 13703 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class
-rw-r--r-- root/root 19111 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java
-rw-r--r-- root/root 7133 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/graph.py
-rw-r--r-- root/root 9487 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kcount.py
-rw-r--r-- root/root 3466 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kmers.py
-rw-r--r-- root/root 16961 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kraken.py
-rw-r--r-- root/root 13330 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/mapping.py
-rw-r--r-- root/root 8365 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/mummer.py
-rw-r--r-- root/root 36646 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/qc.py
-rw-r--r-- root/root 8190 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/qc_external.py
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root 1008 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root 1045 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl
-rwxr-xr-x root/root 41988 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl
-rw-r--r-- root/root 90 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config
-rw-r--r-- root/root 90 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv
-rw-r--r-- root/root 57611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm
-rwxr-xr-x root/root 13201 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh
-rw-r--r-- root/root 1428 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/read_trim.py
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/read_trim/
-rw-r--r-- root/root 3143 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta
-rw-r--r-- root/root 6056 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/seed.py
-rw-r--r-- root/root 5586 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/seed_processor.py
-rw-r--r-- root/root 2443 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_data_runner.py
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/test_run_data/
-rw-r--r-- root/root 672 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa
-rw-r--r-- root/root 9981 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta
-rw-r--r-- root/root 9200 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta
-rw-r--r-- root/root 3813239 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root 4661713 2022-10-08 16:53 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz
-rw-r--r-- root/root 9217 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/share/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/share/doc/iva/
-rw-r--r-- root/root 899 2022-10-08 16:53 ./usr/share/doc/iva/changelog.Debian.gz
-rw-r--r-- root/root 2907 2021-03-25 08:41 ./usr/share/doc/iva/changelog.gz
-rw-r--r-- root/root 1493 2022-10-08 16:53 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/share/man/
drwxr-xr-x root/root 0 2022-10-08 16:53 ./usr/share/man/man1/
-rw-r--r-- root/root 2252 2022-10-08 16:53 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root 1281 2022-10-08 16:53 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root 641 2022-10-08 16:53 ./usr/share/man/man1/iva_qc_make_db.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 37124
Build-Time: 56
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 467
Job: iva_1.0.11+ds-2
Machine Architecture: armhf
Package: iva
Package-Time: 545
Source-Version: 1.0.11+ds-2
Space: 37124
Status: successful
Version: 1.0.11+ds-2
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Finished at 2022-10-14T05:25:14Z
Build needed 00:09:05, 37124k disk space