iva →
1.0.11+ds-3 →
armhf → 2022-12-08 07:41:33
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| iva 1.0.11+ds-3 (armhf) Thu, 08 Dec 2022 07:30:53 +0000 |
+==============================================================================+
Package: iva
Version: 1.0.11+ds-3
Source Version: 1.0.11+ds-3
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-98f93e50-1093-494b-ad6e-9ffdd09b6ce1' 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 [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 11s (2503 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-3 (dsc) [2405 B]
Get:2 http://172.17.4.1/private bookworm-staging/main iva 1.0.11+ds-3 (tar) [8681 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main iva 1.0.11+ds-3 (diff) [5940 B]
Fetched 8689 kB in 1s (9705 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-7TVM4k/iva-1.0.11+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-7TVM4k' 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-PLXZpF/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-PLXZpF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-PLXZpF/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-PLXZpF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (8160 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 libperl5.34 netbase perl-modules-5.34 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 82 not upgraded.
Need to get 844 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [844 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 844 B in 0s (59.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14774 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-networkx, python3-pysam, python3-pytest, 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-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless
dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<<BUILDDIR>>/resolver-PLXZpF/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-PLXZpF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Sources [604 B]
Get:5 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ Packages [685 B]
Fetched 2622 B in 0s (11.6 kB/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 libperl5.34 netbase perl-modules-5.34
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 cpp-12 debhelper default-jdk-headless
default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz
fastaq file fontconfig-config fonts-dejavu-core g++-12 gawk gcc-12
gcc-12-base gettext gettext-base groff-base help2man intltool-debian
java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasan8
libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data
libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libblkid1 libbrotli1
libcapture-tiny-perl libcc1-0 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 libgcc-12-dev
libgcc-s1 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b
libhts3 libhtscodecs2 libicu72 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
libssl3 libstdc++-12-dev libstdc++6 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 libubsan1
libuchardet0 libuuid1 libxml2 m4 man-db media-types mount mummer
openjdk-17-jdk-headless openjdk-17-jre-headless openssl po-debconf python3
python3-attr python3-distutils python3-iniconfig python3-lib2to3
python3-minimal python3-more-itertools python3-networkx python3-numpy
python3-packaging python3-pkg-resources python3-pluggy python3-py
python3-pyparsing python3-pysam python3-pytest python3-setuptools
python3-tomli python3.10 python3.10-minimal samtools smalt ucf util-linux
util-linux-extra
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-12-locales cpp-12-doc
dh-make default-jre flit python3-build python3-installer gcc-12-doc gawk-doc
gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins
alsa-utils libxml-sax-expatxs-perl cups-common low-memory-monitor
liblcms2-utils cryptsetup-bin pcscd libssl-doc libstdc++-12-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
nfs-common openjdk-17-demo openjdk-17-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-attr-doc python-networkx-doc gfortran python-numpy-doc
python3-dev subversion 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 python3-pygments
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 libicu72
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-17-jdk-headless
openjdk-17-jre-headless openssl po-debconf python3 python3-attr
python3-distutils python3-iniconfig python3-lib2to3 python3-minimal
python3-more-itertools python3-networkx python3-numpy python3-packaging
python3-pkg-resources python3-pluggy python3-py python3-pyparsing
python3-pysam python3-pytest python3-setuptools python3-tomli python3.10
python3.10-minimal samtools sbuild-build-depends-iva-dummy smalt ucf
The following packages will be upgraded:
bsdutils cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libblkid1
libcc1-0 libgcc-12-dev libgcc-s1 libgomp1 libmount1 libsmartcols1 libssl3
libstdc++-12-dev libstdc++6 libubsan1 libuuid1 mount util-linux
util-linux-extra
22 upgraded, 126 newly installed, 0 to remove and 60 not upgraded.
Need to get 390 MB of archives.
After this operation, 645 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-PLXZpF/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-4 [83.9 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-4 [91.6 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-4 [98.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-4 [1062 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf liblocale-gettext-perl armhf 1.07-4+b3 [14.6 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-4 [126 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 libcc1-0 armhf 12.2.0-9+rpi1 [32.2 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.2.0-9+rpi1 [95.4 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.2.0-9+rpi1 [8224 B]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.2.0-9+rpi1 [2089 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.2.0-9+rpi1 [861 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.2.0-9+rpi1 [37.2 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.2.0-9+rpi1 [504 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.2.0-9+rpi1 [7913 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.2.0-9+rpi1 [2025 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.2.0-9+rpi1 [725 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.2.0-9+rpi1 [14.2 MB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.2.0-9+rpi1 [7156 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.2.0-9+rpi1 [36.1 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.8-3 [769 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.8-3 [1478 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-4 [27.1 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.8-3 [1597 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.8-3 [506 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-4 [131 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-4 [144 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.7-1 [1349 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libio-string-perl all 1.08-3.1 [11.8 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libdata-stag-perl all 0.14-3 [448 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libexception-class-perl all 1.45-1 [34.6 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libtest-deep-perl all 1.130-2 [49.4 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libtext-diff-perl all 1.45-1 [27.7 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libtest-differences-perl all 0.69-1 [18.9 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libtest-exception-perl all 0.43-3 [16.9 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libtest-warn-perl all 0.37-2 [14.5 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libtest-most-perl all 0.38-1 [25.1 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf bioperl all 1.7.8-1 [246 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates-java all 20220719 [16.1 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.1 [80.8 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.1 [941 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf java-common all 0.73 [6268 B]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-6+b1 [124 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-6+b1 [55.8 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.14.4-1 [211 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-6+b1 [58.5 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.4.2-1+b1 [311 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libnspr4 armhf 2:4.35-1 [90.9 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libnss3 armhf 2:3.85-1 [1094 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libasound2-data all 1.2.8-1 [20.5 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libasound2 armhf 1.2.8-1 [304 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.1-2 [1214 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2+b1 [1832 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libpcsclite1 armhf 1.9.9-1 [58.1 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf openjdk-17-jre-headless armhf 17.0.4+8-1+rpi1 [40.1 MB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf default-jre-headless armhf 2:1.17-73 [2812 B]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf openjdk-17-jdk-headless armhf 17.0.4+8-1+rpi1 [259 MB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf default-jdk-headless armhf 2:1.17-73 [1108 B]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf fastaq all 3.17.0-5 [48.2 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf help2man armhf 1.49.2 [202 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf kmc armhf 3.2.1+dfsg-1 [776 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libbambamc0 armhf 0.0.50-6 [31.0 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-9+rpi1 [238 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.7-1 [2095 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf mummer armhf 3.23+dfsg-7 [618 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.1.0-1 [64.1 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf python3-networkx all 2.6.3-1 [943 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.21.5-2 [3409 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.7-3 [136 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.11.0-1 [89.2 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf python3-pysam armhf 0.17.0+ds-2+b1 [1834 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-2 [17.9 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-4 [218 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf smalt armhf 0.7.6-12 [94.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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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
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Adding debian:ACCVRAIZ1.pem
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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-3) ...
Setting up python3.10 (3.10.8-3) ...
Setting up libstdc++-12-dev:armhf (12.2.0-9+rpi1) ...
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 (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.16.1-1) ...
Setting up python3-pyparsing (3.0.7-3) ...
Setting up gcc-12 (12.2.0-9+rpi1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up libcups2:armhf (2.4.2-1+b1) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up g++-12 (12.2.0-9+rpi1) ...
Setting up python3-pkg-resources (65.5.0-1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up bioperl (1.7.8-1) ...
Setting up python3-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-attr (22.1.0-1) ...
Setting up python3-pysam (0.17.0+ds-2+b1) ...
Setting up python3-setuptools (65.5.0-1) ...
Setting up python3-tomli (2.0.1-2) ...
Setting up python3-py (1.11.0-1) ...
Setting up fastaq (3.17.0-5) ...
Setting up debhelper (13.11.1) ...
Setting up python3-networkx (2.6.3-1) ...
Setting up python3-packaging (21.3-1.1) ...
Setting up python3-numpy (1:1.21.5-2) ...
Setting up python3-pytest (7.1.2-4) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Setting up openjdk-17-jre-headless:armhf (17.0.4+8-1+rpi1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up default-jre-headless (2:1.17-73) ...
Setting up openjdk-17-jdk-headless:armhf (17.0.4+8-1+rpi1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jdk-headless (2:1.17-73) ...
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_12.2.0-9+rpi1 gcc-12_12.2.0-9+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+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_0.21-10 autotools-dev_20220109.1 base-files_12.3+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_2.38.1-4 bsdutils_1:2.38.1-4 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_12.2.0-9+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.11.1 debianutils_5.7-0.3 default-jdk-headless_2:1.17-73 default-jre-headless_2:1.17-73 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-2 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_12.2.0-9+rpi1 gawk_1:5.1.0-1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-9+rpi1 gcc-12-base_12.2.0-9+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_0.21-10 gettext-base_0.21-10 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_1.22.4-9 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 java-common_0.73 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_12.2.0-9+rpi1 libasound2_1.2.8-1 libasound2-data_1.2.8-1 libassuan0_2.5.5-4 libatomic1_12.2.0-9+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_2.38.1-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 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_12.2.0-9+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_7.86.0-2 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_13.11.1 libdeflate0_1.14-1 libdevel-stacktrace-perl_2.0400-2 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexception-class-perl_1.45-1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-2 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-9+rpi1 libgcc-s1_12.2.0-9+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-9+rpi1 libglib2.0-0_2.74.1-2 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-9+rpi1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libharfbuzz0b_5.2.0-2+b1 libhogweed6_3.8.1-2 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu72_72.1-3 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+b3 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_2.38.1-4 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_2:3.85-1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libpcsclite1_1.9.9-1 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.8-3 libpython3.10-stdlib_3.10.8-3 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_2.38.1-4 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.7-1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 libsub-override-perl_0.09-4 libsub-uplevel-perl_0.2800-3 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtest-deep-perl_1.130-2 libtest-differences-perl_0.69-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 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_2.4.7-5 libubsan1_12.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-4 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-17-jdk-headless_17.0.4+8-1+rpi1 openjdk-17-jre-headless_17.0.4+8-1+rpi1 openssl_3.0.7-1 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-attr_22.1.0-1 python3-distutils_3.10.8-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1 python3-more-itertools_8.10.0-2 python3-networkx_2.6.3-1 python3-numpy_1:1.21.5-2 python3-packaging_21.3-1.1 python3-pkg-resources_65.5.0-1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pyparsing_3.0.7-3 python3-pysam_0.17.0+ds-2+b1 python3-pytest_7.1.2-4 python3-setuptools_65.5.0-1 python3-tomli_2.0.1-2 python3.10_3.10.8-3 python3.10-minimal_3.10.8-3 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_1.31 smalt_0.7.6-12 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 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.IVgSSeCH/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 2 17:12:51 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./iva_1.0.11+ds-3.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-3.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-98f93e50-1093-494b-ad6e-9ffdd09b6ce1
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-3
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 170ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SizeFasta.java]]
[parsing completed 10ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 14ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils.java]]
[parsing completed 20ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 37ms]
[loading /modules/java.management/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/jdk.incubator.foreign/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/jdk.jpackage/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/jdk.random/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/java.compiler/module-info.class]
[loading /modules/java.desktop/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/jdk.incubator.vector/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/java.base/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/jdk.nio.mapmode/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[search path for source files: .]
[search path for class files: /usr/lib/jvm/java-17-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/constant/Constable.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/lang/constant/ConstantDesc.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/util/Iterator.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]
[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/util/Optional.class]
[loading /modules/java.base/java/lang/Enum$EnumDesc.class]
[loading /modules/java.base/java/lang/constant/DynamicConstantDesc.class]
[loading /modules/java.base/java/lang/CloneNotSupportedException.class]
[loading /modules/java.base/java/lang/Class.class]
[loading /modules/java.base/java/net/URI.class]
[loading /modules/java.base/java/lang/Process.class]
[loading /modules/java.base/java/lang/Runtime.class]
[loading /modules/java.base/java/lang/StringBuilder.class]
[loading /modules/java.base/java/lang/reflect/GenericDeclaration.class]
[loading /modules/java.base/java/lang/reflect/AnnotatedElement.class]
[loading /modules/java.base/java/lang/reflect/Type.class]
[loading /modules/java.base/java/lang/invoke/TypeDescriptor.class]
[loading /modules/java.base/java/lang/invoke/TypeDescriptor$OfField.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 2669ms]
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 -m pytest --verbose
============================= test session starts ==============================
platform linux -- Python 3.10.8, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/iva-1.0.11+ds
collecting ... collected 160 items
iva/tests/assembly_test.py::TestAssembly::test_contig_contained_in_nucmer_hits PASSED [ 0%]
iva/tests/assembly_test.py::TestAssembly::test_contig_names_size_order PASSED [ 1%]
iva/tests/assembly_test.py::TestAssembly::test_contig_worth_extending PASSED [ 1%]
iva/tests/assembly_test.py::TestAssembly::test_coords_to_new_contig PASSED [ 2%]
iva/tests/assembly_test.py::TestAssembly::test_extend_contigs_with_bam PASSED [ 3%]
iva/tests/assembly_test.py::TestAssembly::test_get_contig_order_by_orfs PASSED [ 3%]
iva/tests/assembly_test.py::TestAssembly::test_get_ref_length PASSED [ 4%]
iva/tests/assembly_test.py::TestAssembly::test_get_ref_length_sam_pair PASSED [ 5%]
iva/tests/assembly_test.py::TestAssembly::test_get_unmapped_pairs PASSED [ 5%]
iva/tests/assembly_test.py::TestAssembly::test_good_intervals_from_strand_coverage PASSED [ 6%]
iva/tests/assembly_test.py::TestAssembly::test_init_and_write PASSED [ 6%]
iva/tests/assembly_test.py::TestAssembly::test_map_reads PASSED [ 7%]
iva/tests/assembly_test.py::TestAssembly::test_merge_overlapping_contigs PASSED [ 8%]
iva/tests/assembly_test.py::TestAssembly::test_read_pair_extend PASSED [ 8%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contained_contigs PASSED [ 9%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contig PASSED [ 10%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contig_from_nucmer_hits PASSED [ 10%]
iva/tests/assembly_test.py::TestAssembly::test_subcontigs_from_strand_bias PASSED [ 11%]
iva/tests/assembly_test.py::TestAssembly::test_trim_contig_for_strand_bias PASSED [ 11%]
iva/tests/assembly_test.py::TestAssembly::test_trim_contigs PASSED [ 12%]
iva/tests/assembly_test.py::TestAssembly::test_trim_strand_biased_ends PASSED [ 13%]
iva/tests/assembly_test.py::TestAssembly::test_worth_extending PASSED [ 13%]
iva/tests/contig_test.py::TestContig::test_add_left_kmer PASSED [ 14%]
iva/tests/contig_test.py::TestContig::test_add_right_kmer PASSED [ 15%]
iva/tests/contig_test.py::TestContig::test_extend PASSED [ 15%]
iva/tests/contig_test.py::TestContig::test_init PASSED [ 16%]
iva/tests/contig_test.py::TestContig::test_len PASSED [ 16%]
iva/tests/contig_trim_test.py::TestContigTrim::test_coverage_to_trimmed_coords PASSED [ 17%]
iva/tests/contig_trim_test.py::TestContigTrim::test_trim_ends PASSED [ 18%]
iva/tests/contig_trim_test.py::TestContigTrim::test_trim_primers_and_adapters PASSED [ 18%]
iva/tests/edge_test.py::TestEdge::test_change_hit_coords_with_intersection PASSED [ 19%]
iva/tests/edge_test.py::TestEdge::test_make_contig_first PASSED [ 20%]
iva/tests/edge_test.py::TestEdge::test_make_contig_forwards PASSED [ 20%]
iva/tests/edge_test.py::TestEdge::test_merge_into PASSED [ 21%]
iva/tests/edge_test.py::TestEdge::test_open_end PASSED [ 21%]
iva/tests/edge_test.py::TestEdge::test_reverse PASSED [ 22%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir PASSED [ 23%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_unzipped PASSED [ 23%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_zipped PASSED [ 24%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file PASSED [ 25%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_unzipped PASSED [ 25%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_zipped PASSED [ 26%]
iva/tests/egg_extract_test.py::TestEggExtract::test_init_and_write PASSED [ 26%]
iva/tests/external_progs_test.py::TestExternalProgs::test_blastn_version PASSED [ 27%]
iva/tests/external_progs_test.py::TestExternalProgs::test_delta_filter_in_path PASSED [ 28%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_in_path PASSED [ 28%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_version PASSED [ 29%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_in_path PASSED [ 30%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_version PASSED [ 30%]
iva/tests/external_progs_test.py::TestExternalProgs::test_makeblastdb_version PASSED [ 31%]
iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_in_path PASSED [ 31%]
iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED [ 32%]
iva/tests/external_progs_test.py::TestExternalProgs::test_r_version PASSED [ 33%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_in_path PASSED [ 33%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 34%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_version PASSED [ 35%]
iva/tests/external_progs_test.py::TestExternalProgs::test_show_coords_in_path PASSED [ 35%]
iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_in_path PASSED [ 36%]
iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_version PASSED [ 36%]
iva/tests/graph_test.py::TestGraph::test_add_and_get_edges PASSED [ 37%]
iva/tests/graph_test.py::TestGraph::test_connected_components PASSED [ 38%]
iva/tests/graph_test.py::TestGraph::test_degree PASSED [ 38%]
iva/tests/graph_test.py::TestGraph::test_edges_are_consistent PASSED [ 39%]
iva/tests/graph_test.py::TestGraph::test_find_simple_path PASSED [ 40%]
iva/tests/graph_test.py::TestGraph::test_get_nodes PASSED [ 40%]
iva/tests/graph_test.py::TestGraph::test_merged_coords_from_simple_nonredundant_path PASSED [ 41%]
iva/tests/graph_test.py::TestGraph::test_node_to_coords PASSED [ 41%]
iva/tests/graph_test.py::TestGraph::test_remove_middle_node PASSED [ 42%]
iva/tests/graph_test.py::TestGraph::test_remove_node PASSED [ 43%]
iva/tests/graph_test.py::TestGraph::test_remove_redundant_nodes_from_simple_path PASSED [ 43%]
iva/tests/graph_test.py::TestGraph::test_simple_path_is_consistent PASSED [ 44%]
iva/tests/kcount_test.py::TestKcount::test_counts_file_to_fasta PASSED [ 45%]
iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fa PASSED [ 45%]
iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fq PASSED [ 46%]
iva/tests/kcount_test.py::TestKcount::test_kmc_to_kmer_counts PASSED [ 46%]
iva/tests/kcount_test.py::TestKcount::test_median PASSED [ 47%]
iva/tests/kmers_test.py::TestKmers::test_append PASSED [ 48%]
iva/tests/kmers_test.py::TestKmers::test_commonest_kmers PASSED [ 48%]
iva/tests/kmers_test.py::TestKmers::test_extend PASSED [ 49%]
iva/tests/kmers_test.py::TestKmers::test_extension PASSED [ 50%]
iva/tests/kmers_test.py::TestKmers::test_init PASSED [ 50%]
iva/tests/kmers_test.py::TestKmers::test_kmer_dict PASSED [ 51%]
iva/tests/kraken_test.py::TestKraken::test_append_to_file PASSED [ 51%]
iva/tests/kraken_test.py::TestKraken::test_count_cds_from_embl PASSED [ 52%]
iva/tests/kraken_test.py::TestKraken::test_genbank_to_taxon_and_gi PASSED [ 53%]
iva/tests/kraken_test.py::TestKraken::test_get_most_common_species_dir PASSED [ 53%]
iva/tests/kraken_test.py::TestKraken::test_get_parent_taxons PASSED [ 54%]
iva/tests/kraken_test.py::TestKraken::test_load_extra_ref_info PASSED [ 55%]
iva/tests/kraken_test.py::TestKraken::test_replace_fasta_header PASSED [ 55%]
iva/tests/kraken_test.py::TestKraken::test_species_to_dir PASSED [ 56%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files PASSED [ 56%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files_region PASSED [ 57%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_region_fasta PASSED [ 58%]
iva/tests/mapping_test.py::TestMapping::test_bam_to_fasta PASSED [ 58%]
iva/tests/mapping_test.py::TestMapping::test_can_extend PASSED [ 59%]
iva/tests/mapping_test.py::TestMapping::test_consensus_base PASSED [ 60%]
iva/tests/mapping_test.py::TestMapping::test_consensus_base_both_strands PASSED [ 60%]
iva/tests/mapping_test.py::TestMapping::test_find_incorrect_ref_bases PASSED [ 61%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd PASSED [ 61%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd_And_rev PASSED [ 62%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_rev PASSED [ 63%]
iva/tests/mapping_test.py::TestMapping::test_get_pair_type PASSED [ 63%]
iva/tests/mapping_test.py::TestMapping::test_get_ref_name PASSED [ 64%]
iva/tests/mapping_test.py::TestMapping::test_map_reads PASSED [ 65%]
iva/tests/mapping_test.py::TestMapping::test_map_reads_and_sort PASSED [ 65%]
iva/tests/mapping_test.py::TestMapping::test_map_reads_wth_flag PASSED [ 66%]
iva/tests/mapping_test.py::TestMapping::test_remove_indels PASSED [ 66%]
iva/tests/mapping_test.py::TestMapping::test_sam_to_fasta PASSED [ 67%]
iva/tests/mapping_test.py::TestMapping::test_smalt_in_path PASSED [ 68%]
iva/tests/mapping_test.py::TestMapping::test_soft_clipped PASSED [ 68%]
iva/tests/mapping_test.py::TestMapping::test_strip_mpileup_coverage_string PASSED [ 69%]
iva/tests/mapping_test.py::TestMapping::test_total_ref_length_from_bam PASSED [ 70%]
iva/tests/mummer_test.py::TestMummer::test_file_read PASSED [ 70%]
iva/tests/mummer_test.py::TestMummer::test_is_at_ends PASSED [ 71%]
iva/tests/mummer_test.py::TestMummer::test_is_self_hit PASSED [ 71%]
iva/tests/mummer_test.py::TestMummer::test_on_same_strand PASSED [ 72%]
iva/tests/mummer_test.py::TestMummer::test_qry_coords PASSED [ 73%]
iva/tests/mummer_test.py::TestMummer::test_ref_coords PASSED [ 73%]
iva/tests/mummer_test.py::TestMummer::test_run_nucmer PASSED [ 74%]
iva/tests/mummer_test.py::TestMummer::test_sort PASSED [ 75%]
iva/tests/mummer_test.py::TestMummer::test_swap PASSED [ 75%]
iva/tests/mummer_test.py::TestMummer::test_to_graph_edge PASSED [ 76%]
iva/tests/qc_external_test.py::TestQcExternal::test_run_gage PASSED [ 76%]
iva/tests/qc_external_test.py::TestQcExternal::test_run_ratt PASSED [ 77%]
iva/tests/qc_test.py::TestQc::test_calculate_cds_assembly_stats PASSED [ 78%]
iva/tests/qc_test.py::TestQc::test_calculate_contig_placement PASSED [ 78%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_positions_covered_by_contigs PASSED [ 79%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_read_coverage PASSED [ 80%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_read_region_coverage PASSED [ 80%]
iva/tests/qc_test.py::TestQc::test_calculate_refseq_assembly_stats PASSED [ 81%]
iva/tests/qc_test.py::TestQc::test_calculate_should_have_assembled PASSED [ 81%]
iva/tests/qc_test.py::TestQc::test_contig_placement_in_reference PASSED [ 82%]
iva/tests/qc_test.py::TestQc::test_contigs_and_bases_that_hit_ref PASSED [ 83%]
iva/tests/qc_test.py::TestQc::test_cov_to_R_string PASSED [ 83%]
iva/tests/qc_test.py::TestQc::test_coverage_list_to_low_cov_intervals PASSED [ 84%]
iva/tests/qc_test.py::TestQc::test_get_R_plot_contig_order_from_contig_placement PASSED [ 85%]
iva/tests/qc_test.py::TestQc::test_get_contig_hits_to_reference PASSED [ 85%]
iva/tests/qc_test.py::TestQc::test_get_overlapping_qry_hits PASSED [ 86%]
iva/tests/qc_test.py::TestQc::test_get_ref_cds_from_gff PASSED [ 86%]
iva/tests/qc_test.py::TestQc::test_get_unique_and_repetitive_from_contig_hits PASSED [ 87%]
iva/tests/qc_test.py::TestQc::test_gff_and_fasta_to_cds PASSED [ 88%]
iva/tests/qc_test.py::TestQc::test_has_orf PASSED [ 88%]
iva/tests/qc_test.py::TestQc::test_hash_nucmer_hits_by_ref PASSED [ 89%]
iva/tests/qc_test.py::TestQc::test_ids_in_order_from_fai PASSED [ 90%]
iva/tests/qc_test.py::TestQc::test_invert_list PASSED [ 90%]
iva/tests/qc_test.py::TestQc::test_map_cds_to_assembly PASSED [ 91%]
iva/tests/qc_test.py::TestQc::test_mummer_coords_file_to_dict PASSED [ 91%]
iva/tests/qc_test.py::TestQc::test_write_cds_seqs PASSED [ 92%]
iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_hit_ref PASSED [ 93%]
iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_not_hit_ref PASSED [ 93%]
iva/tests/qc_test.py::TestQc::test_write_ref_coverage_to_files_for_R PASSED [ 94%]
iva/tests/read_trim_test.py::TestReadTrim::test_run_trimmomatic PASSED [ 95%]
iva/tests/seed_test.py::TestSeed::test_extend PASSED [ 95%]
iva/tests/seed_test.py::TestSeed::test_extend_with_reads_as_single_end PASSED [ 96%]
iva/tests/seed_test.py::TestSeed::test_extension_from_read PASSED [ 96%]
iva/tests/seed_test.py::TestSeed::test_extensions_from_reads_file PASSED [ 97%]
iva/tests/seed_test.py::TestSeed::test_init PASSED [ 98%]
iva/tests/seed_test.py::TestSeed::test_kmc_in_path PASSED [ 98%]
iva/tests/seed_test.py::TestSeed::test_len PASSED [ 99%]
iva/tests/seed_test.py::TestSeed::test_write_fasta PASSED [100%]
=============================== warnings summary ===============================
iva/mapping.py:161
/<<BUILDDIR>>/iva-1.0.11+ds/iva/mapping.py:161: DeprecationWarning: invalid escape sequence '\^'
s = re.sub('\^.', '', s)
iva/external_progs.py:33
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence '\('
'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')),
iva/external_progs.py:34
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence '\('
'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')),
iva/external_progs.py:37
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence '\('
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
iva/external_progs.py:38
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence '\('
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
iva/external_progs.py:40
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence '\d'
'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
iva/external_progs.py:19
/<<BUILDDIR>>/iva-1.0.11+ds/iva/external_progs.py:19: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.version import LooseVersion
iva/kraken.py:360
/<<BUILDDIR>>/iva-1.0.11+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence '\.'
self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl')
iva/kraken.py:415
/<<BUILDDIR>>/iva-1.0.11+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence '\W'
return re.sub('\W', '_', s).strip('_')
iva/test_data_runner.py:20
/<<BUILDDIR>>/iva-1.0.11+ds/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py)
class Tester:
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================== 160 passed, 10 warnings in 17.15s =======================
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
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'
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-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../iva_1.0.11+ds-3_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 2022-12-08T07:41:28Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
iva_1.0.11+ds-3_armhf.changes:
------------------------------
Format: 1.8
Date: Fri, 02 Dec 2022 17:51:23 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.11+ds-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
iva - iterative virus sequence assembler
Closes: 1018382
Changes:
iva (1.0.11+ds-3) unstable; urgency=medium
.
* Team upload.
* d/control: replace nose by pytest. (Closes: #1018382)
* d/rules: fetch and run tests with pytest-3.
* Set upstream metadata fields: Repository-Browse.
Checksums-Sha1:
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b0f8800c9b95ad24d9d961e444c85508e1a24ae4 8581416 iva_1.0.11+ds-3_armhf.deb
Checksums-Sha256:
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Files:
f5e0cd9a9ce1a481738f33fd8b3d2b00 7929 science optional iva_1.0.11+ds-3_armhf.buildinfo
c86f8dff71d1845f4014c937bb7f0808 8581416 science optional iva_1.0.11+ds-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
iva_1.0.11+ds-3_armhf.deb
-------------------------
new Debian package, version 2.0.
size 8581416 bytes: control archive=3012 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-3
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 2022-12-02 16:51 ./
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/bin/
-rwxr-xr-x root/root 17240 2022-12-02 16:51 ./usr/bin/iva
-rwxr-xr-x root/root 6228 2022-12-02 16:51 ./usr/bin/iva_qc
-rwxr-xr-x root/root 2406 2022-12-02 16:51 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root 488 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root 4 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root 0 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root 508 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root 10213 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root 14839 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root 3689 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root 3611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root 2898 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root 2229 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root 640 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root 4727 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root 1303 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root 5920 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root 13712 2022-12-02 16:51 ./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 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root 1008 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root 1045 2022-12-02 16:51 ./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 2022-12-02 16:51 ./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 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root 4661713 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/share/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/doc/iva/
-rw-r--r-- root/root 1024 2022-12-02 16:51 ./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 2022-12-02 16:51 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/man/
drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/man/man1/
-rw-r--r-- root/root 2252 2022-12-02 16:51 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root 1282 2022-12-02 16:51 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root 641 2022-12-02 16:51 ./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: 37160
Build-Time: 59
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 556
Job: iva_1.0.11+ds-3
Machine Architecture: armhf
Package: iva
Package-Time: 635
Source-Version: 1.0.11+ds-3
Space: 37160
Status: successful
Version: 1.0.11+ds-3
--------------------------------------------------------------------------------
Finished at 2022-12-08T07:41:28Z
Build needed 00:10:35, 37160k disk space