Build log for iva (1.0.11+ds-4) on armhf

iva → 1.0.11+ds-4 → armhf → 2023-12-24 05:31:53

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04

+==============================================================================+
| iva 1.0.11+ds-4 (armhf)                      Sun, 24 Dec 2023 05:09:43 +0000 |
+==============================================================================+

Package: iva
Version: 1.0.11+ds-4
Source Version: 1.0.11+ds-4
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-694636ec-20ff-4a12-a512-e27bc7d11d87' with '<<CHROOT>>'

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

Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 30s (961 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/trixie-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 trixie-staging/main iva 1.0.11+ds-4 (dsc) [2263 B]
Get:2 http://172.17.4.1/private trixie-staging/main iva 1.0.11+ds-4 (tar) [8681 kB]
Get:3 http://172.17.4.1/private trixie-staging/main iva 1.0.11+ds-4 (diff) [6012 B]
Fetched 8689 kB in 1s (10.5 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/iva-2YDnad/iva-1.0.11+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/iva-2YDnad' 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-qDfEdg/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-qDfEdg/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-qDfEdg/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2710 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
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 1 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12859 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-qDfEdg/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-qDfEdg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Sources [604 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ Packages [687 B]
Fetched 2624 B in 1s (3564 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install iva build dependencies (apt-based resolver)
---------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  krb5-locales libpam-cap sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional 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 fonts-dejavu-mono 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 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1
  libpipeline1 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal
  libpython3.11-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-distutils python3-iniconfig python3-lib2to3
  python3-minimal python3-networkx python3-numpy python3-packaging
  python3-pkg-resources python3-pluggy python3-pysam python3-pytest
  python3-setuptools python3.11 python3.11-minimal samtools smalt
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make default-jre flit
  python3-build python3-installer python3-wheel gawk-doc gettext-doc
  libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils
  libxml-sax-expatxs-perl cups-common low-memory-monitor liblcms2-utils pcscd
  libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
  less www-browser 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 gfortran python3-dev
  python-setuptools-doc python3.11-venv python3.11-doc binfmt-support cwltool
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 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 fonts-dejavu-mono 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 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1
  libpipeline1 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal
  libpython3.11-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-distutils python3-iniconfig python3-lib2to3
  python3-minimal python3-networkx python3-numpy python3-packaging
  python3-pkg-resources python3-pluggy python3-pysam python3-pytest
  python3-setuptools python3.11 python3.11-minimal samtools
  sbuild-build-depends-iva-dummy smalt
0 upgraded, 120 newly installed, 0 to remove and 1 not upgraded.
Need to get 167 MB of archives.
After this operation, 475 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qDfEdg/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf liblocale-gettext-perl armhf 1.07-6 [14.8 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf gawk armhf 1:5.2.1-2 [595 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.7-2 [801 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.7-2 [1677 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.7-2 [1694 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.7-2 [590 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:13 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-2 [81.2 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf openssl armhf 3.1.4-2 [1375 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf ca-certificates all 20230311 [153 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libio-string-perl all 1.08-4 [12.1 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libdata-stag-perl all 0.14-3 [448 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libbio-perl-perl all 1.7.8-1 [2603 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libdevel-stacktrace-perl all 2.0400-2 [26.8 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libexception-class-perl all 1.45-1 [34.6 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libtest-deep-perl all 1.204-1 [52.9 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libtext-diff-perl all 1.45-2 [27.2 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libtest-differences-perl all 0.71-1 [17.9 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libtest-exception-perl all 0.43-3 [16.9 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libtest-warn-perl all 0.37-2 [14.5 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libtest-most-perl all 0.38-1 [25.1 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf bioperl all 1.7.8-1 [246 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf ca-certificates-java all 20230710 [11.8 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf java-common all 0.75 [6640 B]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libavahi-common-data armhf 0.8-13 [111 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libavahi-common3 armhf 0.8-13 [40.1 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libdbus-1-3 armhf 1.14.10-3 [177 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libavahi-client3 armhf 0.8-13 [42.6 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libcups2 armhf 2.4.7-1 [206 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf liblcms2-2 armhf 2.14-2 [124 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-2 [258 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libnspr4 armhf 2:4.35-1.1 [85.2 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libnss3 armhf 2:3.95-1 [1133 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libasound2-data all 1.2.10-3 [20.7 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libasound2 armhf 1.2.10-3 [309 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.3-1 [1256 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.0.1-1 [2098 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libpcsclite1 armhf 2.0.1-1 [47.6 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf openjdk-17-jre-headless armhf 17.0.9+9-2+rpi1 [40.7 MB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf default-jre-headless armhf 2:1.17-75 [3068 B]
Get:87 http://172.17.4.1/private trixie-staging/main armhf openjdk-17-jdk-headless armhf 17.0.9+9-2+rpi1 [72.0 MB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf default-jdk-headless armhf 2:1.17-75 [1108 B]
Get:89 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231204 [108 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-3 [195 kB]
Ign:97 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-3
Get:98 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.6.0-1 [60.3 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libncurses6 armhf 6.4+20231209-1 [80.5 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf samtools armhf 1.19-1 [593 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf fastaq all 3.17.0-6 [47.5 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf help2man armhf 1.49.3 [198 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf kmc armhf 3.2.3+dfsg-1 [791 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libbambamc0 armhf 0.0.50-6 [31.0 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-7+rpi1 [247 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.1.4-2 [2115 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf mummer armhf 3.23+dfsg-8 [615 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:114 http://172.17.4.1/private trixie-staging/main armhf python3-networkx all 2.8.8-1 [1425 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf python3-numpy armhf 1:1.24.2-2 [3164 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf python3-packaging all 23.2-1 [44.8 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf python3-pluggy all 1.3.0-1 [25.1 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf python3-pysam armhf 0.22.0+ds-1+rpi1 [2903 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf python3-pytest all 7.4.3-2 [239 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf smalt armhf 0.7.6-12 [94.0 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-3 [195 kB]
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Unpacking python3-distutils (3.11.5-1) ...
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Unpacking python3-pkg-resources (68.1.2-2) ...
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Unpacking python3-setuptools (68.1.2-2) ...
Selecting previously unselected package dh-python.
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Unpacking dh-python (6.20231204) ...
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Unpacking libnghttp2-14:armhf (1.58.0-1) ...
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Unpacking libpsl5:armhf (0.21.2-1+b1) ...
Selecting previously unselected package librtmp1:armhf.
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libssh2-1:armhf (1.11.0-3) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
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Unpacking libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Selecting previously unselected package libdeflate0:armhf.
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Unpacking libdeflate0:armhf (1.18-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
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Unpacking libhtscodecs2:armhf (1.6.0-1) ...
Selecting previously unselected package libhts3:armhf.
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Unpacking libhts3:armhf (1.18+ds-1) ...
Selecting previously unselected package libncurses6:armhf.
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Unpacking libncurses6:armhf (6.4+20231209-1) ...
Selecting previously unselected package samtools.
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Unpacking samtools (1.19-1) ...
Selecting previously unselected package fastaq.
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Unpacking fastaq (3.17.0-6) ...
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Unpacking help2man (1.49.3) ...
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Unpacking kmc (3.2.3+dfsg-1) ...
Selecting previously unselected package libbambamc0:armhf.
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Unpacking libbambamc0:armhf (0.0.50-6) ...
Selecting previously unselected package libblas3:armhf.
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Unpacking libblas3:armhf (3.11.0-2) ...
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Unpacking libgfortran5:armhf (13.2.0-7+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
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Unpacking liblapack3:armhf (3.11.0-2) ...
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Unpacking libssl-dev:armhf (3.1.4-2) ...
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Unpacking mummer (3.23+dfsg-8) ...
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Unpacking python3-iniconfig (1.1.1-2) ...
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Unpacking python3-networkx (2.8.8-1) ...
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Unpacking python3-packaging (23.2-1) ...
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Unpacking python3-pluggy (1.3.0-1) ...
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Unpacking python3-pysam (0.22.0+ds-1+rpi1) ...
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Unpacking smalt (0.7.6-12) ...
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Setting up libhtscodecs2:armhf (1.6.0-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.14-2) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-2) ...
Setting up java-common (0.75) ...
Setting up libtest-deep-perl (1.204-1) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up gawk (1:5.2.1-2) ...
Setting up libalgorithm-diff-perl (1.201-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.78.3-1) ...
No schema files found: doing nothing.
Setting up libpython3.11-stdlib:armhf (3.11.7-2) ...
Setting up libdebhelper-perl (13.11.9) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up libasound2-data (1.2.10-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ...
Setting up libnspr4:armhf (2:4.35-1.1) ...
Setting up libtext-diff-perl (1.45-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libavahi-common-data:armhf (0.8-13) ...
Setting up libncurses6:armhf (6.4+20231209-1) ...
Setting up libdbus-1-3:armhf (1.14.10-3) ...
Setting up libbambamc0:armhf (0.0.50-6) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libssl-dev:armhf (3.1.4-2) ...
Setting up libpng16-16:armhf (1.6.40-2) ...
Setting up autopoint (0.21-14) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libpcsclite1:armhf (2.0.1-1) ...
Setting up libgfortran5:armhf (13.2.0-7+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up libcapture-tiny-perl (0.48-2) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libasound2:armhf (1.2.10-3) ...
Setting up mummer (3.23+dfsg-8) ...
Setting up libsub-uplevel-perl (0.2800-3) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-3) ...
Setting up libdevel-stacktrace-perl (2.0400-2) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up openssl (3.1.4-2) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up kmc (3.2.3+dfsg-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up liblocale-gettext-perl (1.07-6) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up smalt (0.7.6-12) ...
Setting up python3.11 (3.11.7-2) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up fontconfig-config (2.14.2-6) ...
Setting up libtest-warn-perl (0.37-2) ...
Setting up libavahi-common3:armhf (0.8-13) ...
Setting up libtest-differences-perl (0.71-1) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up python3 (3.11.4-5) ...
Setting up libnss3:armhf (2:3.95-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
Setting up dh-autoreconf (20) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up python3-packaging (23.2-1) ...
Setting up libtest-exception-perl (0.43-3) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1) ...
Setting up python3-pluggy (1.3.0-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libharfbuzz0b:armhf (8.0.1-1) ...
Setting up ca-certificates-java (20230710) ...
No JRE found. Skipping Java certificates setup.
Setting up python3-lib2to3 (3.11.5-1) ...
Setting up libavahi-client3:armhf (0.8-13) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.11.5-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up python3-pysam (0.22.0+ds-1+rpi1) ...
Setting up python3-setuptools (68.1.2-2) ...
Setting up libtest-most-perl (0.38-1) ...
Setting up python3-pytest (7.4.3-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3-networkx (2.8.8-1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.19-1) ...
Setting up python3-numpy (1:1.24.2-2) ...
Setting up libcups2:armhf (2.4.7-1) ...
Setting up dh-python (6.20231204) ...
Setting up bioperl (1.7.8-1) ...
Setting up fastaq (3.17.0-6) ...
Setting up debhelper (13.11.9) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.14.2-6) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
Setting up openjdk-17-jre-headless:armhf (17.0.9+9-2+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
Processing triggers for ca-certificates-java (20230710) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.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:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.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_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem
Adding debian:E-Tugra_Global_Root_CA_RSA_v3.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_-_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:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.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:ISRG_Root_X2.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: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_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_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:Telia_Root_CA_v2.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:TunTrust_Root_CA.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
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up openjdk-17-jdk-headless:armhf (17.0.9+9-2+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-jre-headless (2:1.17-75) ...
Setting up default-jdk-headless (2:1.17-75) ...
Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20230311) ...
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 (20230710) ...
done.
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bioperl_1.7.8-1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.10 bzip2_1.0.8-5+b2 ca-certificates_20230311 ca-certificates-java_20230710 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-7+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 default-jdk-headless_2:1.17-75 default-jre-headless_2:1.17-75 dh-autoreconf_20 dh-python_6.20231204 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 fastaq_3.17.0-6 file_1:5.45-2 findutils_4.9.0-5 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gawk_1:5.2.1-2 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 gcc-13-base_13.2.0-7+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_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 java-common_0.75 kmc_3.2.3+dfsg-1 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-7+rpi1 libasound2_1.2.10-3 libasound2-data_1.2.10-3 libassuan0_2.5.6-1 libatomic1_13.2.0-7+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libavahi-client3_0.8-13 libavahi-common-data_0.8-13 libavahi-common3_0.8-13 libbambamc0_0.0.50-6 libbinutils_2.41-6+rpi1 libbio-perl-perl_1.7.8-1 libblas3_3.11.0-2 libblkid1_2.39.3-2 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcapture-tiny-perl_0.48-2 libcc1-0_13.2.0-7+rpi1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcups2_2.4.7-1 libcurl3-gnutls_8.4.0-2+rpi1 libdata-stag-perl_0.14-3 libdb5.3_5.3.28+dfsg2-4 libdbus-1-3_1.14.10-3 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdeflate0_1.18-1 libdevel-stacktrace-perl_2.0400-2 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexception-class-perl_1.45-1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.2-6 libfreetype6_2.13.2+dfsg-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-7+rpi1 libgcc-s1_13.2.0-7+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-7+rpi1 libglib2.0-0_2.78.3-1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20.1-5 libharfbuzz0b_8.0.1-1 libhogweed6_3.9.1-2 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libio-string-perl_1.08-4 libisl23_0.26-3 libjansson4_2.14-2 libjpeg62-turbo_1:2.1.5-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 liblapack3_3.11.0-2 liblcms2-2_2.14-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses6_6.4+20231209-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnspr4_2:4.35-1.1 libnss3_2:3.95-1 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libpcsclite1_2.0.1-1 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libpng16-16_1.6.40-2 libpsl5_0.21.2-1+b1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.7-2 libpython3.11-stdlib_3.11.7-2 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsigsegv2_2.14-1 libsmartcols1_2.39.3-2 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-3 libssl-dev_3.1.4-2 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 libsub-override-perl_0.10-1 libsub-uplevel-perl_0.2800-3 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtest-deep-perl_1.204-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-diff-perl_1.45-2 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-7+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.3-2 mummer_3.23+dfsg-8 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 netbase_6.4 openjdk-17-jdk-headless_17.0.9+9-2+rpi1 openjdk-17-jre-headless_17.0.9+9-2+rpi1 openssl_3.1.4-2 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-distutils_3.11.5-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-networkx_2.8.8-1 python3-numpy_1:1.24.2-2 python3-packaging_23.2-1 python3-pkg-resources_68.1.2-2 python3-pluggy_1.3.0-1 python3-pysam_0.22.0+ds-1+rpi1 python3-pytest_7.4.3-2 python3-setuptools_68.1.2-2 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 samtools_1.19-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 smalt_0.7.6-12 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usrmerge_38 util-linux_2.39.3-2 util-linux-extra_2.39.3-2 xz-utils_5.4.5-0.1 zlib1g_1:1.2.13.dfsg-3

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


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

gpgv: Signature made Mon Dec 18 21:30:07 2023 UTC
gpgv:                using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-4.dsc: no acceptable signature found
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-4.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 disc space
----------------

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-694636ec-20ff-4a12-a512-e27bc7d11d87
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.11+ds-4
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 *.egg-info .pytest_cache build
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:310: python3.11 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 387ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SizeFasta.java]]
[parsing completed 31ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 44ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/Utils.java]]
[parsing completed 53ms]
[parsing started SimpleFileObject[/<<BUILDDIR>>/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 102ms]
[loading /modules/java.desktop/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/java.compiler/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/jdk.incubator.vector/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/jdk.random/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/jdk.jpackage/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/java.base/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/java.management/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/jdk.nio.mapmode/module-info.class]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/jdk.incubator.foreign/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 7268ms]
dh_auto_build --
I: pybuild base:310: /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_3.11_iva/build/iva
copying iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/common.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/contig.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/edge.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/graph.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/qc.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/seed.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.11
copying and adjusting scripts/iva -> build/scripts-3.11
copying and adjusting scripts/iva_qc -> build/scripts-3.11
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.11
changing mode of build/scripts-3.11/iva from 644 to 755
changing mode of build/scripts-3.11/iva_qc from 644 to 755
changing mode of build/scripts-3.11/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 3.11.7, pytest-7.4.3, pluggy-1.3.0 -- /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)

../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1
  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import get_distribution

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/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 35.71s =======================
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:310: /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/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
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/python3.11
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/__init__.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/assembly.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/common.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/edge.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/egg_extract.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/external_progs.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/graph.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kcount.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kmers.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kraken.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mummer.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc_external.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed_processor.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_data_runner.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mapping.py -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/colsum.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getCorrectnessStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getMummerStats.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.java -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Pair.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Translate.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$ToProtein.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.class -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/main.ratt.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config.hiv -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt_correction.pm -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/start.ratt.sh -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/embl2gff.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/genbank2embl.pl -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim/adapters.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
creating /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_1.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_2.fq.gz -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /<<BUILDDIR>>/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reference.fasta -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/assembly.py to assembly.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/common.py to common.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig.py to contig.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig_trim.py to contig_trim.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/edge.py to edge.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/egg_extract.py to egg_extract.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/external_progs.py to external_progs.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/graph.py to graph.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kcount.py to kcount.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kmers.py to kmers.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kraken.py to kraken.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mummer.py to mummer.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc.py to qc.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc_external.py to qc_external.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim.py to read_trim.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed.py to seed.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed_processor.py to seed_processor.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-311.pyc
byte-compiling /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mapping.py to mapping.cpython-311.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/python3.11/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-3.11/iva -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.11/iva_qc -> /<<BUILDDIR>>/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.11/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-4_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-4_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../iva_1.0.11+ds-4_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 2023-12-24T05:31:46Z

Finished
--------

I: Built successfully

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


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


iva_1.0.11+ds-4_armhf.changes:
------------------------------

Format: 1.8
Date: Mon, 18 Dec 2023 22:00:38 +0100
Source: iva
Binary: iva
Architecture: armhf
Version: 1.0.11+ds-4
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
 iva        - iterative virus sequence assembler
Closes: 1045886
Changes:
 iva (1.0.11+ds-4) unstable; urgency=medium
 .
   * Enable building twice in a row.
     Closes: #1045886
   * Bump Standards-Version.
   * Bump debian directory copyright date.
Checksums-Sha1:
 4e3e7b0d8ecae4c56cec79f328cd002067af0d97 8034 iva_1.0.11+ds-4_armhf.buildinfo
 cfa82733d7e38433bc9dd2c69e2898404ca46400 8581448 iva_1.0.11+ds-4_armhf.deb
Checksums-Sha256:
 96d5d1b63549fe5b8a7d81f6538dc5874699f4afccd87b04d045cf340f2174b6 8034 iva_1.0.11+ds-4_armhf.buildinfo
 382af26a0f96c2e571a8d56b06532ef947228f4e954abc1ceb8a0f6aefdef95b 8581448 iva_1.0.11+ds-4_armhf.deb
Files:
 a7248304ecf042ab6a0e69fb2f13aab4 8034 science optional iva_1.0.11+ds-4_armhf.buildinfo
 263ee5737b88fa52e2fcd0ee1d78c628 8581448 science optional iva_1.0.11+ds-4_armhf.deb

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


iva_1.0.11+ds-4_armhf.deb
-------------------------

 new Debian package, version 2.0.
 size 8581448 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-4
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 8770
 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 2023-12-18 21:00 ./
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/bin/
-rwxr-xr-x root/root     17240 2023-12-18 21:00 ./usr/bin/iva
-rwxr-xr-x root/root      6228 2023-12-18 21:00 ./usr/bin/iva_qc
-rwxr-xr-x root/root      2406 2023-12-18 21:00 ./usr/bin/iva_qc_make_db
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/lib/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/lib/python3/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/
-rw-r--r-- root/root       488 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt
-rw-r--r-- root/root         0 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt
-rw-r--r-- root/root         4 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt
drwxr-xr-x root/root         0 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/
-rw-r--r-- root/root       508 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class
-rw-r--r-- root/root     10213 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class
-rw-r--r-- root/root     14839 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java
-rw-r--r-- root/root      3689 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class
-rw-r--r-- root/root      3611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java
-rw-r--r-- root/root      2898 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class
-rw-r--r-- root/root      2229 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java
-rw-r--r-- root/root       640 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class
-rw-r--r-- root/root      4727 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class
-rw-r--r-- root/root      1303 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class
-rw-r--r-- root/root      5920 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class
-rw-r--r-- root/root     13712 2023-12-18 21:00 ./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 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/ratt/
-rwxr-xr-x root/root      1008 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl
-rwxr-xr-x root/root      1045 2023-12-18 21:00 ./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 2023-12-18 21:00 ./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 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz
-rw-r--r-- root/root   4661713 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/share/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/share/doc/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/share/doc/iva/
-rw-r--r-- root/root      1086 2023-12-18 21:00 ./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 2023-12-18 21:00 ./usr/share/doc/iva/copyright
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/share/man/
drwxr-xr-x root/root         0 2023-12-18 21:00 ./usr/share/man/man1/
-rw-r--r-- root/root      2252 2023-12-18 21:00 ./usr/share/man/man1/iva.1.gz
-rw-r--r-- root/root      1282 2023-12-18 21:00 ./usr/share/man/man1/iva_qc.1.gz
-rw-r--r-- root/root       642 2023-12-18 21:00 ./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: 37412
Build-Time: 132
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 1130
Job: iva_1.0.11+ds-4
Machine Architecture: armhf
Package: iva
Package-Time: 1323
Source-Version: 1.0.11+ds-4
Space: 37412
Status: successful
Version: 1.0.11+ds-4
--------------------------------------------------------------------------------
Finished at 2023-12-24T05:31:46Z
Build needed 00:22:03, 37412k disc space
Raspbian Package Auto-Building

Build log for iva (1.0.11+ds-4) on armhf
