ragout →
2.3-3 →
armhf → 2021-10-20 08:15:11
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| ragout 2.3-3 (armhf) Wed, 20 Oct 2021 08:03:13 +0000 |
+==============================================================================+
Package: ragout
Version: 2.3-3
Source Version: 2.3-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-26a45ade-247e-4208-a2cf-9b7a0b8ed185' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 25s (1021 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'ragout' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/ragout.git
Please use:
git clone https://salsa.debian.org/med-team/ragout.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 12.3 MB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main ragout 2.3-3 (dsc) [2091 B]
Get:2 http://172.17.0.1/private bookworm-staging/main ragout 2.3-3 (tar) [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main ragout 2.3-3 (diff) [6852 B]
Fetched 12.3 MB in 1s (9822 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ragout-tpHfk7/ragout-2.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ragout-tpHfk7' 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-COaCqi/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-COaCqi/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-COaCqi/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-COaCqi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2632 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 37 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, python3-networkx, python3-setuptools
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, python3-networkx, python3-setuptools
dpkg-deb: building package 'sbuild-build-depends-ragout-dummy' in '/<<BUILDDIR>>/resolver-COaCqi/apt_archive/sbuild-build-depends-ragout-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-ragout-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-COaCqi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Sources [524 B]
Get:5 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ Packages [600 B]
Fetched 2457 B in 1s (3364 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install ragout build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libdebhelper-perl libelf1 libexpat1 libexpat1-dev libffi8
libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmpdec3 libpipeline1
libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev
libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-decorator python3-dev python3-distutils python3-lib2to3
python3-minimal python3-networkx python3-pkg-resources python3-setuptools
python3.9 python3.9-dev python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-toml
gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python-networkx-doc
python-setuptools-doc python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl javascript-common ca-certificates
libltdl-dev libmail-sendmail-perl python3-gdal python3-matplotlib
python3-numpy python3-pydot python3-pygraphviz python3-scipy python3-yaml
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libdebhelper-perl libelf1 libexpat1 libexpat1-dev libffi8
libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmpdec3 libpipeline1
libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev
libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-decorator python3-dev python3-distutils python3-lib2to3
python3-minimal python3-networkx python3-pkg-resources python3-setuptools
python3.9 python3.9-dev python3.9-minimal sbuild-build-depends-ragout-dummy
sensible-utils zlib1g-dev
0 upgraded, 60 newly installed, 0 to remove and 37 not upgraded.
Need to get 30.1 MB of archives.
After this operation, 115 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-COaCqi/apt_archive ./ sbuild-build-depends-ragout-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-3 [21.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf dh-python all 5.20211016.1 [103 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.1-2 [135 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libjs-underscore all 1.9.1~dfsg-4 [100 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.2.0-4 [137 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.7-4+rpi1 [1416 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.7-4+rpi1 [3060 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libpython3-dev armhf 3.9.2-3 [21.7 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf python3-decorator all 4.4.2-2 [15.8 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.7-4+rpi1 [501 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf python3-dev armhf 3.9.2-3 [24.8 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf python3-pkg-resources all 58.2.0-1 [192 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf python3-networkx all 2.5+ds-2 [900 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf python3-setuptools all 58.2.0-1 [396 kB]
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Unpacking sbuild-build-depends-ragout-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-3) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
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Setting up libffi8:armhf (3.4.2-3) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up libjs-underscore (1.9.1~dfsg-4) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython3.9:armhf (3.9.7-4+rpi1) ...
Setting up libjs-sphinxdoc (4.2.0-4) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.9-dev:armhf (3.9.7-4+rpi1) ...
Setting up python3 (3.9.2-3) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up python3-decorator (4.4.2-2) ...
Setting up python3.9-dev (3.9.7-4+rpi1) ...
Setting up python3-lib2to3 (3.9.7-1) ...
Setting up python3-pkg-resources (58.2.0-1) ...
Setting up python3-distutils (3.9.7-1) ...
Setting up dh-python (5.20211016.1) ...
Setting up libpython3-dev:armhf (3.9.2-3) ...
Setting up python3-setuptools (58.2.0-1) ...
Setting up debhelper (13.5.2) ...
Setting up python3-networkx (2.5+ds-2) ...
Setting up python3-dev (3.9.2-3) ...
Setting up sbuild-build-depends-ragout-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20211016.1 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libexpat1-dev_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-sphinxdoc_4.2.0-4 libjs-underscore_1.9.1~dfsg-4 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpython3-dev_3.9.2-3 libpython3-stdlib_3.9.2-3 libpython3.9_3.9.7-4+rpi1 libpython3.9-dev_3.9.7-4+rpi1 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-decorator_4.4.2-2 python3-dev_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3-networkx_2.5+ds-2 python3-pkg-resources_58.2.0-1 python3-setuptools_58.2.0-1 python3.9_3.9.7-4+rpi1 python3.9-dev_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ragout-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.hINljRTz/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 18 11:32:22 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ragout_2.3-3.dsc
dpkg-source: info: extracting ragout in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ragout_2.3.orig.tar.xz
dpkg-source: info: unpacking ragout_2.3-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying connected_component_subgraphs.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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-26a45ade-247e-4208-a2cf-9b7a0b8ed185
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ragout
dpkg-buildpackage: info: source version 2.3-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean || true
I: pybuild base:232: python3.9 setup.py clean
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.9' does not exist -- can't clean it
rm -f bin/ragout-maf2synteny bin/ragout-overlap
rm -rf .pybuild
find . -name "*.o" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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:232: python3.9 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout
copying ragout/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout
copying ragout/__version__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout
copying ragout/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout
copying ragout/six.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph
copying ragout/assembly_graph/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph
copying ragout/assembly_graph/assembly_refine.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/chimera_detector.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/permutation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/repeat_resolver.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/breakpoint_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
copying ragout/breakpoint_graph/inferer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny
copying ragout/maf2synteny/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny
copying ragout/maf2synteny/maf2synteny.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap
copying ragout/overlap/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap
copying ragout/overlap/overlap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers
copying ragout/parsers/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers
copying ragout/parsers/fasta_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers
copying ragout/parsers/phylogeny_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers
copying ragout/parsers/recipe_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny
copying ragout/phylogeny/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny
copying ragout/phylogeny/inferer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny
copying ragout/phylogeny/phylogeny.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder
copying ragout/scaffolder/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder
copying ragout/scaffolder/output_generator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder
copying ragout/scaffolder/scaffolder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder
copying ragout/scaffolder/merge_iters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
copying ragout/shared/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
copying ragout/shared/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
copying ragout/shared/datatypes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
copying ragout/shared/debug.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
copying ragout/shared/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/cactus.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/hal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/maf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/sibelia.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
copying ragout/synteny_backend/synteny_backend.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
copying ragout/newick/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
copying ragout/newick/lexer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
copying ragout/newick/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
copying ragout/newick/tokens.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
copying ragout/newick/tree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests
copying ragout/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests
copying ragout/tests/test_toy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data
copying ragout/tests/data/DH1.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data
copying ragout/tests/data/ecoli.rcp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data
copying ragout/tests/data/mg1655.coords -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data
copying ragout/tests/data/mg1655_contigs.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make -C ragout/overlap/cpp_impl all
make[2]: Entering directory '/<<PKGBUILDDIR>>/ragout/overlap/cpp_impl'
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG build_graph.cpp -o build_graph.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG fasta.cpp -o fasta.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG overlap.cpp -o overlap.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG suffix_array.cpp -o suffix_array.o
g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /<<PKGBUILDDIR>>/bin/ragout-overlap
make[2]: Leaving directory '/<<PKGBUILDDIR>>/ragout/overlap/cpp_impl'
make -C ragout/maf2synteny/cpp_impl all
make[2]: Entering directory '/<<PKGBUILDDIR>>/ragout/maf2synteny/cpp_impl'
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG breakpoint_graph.cpp -o breakpoint_graph.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG compress_algorithms.cpp -o compress_algorithms.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG maf_tools.cpp -o maf_tools.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++0x -Wall -O2 -DNDEBUG permutation.cpp -o permutation.o
g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /<<PKGBUILDDIR>>/bin/ragout-maf2synteny
make[2]: Leaving directory '/<<PKGBUILDDIR>>/ragout/maf2synteny/cpp_impl'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:232: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; python3.9 -m unittest discover -v
----------------------------------------------------------------------
Ran 0 tests in 0.001s
OK
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
running install
running build
running build_py
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make -C ragout/overlap/cpp_impl all
make[2]: Entering directory '/<<PKGBUILDDIR>>/ragout/overlap/cpp_impl'
g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /<<PKGBUILDDIR>>/bin/ragout-overlap
make[2]: Leaving directory '/<<PKGBUILDDIR>>/ragout/overlap/cpp_impl'
make -C ragout/maf2synteny/cpp_impl all
make[2]: Entering directory '/<<PKGBUILDDIR>>/ragout/maf2synteny/cpp_impl'
g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /<<PKGBUILDDIR>>/bin/ragout-maf2synteny
make[2]: Leaving directory '/<<PKGBUILDDIR>>/ragout/maf2synteny/cpp_impl'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
running install_lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/__version__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/main.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/six.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph/assembly_refine.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/assembly_graph/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/chimera_detector.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/permutation.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/repeat_resolver.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/breakpoint_graph.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/inferer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/breakpoint_graph/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny/maf2synteny.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/maf2synteny/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap/overlap.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/overlap/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers/fasta_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers/phylogeny_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers/recipe_parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/parsers/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny/inferer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny/phylogeny.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/phylogeny/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder/output_generator.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder/scaffolder.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder/merge_iters.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/scaffolder/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/config.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/datatypes.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/debug.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/utils.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/shared/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/cactus.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/hal.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/maf.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/sibelia.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/synteny_backend.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/synteny_backend/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/lexer.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/parser.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/tokens.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/tree.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/newick/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/test_toy.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data/DH1.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data/ecoli.rcp -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data/mg1655.coords -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/data/mg1655_contigs.fasta -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/data
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/tests/__pycache__/test_toy.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/__pycache__
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/ragout/__pycache__/__init__.cpython-39.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/__pycache__
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/__version__.py to __version__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/main.py to main.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/six.py to six.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/assembly_graph/assembly_refine.py to assembly_refine.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/chimera_detector.py to chimera_detector.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/permutation.py to permutation.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/repeat_resolver.py to repeat_resolver.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/breakpoint_graph.py to breakpoint_graph.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/breakpoint_graph/inferer.py to inferer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/maf2synteny/maf2synteny.py to maf2synteny.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/overlap/overlap.py to overlap.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/fasta_parser.py to fasta_parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/phylogeny_parser.py to phylogeny_parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/parsers/recipe_parser.py to recipe_parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny/inferer.py to inferer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/phylogeny/phylogeny.py to phylogeny.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/output_generator.py to output_generator.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/scaffolder.py to scaffolder.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/scaffolder/merge_iters.py to merge_iters.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/config.py to config.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/datatypes.py to datatypes.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/debug.py to debug.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/shared/utils.py to utils.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/cactus.py to cactus.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/hal.py to hal.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/maf.py to maf.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/sibelia.py to sibelia.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/synteny_backend/synteny_backend.py to synteny_backend.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/lexer.py to lexer.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/parser.py to parser.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/tokens.py to tokens.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/newick/tree.py to tree.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout/tests/test_toy.py to test_toy.cpython-39.pyc
running install_egg_info
running egg_info
creating ragout.egg-info
writing ragout.egg-info/PKG-INFO
writing dependency_links to ragout.egg-info/dependency_links.txt
writing entry points to ragout.egg-info/entry_points.txt
writing top-level names to ragout.egg-info/top_level.txt
writing manifest file 'ragout.egg-info/SOURCES.txt'
reading manifest file 'ragout.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'ragout.egg-info/SOURCES.txt'
Copying ragout.egg-info to /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.9/dist-packages/ragout-2.3.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ragout script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin
Installing C++ binaries
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
find debian -name LICENSE -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_installman -a -O--buildsystem=pybuild
dh_python3 -a -O--buildsystem=pybuild
I: dh_python3 tools:114: replacing shebang in debian/ragout/usr/bin/ragout
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
dpkg-shlibdeps: warning: debian/ragout/usr/bin/ragout-overlap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/ragout/usr/bin/ragout-maf2synteny contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ragout/usr/bin/ragout-overlap debian/ragout/usr/bin/ragout-maf2synteny were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
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 'ragout' in '../ragout_2.3-3_armhf.deb'.
dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../ragout_2.3-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-10-20T08:15:04Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
ragout_2.3-3_armhf.changes:
---------------------------
Format: 1.8
Date: Mon, 18 Oct 2021 11:12:32 +0200
Source: ragout
Binary: ragout ragout-dbgsym
Architecture: armhf
Version: 2.3-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
ragout - Reference-Assisted Genome Ordering UTility
Changes:
ragout (2.3-3) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
Checksums-Sha1:
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6929cac04cd05ad603ccc22197ee55224d450d6d 5836 ragout_2.3-3_armhf.buildinfo
89460b19461c5d22755ddad19c4db6250a73e2fd 2119540 ragout_2.3-3_armhf.deb
Checksums-Sha256:
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7e219ca5df91184691d1858b395738c0fafe3944c1b2c0e8c877c77d0877e5fc 5836 ragout_2.3-3_armhf.buildinfo
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Files:
f77223de5029b29dd05f350fbfc6c9c9 1275988 debug optional ragout-dbgsym_2.3-3_armhf.deb
2262406a00fa53dc97f0424c7c8ffca3 5836 science optional ragout_2.3-3_armhf.buildinfo
2be15e7268e07d2a9e1bed58c4f55259 2119540 science optional ragout_2.3-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
ragout-dbgsym_2.3-3_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 1275988 bytes: control archive=644 bytes.
404 bytes, 12 lines control
298 bytes, 3 lines md5sums
Package: ragout-dbgsym
Source: ragout
Version: 2.3-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1313
Depends: ragout (= 2.3-3)
Section: debug
Priority: optional
Description: debug symbols for ragout
Build-Ids: 158a71ccb499b2057c5d9e995d3c3853405d6f4c 34164bf2e8ae7a3891fa4e60abe80f95b6cfd97b
drwxr-xr-x root/root 0 2021-10-18 09:12 ./
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 352532 2021-10-18 09:12 ./usr/lib/debug/.build-id/15/8a71ccb499b2057c5d9e995d3c3853405d6f4c.debug
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 949680 2021-10-18 09:12 ./usr/lib/debug/.build-id/34/164bf2e8ae7a3891fa4e60abe80f95b6cfd97b.debug
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 26980 2021-10-18 09:12 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ragout.debug
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/share/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-18 09:12 ./usr/share/doc/ragout-dbgsym -> ragout
ragout_2.3-3_armhf.deb
----------------------
new Debian package, version 2.0.
size 2119540 bytes: control archive=2780 bytes.
1092 bytes, 24 lines control
5527 bytes, 61 lines md5sums
249 bytes, 12 lines * postinst #!/bin/sh
398 bytes, 12 lines * prerm #!/bin/sh
Package: ragout
Version: 2.3-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9641
Depends: libc6 (>= 2.4), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2), python3:any, python3-networkx
Recommends: sibelia
Section: science
Priority: optional
Homepage: https://github.com/fenderglass/Ragout/
Description: Reference-Assisted Genome Ordering UTility
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
chromosome-level scaffolding using multiple references. Given initial
assembly fragments (contigs/scaffolds) and one or multiple related
references (complete or draft), it produces a chromosome-scale assembly
(as a set of scaffolds).
.
The approach is based on the analysis of genome rearrangements (like
inversions or chromosomal translocations) between the input genomes and
reconstructing the most parsimonious structure of the target genome.
.
Ragout now supports both small and large genomes (of mammalian scale
and complexity). The assembly of highly polymorphic genomes is
currently limited.
drwxr-xr-x root/root 0 2021-10-18 09:12 ./
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/bin/
-rwxr-xr-x root/root 787 2021-10-18 09:12 ./usr/bin/ragout
-rwxr-xr-x root/root 95884 2021-10-18 09:12 ./usr/bin/ragout-maf2synteny
-rwxr-xr-x root/root 50828 2021-10-18 09:12 ./usr/bin/ragout-overlap
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/python3/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout-2.3.egg-info/
-rw-r--r-- root/root 287 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout-2.3.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout-2.3.egg-info/dependency_links.txt
-rw-r--r-- root/root 45 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout-2.3.egg-info/entry_points.txt
-rw-r--r-- root/root 201 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout-2.3.egg-info/top_level.txt
drwxr-xr-x root/root 0 2021-10-18 09:12 ./usr/lib/python3/dist-packages/ragout/
-rw-r--r-- root/root 0 2020-03-17 21:36 ./usr/lib/python3/dist-packages/ragout/__init__.py
-rw-r--r-- root/root 20 2020-03-17 21:36 ./usr/lib/python3/dist-packages/ragout/__version__.py
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 124220
Build-Time: 313
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 343
Job: ragout_2.3-3
Machine Architecture: armhf
Package: ragout
Package-Time: 711
Source-Version: 2.3-3
Space: 124220
Status: successful
Version: 2.3-3
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Finished at 2021-10-20T08:15:04Z
Build needed 00:11:51, 124220k disc space