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When Building python-biopython as much tests as possible should be run
to confirm the integrity of the build result. There are three types of
tests that can not be run:
1. which need online access since the build should work in an
offline chroot
2. tests needing a ready setup database server (MySQL and PostgreSQL)
3. non-free tools
4. tools that are not packaged for Debian yet
5. packages only available on some architectures are only tested there
6. packages failing tests for some other reasons (phyml)
The according tests are moved away from the test directory in the
debian/rules file. Please look there if you want to know what tests
are affected.
Since the Build of the package is done in a chroot and in this chroot
the setup of the database servers is not done it is not possible to run
the database connection tests (item 2.) This affects the tests:
BioSQL_MySQLdb for MySQL connections
BioSQL_psycopg2 for PostgreSQL connections
The non-free tools (item 3.) which are packaged are:
paml for test_PAML_tools.py
embassy-phylip for test_EmbossPhylipNew.py
you might like to install these manually if you are interested in these
tests.
The tools which are not packaged yet (item 4.) are:
MSAProbs: http://msaprobs.sourceforge.net/
naccess: http://www.e-lucid.com/i/software/bioinformatics/naccess.html
It says: A non-commercial use only licence for academic
researchers is available from the following website:
http://www.bioinf.manchester.ac.uk/naccess/
but the later site seems to have no content
Dfdist: http://tomato.biol.trinity.edu/programs/index.php/DFDIST
fdist2: It will be described at
https://courses.washington.edu/popgen/Software.htm
as "relatively old but still widely used program based on
Beaumont & Nichols 1996. Uses simuations to derive confidence
limits around mean FSTs - outliers from these limits may be
under selection.
The linked page is not available.
GenePop: http://genepop.curtin.edu.au/
Download at http://kimura.univ-montp2.fr/~rousset/Genepop.htm
Recently updated CeCILL Licence
SIMCOAL2: http://cmpg.unibe.ch/software/simcoal2/
XXmotif: http://xxmotif.genzentrum.lmu.de/index.php?id=about
http://xxmotif.genzentrum.lmu.de/index.php?id=download
fastsimcoal: Non-free, see
https://lists.debian.org/debian-med/2014/09/msg00016.html
But it does not need to be explicitly excluded since the
test suite itself checks the existence
There is a package only available on amd64 architectures:
bwa: The package is limited to amd64 only.
So the Build-Depends from bwa is only on these architectures and the
test is consequently only run there.
As described in Bug https://bugs.debian.org/813262 there is a problem
with phyml when using recent libhmsbeagle and the test is running in a
chroot that has no proper GPU (emulator). So for the moment we also
need to exclude phyml from testing.
-- Andreas Tille <tille@debian.org> Tue, 04 Mar 2014 11:16:02 +0100
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