PhyML error - does that ring any bell? Re: RFS: python-biopython
Hello,
I need to thank you for this update. I had not looked at BioPython for a
loooonnggg time. Pretty impressive how it all developed.
I found this
Bio.PDB.mmtf docstring test ... skipped, missing Python dependency
Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python
dependency
Bio.PDB.mmtf.mmtfio docstring test ... skipped, missing Python dependency
to suggest packaging https://github.com/rcsb/mmtf-python - sigh. Any
takers? Would be quite a fit for next week's hackathon, I presume.
The test ran just fine on my local cowbuilder, but when compiling
directly there is an issue with PhyML - excluded as a dependency for
non-Intel platforms. I did not feel like investigating that, but I
sense at some point we should.
Uploaded.
Best,
Steffen
BioSQL docstring test ... ok
BioSQL.BioSeq docstring test ... ok
BioSQL.BioSeqDatabase docstring test ... ok
BioSQL.DBUtils docstring test ... ok
BioSQL.Loader docstring test ... ok
======================================================================
FAIL: test_phyml (test_phyml_tool.AppTests)
Run PhyML using the wrapper.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Tests/test_phyml_tool.py",
line 51, in test_phyml
self.assertEqual(len(err), 0)
AssertionError: 192 != 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Tests/test_phyml_tool.py",
line 60, in test_phyml
self.fail("PhyML wrapper error: %s" % exc)
AssertionError: PhyML wrapper error: 192 != 0
----------------------------------------------------------------------
Ran 515 tests in 266.465 seconds
FAILED (failures = 1)
Skipping any tests requiring internet access
Python version: 3.8.3 (default, May 14 2020, 11:03:12)
[GCC 9.3.0]
Operating system: posix linux
E: pybuild pybuild:352: test: plugin custom failed with: exit code=1:
set -e; \
mkdir -p
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/home;
\
mkdir -p
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Doc/examples;
\
cp -a Doc/Tutorial.tex
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Doc;
\
cp -a Doc/Tutorial
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Doc;
\
cp -a Doc/examples
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Doc;
\
cp -a Tests
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build; \
cd
/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Tests;
\
env DIALIGN2_DIR=/usr/share/dialign
EMBOSS_ROOT=/usr/lib/emboss
HOME=/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/home
python3.
8 run_tests.py --offline
dh_auto_test: error: pybuild --test -i python{version} -p 3.8 --test
--system=custom "--test-args=set -e; \\\
mkdir -p {build_dir}/home; \\\
mkdir -p {build_dir}/Doc/examples; \\\
cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\
cp -a Doc/Tutorial {build_dir}/Doc; \\\
cp -a Doc/examples {build_dir}/Doc; \\\
cp -a Tests {build_dir}; \\\
cd {build_dir}/Tests; \\\
env DIALIGN2_DIR=/usr/share/dialign
EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter}
run_tests.py --offline" returned exit code 13
On 12.06.20 18:39, Étienne Mollier wrote:
Hi Steffen,
Steffen Möller, on 2020-06-12 18:31:57 +0200:
I am at it - do you mind me adding you to the list of maintainers?
I suppose you meant the Uploaders field ? Sure, if it helps.
Kind Regards,
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