Re: RoSA ante portas - happily pass this on
Hi Andreas, hi Dylan,
On 04.07.20 10:11, Dylan Aïssi wrote:
Hi Andreas,
Le sam. 4 juil. 2020 à 09:43, Andreas Tille <andreas@an3as.eu> a écrit :
@Dylan: Any idea how to fix
E: r-other-rosa: requires-r-api
\o/ this tag is finally useful :-)
I pushed a change that should fix this issue. I was not able to test
because r-cran-lsd is not available (still in NEW). Could you try this
change for me?
Lintian still is
lintian ../rosa_1.0-1_amd64.changes
E: r-other-rosa: requires-r-api
W: python3-rosa:
executable-not-elf-or-scriptusr/lib/python3/dist-packages/rosa/tests/Data/intronfile.csv
(<- fixed now)
W: python3-rosa: no-manual-pageusr/bin/antisense_job
W: python3-rosa: no-manual-pageusr/bin/count_spliced
W: python3-rosa: no-manual-pageusr/bin/make_annotation
I added r-cran-lsd to med.functional.domains, should there be any
further interim demand.
The rosa package was renamed to r-other-rosa. In analogy to how we deal
with python packages that live on their own - isn't a mere "rosa"
package missing? I have aded that now, which added
W: rosa: empty-binary-package
with dependencies on r-other-rosa and python3-rosa. My initial attempt
was to only have a rosa package but dh-r or pybuild kept overwriting
each other's variables. That is where my time went.
The testing refers to python that makes problems. I tried
cd python; ln -s ../debian .; PYTHONPATH=$(pwd) pytest-3
and get
=======================================================================================
ERRORS
========================================================================================
____________________________________________________________________
ERROR collecting rosa/tests/test_antisense.py
____________________________________________________________________
ImportError while importing test module
'/home/moeller/git/med-team/rosa/rosa/python/rosa/tests/test_antisense.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
rosa/tests/test_antisense.py:27: in <module>
from rosa.antisense import Antisense
rosa/antisense.py:32: in <module>
from runcommand import RunCommand
E ModuleNotFoundError: No module named 'runcommand'
____________________________________________________________________
ERROR collecting rosa/tests/test_gffparser.py
____________________________________________________________________
ImportError while importing test module
'/home/moeller/git/med-team/rosa/rosa/python/rosa/tests/test_gffparser.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
rosa/tests/test_gffparser.py:29: in <module>
from rosa.gffparser import GffParser
rosa/gffparser.py:22: in <module>
from parser import Parser
E ImportError: cannot import name 'Parser' from 'parser'
(/usr/lib/python3.8/lib-dynload/parser.cpython-38-x86_64-linux-gnu.so)
____________________________________________________________________
ERROR collecting rosa/tests/test_gtfparser.py
____________________________________________________________________
ImportError while importing test module
'/home/moeller/git/med-team/rosa/rosa/python/rosa/tests/test_gtfparser.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
rosa/tests/test_gtfparser.py:29: in <module>
from rosa.gtfparser import GtfParser
rosa/gtfparser.py:22: in <module>
from parser import Parser
E ImportError: cannot import name 'Parser' from 'parser'
(/usr/lib/python3.8/lib-dynload/parser.cpython-38-x86_64-linux-gnu.so)
______________________________________________________________________
ERROR collecting rosa/tests/test_prune.py
______________________________________________________________________
ImportError while importing test module
'/home/moeller/git/med-team/rosa/rosa/python/rosa/tests/test_prune.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
rosa/tests/test_prune.py:27: in <module>
from rosa.antisense import Antisense
rosa/antisense.py:32: in <module>
from runcommand import RunCommand
E ModuleNotFoundError: No module named 'runcommand'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Interrupted: 4 errors during collection
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
I inform upstream about the .csv being executable
(https://github.com/bartongroup/RoSA/issues/11).
Best,
Steffen
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