Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Hi Pierre, a, now I've got it! Great it runs now. Uploaded thanks to your hint, Andreas. On Mon, Apr 20, 2020 at 06:24:00PM +0200, Pierre Gruet wrote: > Hi Andreas, > > Le 20/04/2020 à 12:08, Andreas Tille a écrit : > > > > Thanks a lot for checking. The issue is that we can not build the recent > > upstream version as I wrote in > > > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 > > > > Most probably that's *not* a problem of python-cobra but rather of > > python2-sbml5 (I think Liubov in CC found this out but I simply forgot). > > If you have any spare resources could you please verify this? Please > > checkout latest Git > > > >https://salsa.debian.org/med-team/python-cobra > > > > Sorry for maybe explaining things unclearly in my previous email, but what > you suggest is what I did: I took your packaging of version 0.18.0-1 in > Salsa, and I could build it without a problem in a sid chroot. > Some test have ``xfail'' result, but none has ``fail''. > > I understand the problem you showed in > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 > > means some module could not be loaded, but as I did not encounter this > problem while building, I wrote to you this morning in order to try to > understand the reason. > > > > > Kind regards and thanks again for your attempt to help > > > > Andreas. > > > > I hope this can help, or at least that we can understand the reason why we > have different results at a 16-day interval. > > All the best, > Pierre > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Hi Andreas, Le 20/04/2020 à 12:08, Andreas Tille a écrit : > > Thanks a lot for checking. The issue is that we can not build the recent > upstream version as I wrote in > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 > > Most probably that's *not* a problem of python-cobra but rather of > python2-sbml5 (I think Liubov in CC found this out but I simply forgot). > If you have any spare resources could you please verify this? Please > checkout latest Git > >https://salsa.debian.org/med-team/python-cobra > Sorry for maybe explaining things unclearly in my previous email, but what you suggest is what I did: I took your packaging of version 0.18.0-1 in Salsa, and I could build it without a problem in a sid chroot. Some test have ``xfail'' result, but none has ``fail''. I understand the problem you showed in https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 means some module could not be loaded, but as I did not encounter this problem while building, I wrote to you this morning in order to try to understand the reason. > > Kind regards and thanks again for your attempt to help > > Andreas. > I hope this can help, or at least that we can understand the reason why we have different results at a 16-day interval. All the best, Pierre
Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Hi Pierre, On Mon, Apr 20, 2020 at 11:35:33AM +0200, Pierre Gruet wrote: > I gave it a try this morning but was not able to reproduce your issue in a > sid chroot, with the most recent version of python-cobra that is packaged in > the Salsa repository. > The test session can be successfully launched in my chroot. Yet, I see that > some tests do not pass, which is maybe another libsbml-related matter. This > does not prevent the build from being done. > > Could you please either try again or give details on your configuration for > reproducing the issue? Thanks a lot for checking. The issue is that we can not build the recent upstream version as I wrote in https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656#10 Most probably that's *not* a problem of python-cobra but rather of python2-sbml5 (I think Liubov in CC found this out but I simply forgot). If you have any spare resources could you please verify this? Please checkout latest Git https://salsa.debian.org/med-team/python-cobra Kind regards and thanks again for your attempt to help Andreas. -- http://fam-tille.de
Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Hi Andreas, I gave it a try this morning but was not able to reproduce your issue in a sid chroot, with the most recent version of python-cobra that is packaged in the Salsa repository. The test session can be successfully launched in my chroot. Yet, I see that some tests do not pass, which is maybe another libsbml-related matter. This does not prevent the build from being done. Could you please either try again or give details on your configuration for reproducing the issue? All the best, Pierre
Processed: Re: Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Processing control commands: > tags -1 help Bug #955656 [src:python-cobra] python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib' Added tag(s) help. -- 955656: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=955656 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Control: tags -1 help
Hi,
this bug is fixed in Git. Unfortunately there is an issue with python3-libsbml
which prevents successful building:
ERROR collecting test session _
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:440: in
_importconftest
return self._conftestpath2mod[conftestpath]
E KeyError:
local('/build/python-cobra-0.18.0/.pybuild/cpython3_3.7_cobra/build/cobra/test/conftest.py')
During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:446: in
_importconftest
mod = conftestpath.pyimport()
/usr/lib/python3/dist-packages/py/_path/local.py:701: in pyimport
__import__(modname)
cobra/__init__.py:40: in
from cobra import io
cobra/io/__init__.py:8: in
from cobra.io.sbml import read_sbml_model, write_sbml_model, \
cobra/io/sbml.py:41: in
import libsbml
/usr/lib/python3/dist-packages/libsbml/libsbml.py:22: in
import _libsbml
E ModuleNotFoundError: No module named '_libsbml'
During handling of the above exception, another exception occurred:
/usr/lib/python3/dist-packages/py/_path/common.py:383: in visit
for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
/usr/lib/python3/dist-packages/py/_path/common.py:435: in gen
for p in self.gen(subdir):
/usr/lib/python3/dist-packages/py/_path/common.py:424: in gen
dirs = self.optsort([p for p in entries
/usr/lib/python3/dist-packages/py/_path/common.py:425: in
if p.check(dir=1) and (rec is None or rec(p))])
/usr/lib/python3/dist-packages/_pytest/main.py:667: in _recurse
ihook = self.gethookproxy(dirpath)
/usr/lib/python3/dist-packages/_pytest/main.py:482: in gethookproxy
my_conftestmodules = pm._getconftestmodules(fspath)
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:424: in
_getconftestmodules
mod = self._importconftest(conftestpath.realpath())
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:463: in
_importconftest
raise ConftestImportFailure(conftestpath, sys.exc_info())
E _pytest.config.ConftestImportFailure:
(local('/build/python-cobra-0.18.0/.pybuild/cpython3_3.7_cobra/build/cobra/test/conftest.py'),
(, ModuleNotFoundError("No module named
'_libsbml'"), ))
=== warnings summary ===
Any help is really welcome
Andreas.
--
http://fam-tille.de
Bug#955656: python-cobra: FTBFS: E ModuleNotFoundError: No module named 'matplotlib'
Source: python-cobra Version: 0.14.2-2 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200402 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > debian/rules build > dh build --with python3 --buildsystem=pybuild >dh_update_autotools_config -O--buildsystem=pybuild >dh_autoreconf -O--buildsystem=pybuild >dh_auto_configure -O--buildsystem=pybuild > I: pybuild base:217: python3.7 setup.py config > running config > I: pybuild base:217: python3.8 setup.py config > running config >dh_auto_build -O--buildsystem=pybuild > I: pybuild base:217: /usr/bin/python3.7 setup.py build > running build > running build_py > creating /<>/.pybuild/cpython3_3.7_cobra/build/cobra > copying cobra/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra > copying cobra/exceptions.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra > creating /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > copying cobra/util/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > copying cobra/util/array.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > copying cobra/util/util.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > copying cobra/util/solver.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > copying cobra/util/context.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/util > creating /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/configuration.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/object.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/species.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/singleton.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/gene.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/dictlist.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/metabolite.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/reaction.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/model.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/formula.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > copying cobra/core/solution.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/core > creating > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/geometric.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/room.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/loopless.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/deletion.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/gapfilling.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/phenotype_phase_plane.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/variability.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/sampling.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/parsimonious.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/summary.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/moma.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > copying cobra/flux_analysis/reaction.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis > creating /<>/.pybuild/cpython3_3.7_cobra/build/cobra/test > copying cobra/test/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/test > copying cobra/test/test_manipulation.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/test > copying cobra/test/test_medium.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/test > copying cobra/test/conftest.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/test > creating /<>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation > copying cobra/manipulation/validate.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation > copying cobra/manipulation/modify.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation > copying cobra/manipulation/__init__.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation > copying cobra/manipulation/delete.py -> > /<>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation > copying cobra/manipulation/annotate.py -> >
