[Debian-med-packaging] Bug#917093: matplotlib2 breaks graphlan autopkgtest

[Andreas Tille]

Control: tags -1 help
Control: tags -1 upstream
Control: forwarded -1 Nicola Segata <nicola.segata at unitn.it>

Hi Nicola,

I'd like to forward a bug report against the Debian packaged graphlan.
(I admit I have not found a way to report issues publicly on bitbucket.)

The packaged code is identical with tag 1.1.3 (Commit c1fa530).

Any hint how to make graphlan compatible with latest matplotlib?

Kind regards

       Andreas.

On Sat, Dec 22, 2018 at 03:17:57PM +0100, Paul Gevers wrote:
> 
> With a recent upload of matplotlib2 the autopkgtest of graphlan fails in
> testing when that autopkgtest is run with the binary packages of
> matplotlib2 from unstable. It passes when run with only packages from
> testing. In tabular form:
>                        pass            fail
> matplotlib2            NA              2.2.3-4
> matplotlib             from testing    NA
> graphlan               from testing    1.1.3-1
> all others             from testing    from testing
> 
> I copied some of the output at the bottom of this report.
> 
> Currently this regression is contributing to the delay of the migration
> of matplotlib2 (and matplotlib) to testing [1]. Due to the nature of
> this issue, I filed this bug report against both packages. Can you
> please investigate the situation and reassign the bug to the right
> package? If needed, please change the bug's severity.
> 
> More information about this bug and the reason for filing it can be found on
> https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
> 
> Paul
> 
> [1] https://qa.debian.org/excuses.php?package=matplotlib2
> 
> https://ci.debian.net/data/autopkgtest/testing/amd64/g/graphlan/1563802/log.gz
> 
> autopkgtest [04:48:34]: test run-unit-test: [-----------------------
> Test script ./hmp_metahit/PIPELINE.sh requires export2graphlan which is
> not available.
> Running test script ./gut_microbiome/run.sh .
> /usr/lib/python2.7/dist-packages/matplotlib/__init__.py:1005:
> UserWarning: could not find rc file; returning defaults
>   warnings.warn(message)
> Traceback (most recent call last):
>   File "/usr/bin/graphlan_annotate", line 26, in <module>
>     from src.graphlan_lib import CircTree as CTree
>   File "/usr/share/graphlan/src/graphlan_lib.py", line 27, in <module>
>     from pylab import *
>   File "/usr/lib/python2.7/dist-packages/pylab.py", line 1, in <module>
>     from matplotlib.pylab import *
>   File "/usr/lib/python2.7/dist-packages/matplotlib/pylab.py", line 252,
> in <module>
>     from matplotlib import cbook, mlab, pyplot as plt
>   File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 31,
> in <module>
>     import matplotlib.colorbar
>   File "/usr/lib/python2.7/dist-packages/matplotlib/colorbar.py", line
> 36, in <module>
>     import matplotlib.contour as contour
>   File "/usr/lib/python2.7/dist-packages/matplotlib/contour.py", line
> 20, in <module>
>     import matplotlib.font_manager as font_manager
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1472, in <module>
>     _rebuild()
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1453, in _rebuild
>     fontManager = FontManager()
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1057, in __init__
>     paths = [os.path.join(rcParams['datapath'], 'fonts', 'ttf'),
>   File "/usr/lib/python2.7/posixpath.py", line 70, in join
>     elif path == '' or path.endswith('/'):
> AttributeError: 'NoneType' object has no attribute 'endswith'
> /usr/lib/python2.7/dist-packages/matplotlib/__init__.py:1005:
> UserWarning: could not find rc file; returning defaults
>   warnings.warn(message)
> Traceback (most recent call last):
>   File "/usr/bin/graphlan", line 29, in <module>
>     from src.graphlan_lib import CircTree as CTree
>   File "/usr/share/graphlan/src/graphlan_lib.py", line 27, in <module>
>     from pylab import *
>   File "/usr/lib/python2.7/dist-packages/pylab.py", line 1, in <module>
>     from matplotlib.pylab import *
>   File "/usr/lib/python2.7/dist-packages/matplotlib/pylab.py", line 252,
> in <module>
>     from matplotlib import cbook, mlab, pyplot as plt
>   File "/usr/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 31,
> in <module>
>     import matplotlib.colorbar
>   File "/usr/lib/python2.7/dist-packages/matplotlib/colorbar.py", line
> 36, in <module>
>     import matplotlib.contour as contour
>   File "/usr/lib/python2.7/dist-packages/matplotlib/contour.py", line
> 20, in <module>
>     import matplotlib.font_manager as font_manager
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1472, in <module>
>     _rebuild()
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1453, in _rebuild
>     fontManager = FontManager()
>   File "/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py",
> line 1057, in __init__
>     paths = [os.path.join(rcParams['datapath'], 'fonts', 'ttf'),
>   File "/usr/lib/python2.7/posixpath.py", line 70, in join
>     elif path == '' or path.endswith('/'):
> AttributeError: 'NoneType' object has no attribute 'endswith'
> autopkgtest [04:48:35]: test run-unit-test: -----------------------]
> 




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