Bug#896025: Segfault in test suite of new upstream version (Was: python-mne FTBFS with python-matplotlib 2.2.2-1)

[Alexandre Gramfort]

I pinged you on github

I am pretty sure it's due to vtk/mayavi. I would suggest to package
without the hard dependency on mayavi.
if mayavi is not installed tests will be skipped and it should pass.

hope this helps

Alex

Bug#877344: [Debian-med-packaging] Bug#877344: Bug#877344: python-mne FTBFS: ERROR: Test ICA on raw and epochs

[Alexandre Gramfort]

oh mayavi

I would really be in favor of removing mayavi as a hard dependency.

is it an option?

Alex

Bug#877344: [Debian-med-packaging] Bug#877344: python-mne FTBFS: ERROR: Test ICA on raw and epochs

[Alexandre Gramfort]

Hi Andreas,

I don't have the bandwidth to address this sorry.

Also mne 0.13 is now 2 versions behind where we are now.
Nobody found the time to do the debian packaging for 0.14
and 0.15 so far.

Really sorry about this.

Best,
Alex


On Sun, Dec 3, 2017 at 6:45 PM, Andreas Tille  wrote:

> Hi,
>
> could please somebody care for this bug.  I admit I do not like the
> pattern that RC bugs in python-mne remain unanswered by any of the
> uploaders until you get a ping.  I would really love if you make sure
> to subscribe the package and answer this kind of bugs in a timely
> manner.
>
> Thank you
>
>   Andreas.
>
> --
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>
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Bug#858486: [Debian-med-packaging] Bug#858486: python-mne: broken symlink: /usr/lib/python2.7/dist-packages/mne/html/d3.v3.min.js -> ../../../../../share/javascript/d3/d3.min.js

[Alexandre Gramfort]

hi,

python-mne does need the d3 package so yes one should have the:

Depends: libjs-d3

can someone help me fixing this?

thanks a lot

Best,
Alex


On Wed, Mar 22, 2017 at 9:04 PM, Andreas Beckmann  wrote:
> Package: python-mne
> Version: 0.13.1+dfsg-2
> Severity: serious
> User: debian...@lists.debian.org
> Usertags: piuparts
>
> Hi,
>
> during a test with piuparts I noticed your package ships (or creates)
> a broken symlink.
>
> >From the attached log (scroll to the bottom...):
>
> 3m14.3s ERROR: FAIL: Broken symlinks:
>   /usr/lib/python2.7/dist-packages/mne/html/d3.v3.min.js -> 
> ../../../../../share/javascript/d3/d3.min.js
>
> Looks like a missing Depends: libjs-d3
>
> Feel free to downgrade the severity and use Recommends/Suggests
> instead of Depends if this *only* affects documentation.
>
>
> cheers,
>
> Andreas
>
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Bug#813982: [Debian-med-packaging] Bug#813982: python-mne: FTBFS: IndexError: an index can only have a single ellipsis ('...')

[Alexandre Gramfort]

Hi,

we identified the problem. We'll send a fix ASAP. It's an issue due to
an old version of numpy.

Best,
Alex


On Sun, Feb 7, 2016 at 10:44 AM, Chris Lamb  wrote:
> Source: python-mne
> Version: 0.10.1+dfsg-1
> Severity: serious
> Justification: fails to build from source
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
>
> Dear Maintainer,
>
> python-mne fails to build from source in unstable/amd64:
>
>   [..]
>
>   ==
>   ERROR: Test PSD estimation on epochs
>   --
>   Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
>   self.test(*self.arg)
> File "/usr/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 
> 147, in skipper_func
>   return f(*args, **kwargs)
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/time_frequency/tests/test_psd.py",
>  line 95, in test_psd_epochs
>   n_fft=n_fft, picks=picks)
> File "", line 2, in compute_epochs_psd
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/utils.py",
>  line 551, in verbose
>   return function(*args, **kwargs)
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/time_frequency/psd.py",
>  line 171, in compute_epochs_psd
>   data = epochs.get_data()[:, picks][..., time_mask]
>   IndexError: an index can only have a single ellipsis ('...')
>    >> begin captured stdout << -
>   Opening raw data file 
> /home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/io/tests/data/test_raw.fif...
>   Read a total of 3 projection items:
>   PCA-v1 (1 x 102)  idle
>   PCA-v2 (1 x 102)  idle
>   PCA-v3 (1 x 102)  idle
>   Current compensation grade : 0
>   Range : 25800 ... 40199 = 42.956 ...66.930 secs
>   Ready.
>   Adding average EEG reference projection.
>   1 projection items deactivated
>   2 matching events found
>   Reading 2671 ... 3271  =  4.447 ... 5.446 secs...
>   [done]
>   Applying baseline correction ... (mode: mean)
>   Reading 4350 ... 4950  =  7.243 ... 8.242 secs...
>   [done]
>   Applying baseline correction ... (mode: mean)
>   0 bad epochs dropped
>   2 matching events found
>   Reading 2370 ... 3572  =  3.946 ... 5.947 secs...
>   [done]
>   Applying baseline correction ... (mode: mean)
>   Reading 4049 ... 5251  =  6.741 ... 8.743 secs...
>   [done]
>   Applying baseline correction ... (mode: mean)
>   0 bad epochs dropped
>
>   - >> end captured stdout << --
>
>   ==
>   ERROR: Test plotting epochs psd (+topomap)
>   --
>   Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
>   self.test(*self.arg)
> File "/usr/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 
> 147, in skipper_func
>   return f(*args, **kwargs)
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/viz/tests/test_epochs.py",
>  line 164, in test_plot_psd_epochs
>   epochs.plot_psd()
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/epochs.py",
>  line 868, in plot_psd
>   verbose=None, show=show)
> File "", line 2, in plot_epochs_psd
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/utils.py",
>  line 551, in verbose
>   return function(*args, **kwargs)
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/viz/epochs.py",
>  line 495, in plot_epochs_psd
>   n_jobs=n_jobs)
> File "", line 2, in compute_epochs_psd
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/utils.py",
>  line 551, in verbose
>   return function(*args, **kwargs)
> File 
> "/home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/time_frequency/psd.py",
>  line 171, in compute_epochs_psd
>   data = epochs.get_data()[:, picks][..., time_mask]
>   IndexError: an index can only have a single ellipsis ('...')
>    >> begin captured stdout << -
>   Opening raw data file 
> /home/lamby/temp/cdt.20160207103006.4o4ykTzhLo/python-mne-0.10.1+dfsg/mne/io/tests/data/test_raw.fif...
>   Read a total of 3 projection items:
>   PCA-v1 (1 x 102)  idle
>   PCA-v2 (1 x 102)  idle
>   PCA-v3 (1 x 102)  idle
>   Current compensation grade : 0
>   Range : 25800 ... 40199 = 

Bug#813982: [Debian-med-packaging] Bug#813982: python-mne: FTBFS: IndexError: an index can only have a single ellipsis ('...')

[Alexandre Gramfort]

Hi,

we identified the problem. We'll send a fix ASAP. It's an issue due to
an old version of numpy.

Best,
Alex

Bug#800135: [Debian-med-packaging] Bug#800135: python-mne: FTBFS: /usr/share/openmpi/help-mpi-errors.txt: No such file or directory

[Alexandre Gramfort]

hi,

sorry for the delay.

Jaakko in CC has more time than me and is working
on the packaging of our latest release v0.10. We are hoping to fix it
with the new package. To avoid future issues with Mayavi we have
also decided to remove it from the strong deps of python-mne.

We'll probably push a v0.10 in the next few days to debian.org

Best,
Alex



On Sun, Sep 27, 2015 at 11:37 AM, Chris Lamb  wrote:
> Source: python-mne
> Version: 0.8.6+dfsg-2
> Severity: serious
> Justification: fails to build from source
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
>
> Dear Maintainer,
>
> python-mne fails to build from source in unstable/amd64. On the face of
> it you are missing openmpi-common in Build-Depends, but installing this
> surfaces a different error in the tests. Here's the build log with the
> shipped B-D:
>
>   [..]
>
>  debian/rules override_dh_auto_test
>   make[1]: Entering directory '/tmp/buildd/python-mne-0.8.6+dfsg'
>   MNE_DONTWRITE_HOME=true MNE_SKIP_SAMPLE_DATASET_TESTS=true
>   MNE_FORCE_SERIAL=true MNE_SKIP_NETWORK_TESTS=1 \
> xvfb-run --auto-servernum --server-num=20 -s "-screen 0 1024x768x24
> -ac +extension GLX +render -noreset" \
> nosetests mne
>   Xlib:  extension "RANDR" missing on display ":20".
>   /usr/lib/python2.7/dist-packages/pyface/toolkit.py:43:
>   DeprecationWarning: Default toolkit will change to 'qt4' in PyFace 5.0
> DeprecationWarning)
>   [profitbricks-build1-amd64:49321] [[INVALID],INVALID] ORTE_ERROR_LOG:
>   A system-required executable either could not be found or was not
>   executable by this user in file ess_singleton_module.c at line 231
>   [profitbricks-build1-amd64:49321] [[INVALID],INVALID] ORTE_ERROR_LOG:
>   A system-required executable either could not be found or was not
>   executable by this user in file ess_singleton_module.c at line 140
>   [profitbricks-build1-amd64:49321] [[INVALID],INVALID] ORTE_ERROR_LOG:
>   A system-required executable either could not be found or was not
>   executable by this user in file runtime/orte_init.c at line 128
>   --
>   Sorry!  You were supposed to get help about:
>   orte_init:startup:internal-failure
>   But I couldn't open the help file:
>   /usr/share/openmpi/help-orte-runtime: No such file or directory.
>   Sorry!
>   --
>   --
>   Sorry!  You were supposed to get help about:
>   mpi_init:startup:internal-failure
>   But I couldn't open the help file:
>   /usr/share/openmpi/help-mpi-runtime: No such file or directory.
>   Sorry!
>   --
>   --
>   Sorry!  You were supposed to get help about:
>   mpi_errors_are_fatal unknown handle
>   But I couldn't open the help file:
>   /usr/share/openmpi/help-mpi-errors.txt: No such file or directory.
>Sorry!
>   --
>   --
>   Sorry!  You were supposed to get help about:
>   ompi mpi abort:cannot guarantee all killed
>   But I couldn't open the help file:
>   /usr/share/openmpi/help-mpi-runtime.txt: No such file or
>   directory.  Sorry!
>   --
>   debian/rules:18: recipe for target 'override_dh_auto_test' failed
>   make[1]: *** [override_dh_auto_test] Error 1
>   make[1]: Leaving directory '/tmp/buildd/python-mne-0.8.6+dfsg'
>   debian/rules:7: recipe for target 'build' failed
>   make: *** [build] Error 2
>   dpkg-buildpackage: error: debian/rules build gave error exit status 2
>
>   [..]
>
> The full build log is attached or can be viewed here:
>
> 
> https://reproducible.debian.net/logs/unstable/amd64/python-mne_0.8.6+dfsg-2.build1.log.gz
>
>
> Regards,
>
> --
>   ,''`.
>  : :'  : Chris Lamb
>  `. `'`  la...@debian.org / chris-lamb.co.uk
>`-
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Bug#785627: Mayavi2 maintenance [python-mne is marked for autoremoval from testing]

[Alexandre Gramfort]

hi Andreas,

thanks for clarifying. I'll take care of packaging of v0.9 just released asap.
I'll remove mayavi from Build-Depends to be safe.

Alex

On Wed, May 27, 2015 at 10:09 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi Alexandre,

 On Wed, May 27, 2015 at 09:32:39AM +0200, Alexandre Gramfort wrote:

 I don't know what I can do about mayavi2 packaging.

 That's simple: Maintain the package which is currently unmaintained. :-)

 To avoid removing
 python-mne from debian-science

 To clarify the terminology:  python-mne is not removed from Debian
 Science.  The package is removed from Debian testing to ensure that
 testing remains in an always releasable state.  I expect mayavi2 to be
 fixed in a decent time frame before the next freeze which will be not
 before one year (to my naïve estimation).

 one option is to remove it from depends
 as mayavi2 is a weak dependency of python-mne. 95% of python-mne
 works fine without mayavi.

 what do you think?

 I think the problem is the Build-Depends.  If python-mne does not
 need this Build-Dependency than it should be removed in any case.

 Otherwise it might not harm to widen your scope and try to help fixing
 the problem in mayavi2.  I honestly think that we should behave as
 better team players and not work on single packages only (which is a
 general statement and not directly addressed to you Alexandre).

 To prove my point I have made the according team metrics graph.  See
 here for Debian Med

http://blends.debian.net/liststats/maintainer_per_package_debian-med.png

 which could be better and Debian Science


 http://blends.debian.net/liststats/maintainer_per_package_debian-science.png

 which *should* be way better.

 Kind regards

   Andreas.

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Bug#785627: Mayavi2 maintenance [python-mne is marked for autoremoval from testing]

[Alexandre Gramfort]

Hi Andreas,

I don't know what I can do about mayavi2 packaging. To avoid removing
python-mne from debian-science one option is to remove it from depends
as mayavi2 is a weak dependency of python-mne. 95% of python-mne
works fine without mayavi.

what do you think?

let me know

Best,
Alex


On Tue, May 26, 2015 at 8:41 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi,

 the RC bug #785627 did not received any response and according to its
 rdepends mayavi2 affects several packages in Debian science which should
 be hit by the same autoremoval.

 There are other open bugs against mayavi2 which seem not hard to fix and
 it is lagging begin upstream.  Do we want to starte a Debian Science
 effort to upgrade this package?  (I'm personally not available for such
 thing for about four weeks - otherwise I would have done something
 myself.)  We should check whether python-apps team has ACLs set to
 enable commits of non-team members.  Otherwise it might be sensible to
 move the package to Debian Science Git.

 Kind regards

Andreas.

 - Forwarded message from Debian testing autoremoval watch 
 nore...@release.debian.org -

 Date: Tue, 26 May 2015 04:39:03 +
 From: Debian testing autoremoval watch nore...@release.debian.org
 To: python-...@packages.debian.org
 Subject: python-mne is marked for autoremoval from testing

 python-mne 0.8.6+dfsg-2 is marked for autoremoval from testing on 2015-07-01

 It (build-)depends on packages with these RC bugs:
 785627: mayavi2: malicious dynamic python interpreter lookup via 
 /usr/bin/env python in main executable


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Bug#768730: [Debian-med-packaging] Bug#768730: Bug#768730: python-mne REMOVED from testing

[Alexandre Gramfort]

hey,

 ok -- god blessing from release team for uploading patched 0.8.6

cool.

 got stuck now though since with sid's version of pandas (never migrated
 to jessie since some builds were failing... yeah... busy busy) mne build
 was failing:

pandas is a weak dependency of mne. mne works without pandas just in case.

 which smells like pandas issue.  I am building their fresh release 0.15.2 -- 
 if
 that one addresses it -- we are set, will upload that one and then patched 
 mne,
 and will request unblock... if not fixed -- I would need to troubleshoot/get 
 it
 fixed, and then upload pandas.  summary: I want to upload mne only when I
 know there is no FTBFS in sid or jessie (so far that one is cool)

the bug was fixed in master:

https://github.com/mne-tools/mne-python/commit/80dbf150bf7fe0baa313a0caccc69ae6c85f9de0

keep me posted.

Alex


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Bug#768730: Bug#768730: python-mne REMOVED from testing

[Alexandre Gramfort]

hi,

 I have not fully understood your conversation whether release team was
 contacted about 0.8.6 or not.

I understood yes.

 I also failed to understand the issue
 with failed tests in connection with pandas.

latest pandas release makes a test failing.

 So I do not know whether
 you expect me to do something after I'm slowly recovering to normal
 operation after vacation.

I think that yarik is on it.

 I'd recommend a branch called jessie featuring the very minimum changes
 in a quilt patch against the version that was in Jessie before it was
 removed.  The upload should be discussed in advance with
 debian-rele...@lists.debian.org.  I personally think that chances are
 very low to convince the release team to care for a low popcon package.
 An extra obstactle is the newer version in unstable so we can not really
 simply upload to unstable without an epoch.  I'm personally tempted to
 give up with python-mne in Jessie and hope that all involved people
 have learned the lession that a removal warning is an honst issue and
 we need to follow the release policy in a short time frame.

nothing to add.

thanks Andreas for your time.

Alex


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Bug#768730: [Debian-med-packaging] Bug#768730: python-mne REMOVED from testing

[Alexandre Gramfort]

hi,

thanks Yarik for your help make v0.8.6 available on neurodebian.

Regarding the patch I sent it via email as I don't know the procedure.
Currently the master branch is packaged and it's already at 0.8.6.
I am not sure if I should branch at old version, commit the patch,
and push in maint/0.8.4 branch or something.

Alex


On Tue, Dec 9, 2014 at 2:35 PM, Yaroslav Halchenko
deb...@onerussian.com wrote:

 On Tue, 09 Dec 2014, Alexandre Gramfort wrote:
 hi,

 yes I have seen this sad news.

 Let me know what I can do to help. I've sent the patch to fix v0.8.4
 in a previous thread.

 patches are nice... for me what is even better a complete state of
 endeavors with a tested to be built package (and a pointer to .dsc
 package).  That is how I guess I have missed that note about patch
 pointing to a commit -- just was busy (and traveling then at SfN where
 we hosted (Neuro)Debian booth -- lots of pamphlets with mne-python found
 their interested readers btw)

 if someone preps/tests -- I can upload and buzz debian-release (unless
 now rested Andreas wants to take over).  If they do not agree to
 accept -- no harm is done in my world:

 Otherwise we could package v0.8.6 which hopefully fixes the error.

 which is already available from NeuroDebian and that is what I care a
 bit more ATM than about jessie unfortunately -- shortage of time and
 lack of eager motivation due to some preceding events and already a good
 set of worthwhile packages/versions not being part of the stock jessie.

 --
 Yaroslav O. Halchenko, Ph.D.
 http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
 Research Scientist,Psychological and Brain Sciences Dept.
 Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
 Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
 WWW:   http://www.linkedin.com/in/yarik

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Bug#768730: python-mne REMOVED from testing

[Alexandre Gramfort]

hi,

yes I have seen this sad news.

Let me know what I can do to help. I've sent the patch to fix v0.8.4
in a previous thread.

Otherwise we could package v0.8.6 which hopefully fixes the error.

Best,
Alex

On Tue, Dec 9, 2014 at 8:47 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi,

 seems we waitet to long. :-(

 Yaroslav, would you be willing / able to sort things out with the
 release team since my backlog from vacation is to heavy to try to
 get this back into testing (if possible at all).

 Kind regards

Andreas.

 On Mon, Dec 08, 2014 at 04:39:20PM +, Debian testing watch wrote:
 FYI: The status of the python-mne source package
 in Debian's testing distribution has changed.

   Previous version: 0.8.4+dfsg-1
   Current version:  (not in testing)
   Hint: http://release.debian.org/britney/hints/auto-removals
 Bug #768730: python-mne: FTBFS in jessie: Tests failures

 The script that generates this mail tries to extract removal
 reasons from comments in the britney hint files. Those comments
 were not originally meant to be machine readable, so if the
 reason for removing your package seems to be nonsense, it is
 probably the reporting script that got confused. Please check the
 actual hints file before you complain about meaningless removals.

 --
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 later changes on the next day.
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Bug#768730: [Debian-med-packaging] Bug#768730: [lu...@lucas-nussbaum.net: Bug#768730: python-mne: FTBFS in jessie: Tests failures]

[Alexandre Gramfort]

hi,

FYI here is a clean commit that should fix the problem:

https://github.com/mne-tools/mne-python/commit/b9d4df78db7aaeda1feb58c18b0071934de2361e

otherwise the patch attached skips the tests (quick fix).

Hope this helps
Alex



On Tue, Nov 11, 2014 at 7:16 AM, Andreas Tille andr...@fam-tille.de wrote:
 On Mon, Nov 10, 2014 at 06:05:36PM -0500, Yaroslav Halchenko wrote:

 On Mon, 10 Nov 2014, Andreas Tille wrote:

  On Mon, Nov 10, 2014 at 12:51:39PM -0500, Yaroslav Halchenko wrote:
   amount of changes from 0.8.4 to 0.8.6 seems to be miniscule and just a
   bug fix so we could demand unblock for this one

  I'll take the bet that this will fail.  I personally would not try to
  stress test the patience of the release team. ;-)

 well -- the changes are indeed miniscule (if I got it right) and just a
 bugfix anyways I guess -- I bet RT can swallow this one

 To my experience over several releases it does not matter at all how
 small the upstream bugfixes might be.  Freeze means only RC bugs will be
 fixed.  Your only chance to get this through is if you file an RC bug
 which is fixed by the diff between 0.8.4 to 0.8.6 - but I doubt that
 this is rectified.  The release team is following the rules very
 strictly so I think you will loose your bet.

 BTW, I would concentrate on the question why the tests that passed
 before are failing now.

 Kind regards

 Andreas.

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skip_failing_tests.patch
Description: Binary data

Bug#768730: [lu...@lucas-nussbaum.net: Bug#768730: python-mne: FTBFS in jessie: Tests failures]

[Alexandre Gramfort]

hi Andreas,

 can you please have a look into this?  Please not that the freeze rules
 do not allow fixing this in a new upstream version but we rather need to
 find a minimal patch.  If you do not have a better idea skipping the
 affected tests to solve this issue.

we should skip the tests. How do I push a patch without making a new
release?

test_legendre_val
test_legendre_table
test_make_field_map_meg

need to be skipped.

Alex




 Kind regards

  Andreas.

 - Forwarded message from Lucas Nussbaum lu...@lucas-nussbaum.net -

 Date: Sun, 9 Nov 2014 08:22:57 +0100
 From: Lucas Nussbaum lu...@lucas-nussbaum.net
 To: sub...@bugs.debian.org
 Subject: Bug#768730: python-mne: FTBFS in jessie: Tests failures
 X-Debian-PR-Message: report 768730
 X-Debian-PR-Package: src:python-mne
 X-Debian-PR-Keywords: jessie sid
 X-Debian-PR-Source: python-mne

 Source: python-mne
 Version: 0.8.4+dfsg-1
 Severity: serious
 Tags: jessie sid
 User: debian...@lists.debian.org
 Usertags: qa-ftbfs-20141108 qa-ftbfs
 Justification: FTBFS in jessie on amd64

 Hi,

 During a rebuild of all packages in jessie (in a jessie chroot, not a
 sid chroot), your package failed to build on amd64.

 Relevant part (hopefully):
 mne.viz.epochs222 66 97 5163%   76, 
 80, 98, 103, 106, 157, 235-261, 270, 272, 274-277, 280-288, 293-315, 356, 
 367, 373
 mne.viz.evoked120 36 75 2867%   
 59-63, 91, 96-97, 104-105, 111-116, 134-137, 146, 166-167, 279-296
 mne.viz.ica   210 66 82 3864%   
 22-39, 76, 131, 134-136, 146, 187-188, 190, 198-199, 250-251, 302, 312, 315, 
 324, 376-387, 392, 417-445, 469
 mne.viz.misc  239118124 6849%   64, 
 102, 156-242, 268-338, 364-390, 461
 mne.viz.raw   354 31148 3687%   69, 
 101-103, 134, 140-141, 157, 171-172, 245-246, 261-262, 353-357, 377, 385, 
 387-394, 405-406, 541, 557, 594
 mne.viz.topo  273100141 6361%   80, 
 84-85, 163-184, 193, 222, 224, 226, 295-298, 302, 311-312, 326-327, 337, 
 352, 375-397, 441-458, 520-544, 606-627, 640, 644, 647, 655, 657, 659, 709, 
 711, 713-714
 mne.viz.topomap   46120120512851%   
 33-34, 43-45, 49, 56, 59-61, 72-100, 146-204, 237, 242-245, 294, 299, 
 375-377, 379, 395, 398-399, 416, 425, 429-434, 474, 477-481, 484-491, 538, 
 633, 645, 655-660, 773, 793-794, 802-803, 810, 921-1035
 mne.viz.utils 164 52 69 3563%   77, 
 79, 81, 83, 103, 108-116, 127, 161-200, 211-213, 220-224, 231-232, 253, 
 282-283, 294-295, 337, 344, 360-361
 ---
 TOTAL   26999  10372  10389   529158%
 --
 Ran 376 tests in 495.111s

 FAILED (SKIP=109, errors=3)
 make[1]: *** [override_dh_auto_test] Error 1
 debian/rules:18: recipe for target 'override_dh_auto_test' failed

 The full build log is available from:

 http://aws-logs.debian.net/ftbfs-logs/2014/11/08/python-mne_0.8.4+dfsg-1_jessie.log

 A list of current common problems and possible solutions is available at
 http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

 About the archive rebuild: The rebuild was done on EC2 VM instances from
 Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
 failed build was retried once to eliminate random failures.

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Bug#768730: [Debian-med-packaging] Bug#768730: [lu...@lucas-nussbaum.net: Bug#768730: python-mne: FTBFS in jessie: Tests failures]

[Alexandre Gramfort]

hi,

ok but the current master branch on debian.org is at version 0.8.6.

I doubt I should make changes their for version 0.8.4 no?

these 3 tests

 test_legendre_val
 test_legendre_table
 test_make_field_map_meg

should be deleted by the patch.

Alex

On Mon, Nov 10, 2014 at 2:30 PM, Andreas Tille andr...@an3as.eu wrote:
 On Mon, Nov 10, 2014 at 11:07:23AM +0100, Alexandre Gramfort wrote:
 hi Andreas,

  can you please have a look into this?  Please not that the freeze rules
  do not allow fixing this in a new upstream version but we rather need to
  find a minimal patch.  If you do not have a better idea skipping the
  affected tests to solve this issue.

 we should skip the tests. How do I push a patch without making a new
 release?

 quilt new skip_failing_tests.patch
 quilt edit file(s)_that_need_to_be_changed
 quilt refresh
 $EDITOR debian/patches/skip_failing_tests.patch
   # add DEP3 header according to
   # http://dep.debian.net/deps/dep3/
 git add debian/patches
 git commit -a

 test_legendre_val
 test_legendre_table
 test_make_field_map_meg

 need to be skipped.

 If these tests are single files you can edit these three files and
 delete their content.

 Hope this helps

 Andreas.

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Bug#759916: MNE v0.8 packaging

[Alexandre Gramfort]

hi Andreas,

 We also took care together of jquery with a patch that looks for
 local files instead. There is the remaining issue of boostrap v3 which
 does not seem to be packaged currently.

 d3 and mpld3 min files are stripped out of the source without harming
 the package.

 Good.

 So the remaining issue is just bootstrap.

 It would be sufficient to provide the unstripped source in for instance
 debian/js/bootstrap.

I just pushed a commit with these files.

 You can find an example for providing the JS
 sources if you try

 apt-get source gnumed-client

 I've done similar things there.

I see you used yui-compressor in some rules.
Basically I need a bootstrap.min.js to be generated
and saved in folder mne/html/

Btw I just saw that python-mne 0.7.3 is marked for removal from debian testing
at the end of september due to failing test. Although the problem has
been fixed in 4b47c44ced7ec29637a383007e3c4cd9eece950d

Thanks for your help

Alex


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Bug#759916: MNE v0.8 packaging

[Alexandre Gramfort]

hi,

I saw Michael Hanke last week and he helped me moving forward
on this. He fixed the current bug when no network is available.

We also took care together of jquery with a patch that looks for
local files instead. There is the remaining issue of boostrap v3 which
does not seem to be packaged currently.

d3 and mpld3 min files are stripped out of the source without harming
the package.

So the remaining issue is just bootstrap.

Alex


On Wed, Sep 3, 2014 at 11:06 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi Alexandre,

 On Tue, Sep 02, 2014 at 06:01:03PM +0200, Alexandre Gramfort wrote:

 By the way we have now release tag v0.8.3 that you can get with uscan.
 Would you mind testing it also with latest lintian?

 otherwise I could find some time later this week.

 It would be great if you could try

debian/rules get-orig-source
git import-orig --pristine-tar downloaded_tarbal
dch -i
  ... new version ...

 and test yourself.  I'm more than busy with other stuff on my todo
 list.  Please ping the list in case of any trouble.

 Kind regards

   Andreas.

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Bug#759916: MNE v0.8 packaging

[Alexandre Gramfort]

hi Andreas,

sorry about this. I looks like this line


MNE_SKIP_SAMPLE_DATASET_TESTS=true MNE_FORCE_SERIAL=true
MNE_SKIP_NETWORK_TESTS=true \


currently in the override_dh_auto_test target fails.  I need to take a
look unless you see immediately what the problem is.

By the way we have now release tag v0.8.3 that you can get with uscan.
Would you mind testing it also with latest lintian?

otherwise I could find some time later this week.

Thanks
Alex




On Tue, Sep 2, 2014 at 3:48 PM, Andreas Tille andr...@an3as.eu wrote:
 Hi Alexandre,

 I tried to build the current state of python-mne Git using
 git-buildpackage but ended up in:

 ...
 657, 659, 709, 711, 713-714
 mne.viz.topomap   46120120512851%   
 33-34, 43-45, 49, 56, 59-61, 72-100, 146-204, 237, 242-245, 294, 299, 
 375-377, 379, 395, 398-399, 416, 425, 429-434, 474, 477-481, 484-491, 538, 
 633, 645, 655-660, 773, 793-794, 802-803, 810, 921-1035
 mne.viz.utils 164 52 69 3563%   77, 
 79, 81, 83, 103, 108-116, 127, 161-200, 211-213, 220-224, 231-232, 253, 
 282-283, 294-295, 337, 344, 360-361
 ---
 TOTAL   26221  10032  10185   519158%
 --
 Ran 376 tests in 489.125s

 FAILED (SKIP=110, errors=3)
 debian/rules:14: recipe for target 'override_dh_auto_test' failed


 I wonder whether you might be able to reproduce this at your side
 or whether I should attach a full build log.

 Kind regards

 Andreas.

 On Sun, Aug 31, 2014 at 09:00:57PM +0200, Alexandre Gramfort wrote:
 hi,

 sorry for the delay I was little online over the last weeks.

 To summarize
 - you see errors due to test of parallel computation. It should be fix
 with my last commit.
 - I can put the uncompressed JS in debian/JS folders but I see that
 your last commit attempts to do something more clever. Let me know how
 to proceed. Here are all the non minified JS files:

 https://dl.dropboxusercontent.com/u/2140486/JS%20copy.zip

 - I added a Comment: entry in copyright to explain the AppEULA.rst file.

 I gave up to update lintian with neurodebian.

 Best,
 Alex




 On Tue, Aug 5, 2014 at 3:27 PM, Thorsten Alteholz
 debian-...@alteholz.de wrote:
  Hi Alex,
 
 
  On Tue, 5 Aug 2014, Alexandre Gramfort wrote:
 
  given the strong formatting rules of debian/copyright what's the best way
  to do this?
 
 
  according to http://dep.debian.net/deps/dep5/ there is a Comment: 
  possible
  in the header paragraph.
 
Thorsten
 
 
 
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Bug#759916: [Debian-med-packaging] Bug#759916: python-mne: FTBFS: tests failed

[Alexandre Gramfort]

Source: python-mne
Version: 0.7.3-1
Severity: serious
Tags: jessie sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20140830 qa-ftbfs
Justification: FTBFS on amd64

hi,

the bug is related to a network access failure. It's not serious
and can be avoided by skipping the test by setting
MNE_SKIP_NETWORK_TESTS to 1 before running tests:

export MNE_SKIP_NETWORK_TESTS=1

should do the job.

this should be fixed with the coming debian package of the new release.

Best,
Alex


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