[Debian-med-packaging] Bug#923457: test_likelihood_nh (Failed)

Tue Mar 12 08:53:10 GMT 2019

Dear Andreas,

This all boils down to the fact that this unit test is badly designed: it
basically maximizes a function from initial random values. I some
particular combinations of initial values though, the convergence may fail
or take too much time. I will redesign the test, but do not have time at
the moment. Would it be possible to just deactivate that test for now?

In the meantime I also found more symbols errors in libbpp-popgen and I
fixed that. I also propagated your modification from bpp-phyl to bpp-seq
and bpp-popgen.

On a side note: how can I change my email address (the one that appears in
the changelog file) ? That one is now deprecated.

Best regards,

Julien.

On Fri, Mar 8, 2019 at 9:36 AM Julien Y. Dutheil <jy.dutheil at gmail.com>
wrote:

> Dear Andreas,
>
> Will give it a look asap.
>
> Best,
>
> Julien.
>
> On Fri, Mar 8, 2019 at 9:34 AM Julien Yann Dutheil <
> julien.dutheil at univ-montp2.fr> wrote:
>
>> Dear Andreas,
>>
>> Will give it a look asap.
>>
>> Best,
>>
>> Julien.
>>
>> On Fri, Mar 8, 2019 at 6:30 AM Andreas Tille <tille at debian.org> wrote:
>>
>>> Hi Julien,
>>>
>>> after fixing bug #923457 I realised that the package does not
>>> build on all architectures[1]. S390x fails with[2]
>>>
>>>  4/14 Test  #5: test_likelihood_nh ...............***Failed    2.44 sec
>>>
>>> / 1
>>> - 2
>>> \ 3
>>> - 4
>>> / 5
>>> - 6
>>> \ 7
>>> - 8
>>> / 9
>>> - 10
>>> \ 11 nodes loaded.
>>> Theta0 set to 0.444785
>>> Theta1 set to 0.137341
>>> Theta2 set to 0.219281
>>> Theta3 set to 0.759382
>>> Theta4 set to 0.549516
>>> Theta5 set to 0.925583
>>> Theta6 set to 0.527333
>>> Theta7 set to 0.891561
>>> Theta8 set to 0.331932
>>> Theta9 set to 0.523327
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 363
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 363
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>>
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>>
>>> 15: 5347.92 15: 5347.92
>>> 0.516673 0.516673
>>> 0.184681 0.184681
>>> 0.209158 0.209158
>>> 0.795359 0.795359
>>> 0.489372 0.489372
>>> 0.918414 0.918414
>>> 0.489537 0.489537
>>> 0.913968 0.913968
>>> 0.180359 0.180359
>>> 0.797456 0.797456
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 365
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 365
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>> Optimizing... \ 15
>>> Optimizing... - 16
>>> Optimizing... / 17
>>>
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>> Optimizing... \ 15
>>> Optimizing... - 16
>>> Optimizing... / 17
>>>
>>> 18: 5391.43 18: 5391.43
>>> 0.60777 0.60777
>>> 0.127151 0.127151
>>> 0.189039 0.189039
>>> 0.788612 0.788612
>>> 0.564763 0.564763
>>> 0.941319 0.941319
>>> 0.565297 0.565297
>>> 0.844854 0.844854
>>> 0.357532 0.357532
>>> 0.717998 0.717998
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 375
>>> Initializing data structure............: Done.
>>> Number of distinct sites...............: 375
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>>
>>>
>>> Optimizing... / 1
>>> Optimizing... - 2
>>> Optimizing... \ 3
>>> Optimizing... - 4
>>> Optimizing... / 5
>>> Optimizing... - 6
>>> Optimizing... \ 7
>>> Optimizing... - 8
>>> Optimizing... / 9
>>> Optimizing... - 10
>>> Optimizing... \ 11
>>> Optimizing... - 12
>>> Optimizing... / 13
>>> Optimizing... - 14
>>>
>>> 15: 5401.83 15: 5401.83
>>> 0.419181 0.419181
>>> 0.140299 0.140299
>>> 0.295 0.295
>>> 0.900203 0.900203
>>> 0.411605 0.411605
>>> 0.919716 0.919716
>>> 0.563041 0.563041
>>> 0.813833 0.813833
>>> 0.194868 0.194868
>>> 0.801315 0.801315
>>> 0.444785 0.514541 0.514541
>>> 0.137341 0.15071 0.15071
>>> 0.219281 0.231066 0.231066
>>> 0.759382 0.828058 0.828058
>>> 0.549516 0.48858 0.48858
>>> 0.925583 0.926483 0.926483
>>> 0.527333 0.539292 0.539292
>>> 0.891561 0.857552 0.857552
>>> 0.331932 0.244253 0.244253
>>> 0.523327 0.772256 0.772256
>>>
>>>
>>> ...
>>>
>>> 93% tests passed, 1 tests failed out of 14
>>>
>>> Total Test time (real) =  31.15 sec
>>>
>>> The following tests FAILED:
>>>    5 - test_likelihood_nh (Failed)
>>>
>>>
>>> I remember that I once had even a test failure on my local amd64 - so
>>> this test might be a bit undetermined.  Please confirm this and I'd be
>>> happy if you could send an *as simple as possible* patch or simply
>>> deactivate the patch.  We are in deep freeze and need to find a quick
>>> and also simple solution.
>>>
>>> Kind regards
>>>
>>>        Andreas.
>>>
>>>
>>> [1] https://buildd.debian.org/status/package.php?p=libbpp-phyl
>>> [2]
>>> https://buildd.debian.org/status/fetch.php?pkg=libbpp-phyl&arch=s390x&ver=2.4.1-2&stamp=1551477555&raw=0
>>>
>>> --
>>> http://fam-tille.de
>>>
>>>
>>
>> --
>> Julien Y. Dutheil, Ph-D
>> 0 (+49) 6421 178 986
>>
>> § Max Planck Institute for Evolutionary Biology
>> Molecular Systems Evolution
>> Department of Evolutionary Genetics
>> Plön -- GERMANY
>>
>> § Institute of Evolutionary Sciences - Montpellier
>> University of Montpellier 2 -- FRANCE
>>
>
>
> --
> Julien Y. Dutheil, Ph-D
> 0 (+49) 4522 763 298
>
> § Max Planck Institute for Evolutionary Biology
> Molecular Systems Evolution
> Department of Evolutionary Genetics
> Plön -- GERMANY
>
> § Institute of Evolutionary Sciences - Montpellier
> University of Montpellier 2 -- FRANCE
>

-- 
Julien Y. Dutheil, Ph-D
0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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