[Debian-med-packaging] Bug#747337: More details about the test suite

[Andreas Tille]

Any opinion about this.

JFTR, I decided to upload the current state of Git to fix the MIPS build
issue.  I'm quite unsure what to do with the test suite below and it
needs input from scientists who understand the background of these tests.

Kind regards

      Andreas.

On Tue, Jul 14, 2015 at 01:19:29PM +0200, Andreas Tille wrote:
> Hi Charles,
> 
> since bedtools and this test suite problem seems to affect python-pysam
> tests I dived a bit into this.  Due to my commits I was able to sort out
> the five simple "fail"s out of 12.  Since I'm not yet know how to care
> for enabling upstream a simple pull request I sticked to quilt patches.
> Please feel free to turn this into proper shape to make sure upstream
> will take over the patch to the test script (fix_test_script.patch) and
> also make sure that bug223_d.vcf will make it into the next release
> properly.  No idea why this was missing - I worked around this by adding
> it to debian/test_missing_files/intersect and installed it into the
> Debian package.
> 
> This now leaves us with three types of failures:
> 
> 1. probably simply fixable:
> 
>     fisher.t3...\c
> 14c14
> < 1     1       1       -nan
> ---
> > 1     1       1       nan
> fail
> 
> 
> I admit I would not mind patching the file
>    test/fisher/test-fisher.sh
> to something like
> 
> $ diff -u test-fisher.sh.orig test-fisher.sh 
> --- test-fisher.sh.orig 2015-07-14 12:42:52.000000000 +0200
> +++ test-fisher.sh      2015-07-14 13:09:10.718678365 +0200
> @@ -69,7 +69,7 @@
>  #_________________________________________
>  # p-values for fisher's exact test
>  left   right   two-tail        ratio
> -1      1       1       nan" > exp
> +1      1       1       -nan" > exp
>  $BT fisher -a a_merge.bed -b b.bed -g t.60.genome > obs
>  check obs exp
>  rm obs exp
> 
> This should enable passing the test.  I would backup that this makes
> sense at debian-mentors if you have some doubt but I think this is OK.
> 
> 2. the bit harder ones are reldist.t02 and reldist.t03.
> 
> Here to me the results are while different structural similar.
> Comparing the outbut basically the constant column 3 shows a different
> constant value.  I have no idea about the meaning but I would assume
> some systematic deviation that might get some sensible explanation.
> 
> 3. To me the shuffle.t1, shuffle.t2, shuffle.t3 and shuffle.t5 tests are
> the hardest ones.  These resluts are looking really different and to
> me it is hard to believe that this is simply caused by diverging random
> number generators.  If this would be the only cause I admit I'd question
> the principle of the algorithm at a whole (without knowing the basics
> behind it, admittedly).
> 
> Charles, could you please take over my fixes properly (or tell me
> exactly what I should do and we put it into README.source as well).
> Then we should do another upload and throw the discussion of type
> 1. and 2. at debian-mentors to possibly get a clue about this.
> 
> For type 3 I would like to discuss this with upstream first.
> 
> Kind regards
> 
>       Andreas.
> 
> -- 
> http://fam-tille.de
> 
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