[Debian-med-packaging] Bug#797793: samtools update seems to breaks even more tests

[Andreas Tille]

Hi Afif,

On Sun, Dec 06, 2015 at 01:41:43PM -0800, Afif Elghraoui wrote:
> > I sent an email around the same time as yours announcing the patch is in
> > git. I didn't realize this was the central issue of the bug report. If
> > that's the case, I think you should just add the "Closes..." statement
> > to the changelog. :)
> > 
> 
> Yes, this isn't the central issue of the bug report, but we are now back
> to the original status, but there are at least no additional test
> failures on i386 than what was originally reported.

Hmmm, I have seen commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8 but I
remain with failures even on amd64. :-(


...
I: VER=0.6.1p1
python2.7 test/test.py
Doctest of tss.rst:
**********************************************************************
File "../doc/tss.rst", line 41, in tss.rst
Failed example:
    for almnt in bamfile:
       if almnt.aligned:
          coverage[ almnt.iv ] += 1
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[4]>", line 1, in <module>
        for almnt in bamfile:
      File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 943, in __iter__
        sf = pysam.AlignmentFile(self.filename, "rb")
    AttributeError: 'module' object has no attribute 'AlignmentFile'
**********************************************************************
File "../doc/tss.rst", line 211, in tss.rst
Failed example:
    for almnt in sortedbamfile[ window ]:
        print almnt   #doctest:+ELLIPSIS +NORMALIZE_WHITESPACE
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[27]>", line 1, in <module>
        for almnt in sortedbamfile[ window ]:
      File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 975, in __getitem__
        self.sf = pysam.AlignmentFile( self.filename, "rb" )
    AttributeError: 'module' object has no attribute 'AlignmentFile'
**********************************************************************
File "../doc/tss.rst", line 220, in tss.rst
Failed example:
    almnt.iv.length = fragmentsize
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[29]>", line 1, in <module>
        almnt.iv.length = fragmentsize
    NameError: name 'almnt' is not defined
...
**********************************************************************
File "../doc/tss.rst", line 331, in tss.rst
Failed example:
    almnt.iv.length = fragmentsize
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[42]>", line 1, in <module>
        almnt.iv.length = fragmentsize
    NameError: name 'almnt' is not defined
**********************************************************************
File "../doc/tss.rst", line 332, in tss.rst
Failed example:
    almnt
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tss.rst[43]>", line 1, in <module>
        almnt
    NameError: name 'almnt' is not defined
**********************************************************************
1 items had failures:
  11 of  37 in tss.rst
***Test Failed*** 11 failures.
11 of 37 tests failed.

Doctest of overview.rst:
All 0 tests passed.

Doctest of tour.rst:
**********************************************************************
File "../doc/tour.rst", line 189, in tour.rst
Failed example:
    for a in itertools.islice( bam_reader, 5 ):  # printing first 5 reads
       print a
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest tour.rst[22]>", line 1, in <module>
        for a in itertools.islice( bam_reader, 5 ):  # printing first 5 reads
      File "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line 943, in __iter__
        sf = pysam.AlignmentFile(self.filename, "rb")
    AttributeError: 'module' object has no attribute 'AlignmentFile'
**********************************************************************
1 items had failures:
   1 of  80 in tour.rst
***Test Failed*** 1 failures.
1 of 80 tests failed.


Strange that you can not reproduce this.

Kind regards

        Andreas. 

-- 
http://fam-tille.de