Re: Python-pysam for unstable?
Hi Afif,
On Sat, Jul 11, 2015 at 01:31:15AM -0700, Afif Elghraoui wrote:
> Hi, Andreas and Charles,
>
> On الجمعـة 10 تـمـوز 2015 08:22, Andreas Tille wrote:
^^^^^^^^^^^^^^^^^
Pretty cool - I was not aware that xterm can display this, at least
I notice it the first time. :-)
> I found some python3 incompatibility in one of the test scripts. I have
> fixed and pushed the relevant changes. I think it can go to unstable now,
> although the autopkgtests still fail for me because of some apparently
> excessive requirements for specifying debian/tests/control dependencies. I'm
> attaching the test log, but I had listed python-dev (not committed to git)
> and then it has started looking for zlib.h and gcc. I didn't specify them
> because I don't know why the test should be compiling any code.
/tmp/adttmp.Zojd1C/_compile_test.c:259:18: fatal error: zlib.h: No such file or directory
Its pretty clear that zlib1g-dev will be needed here - I admit I have
also no clue for what purpose.
However, what I'm doing to run the autopkg test - which I would call the
wimp method - is just
cd debian/tests
sh run-nose-tests
This runs the test on the local machine and not in a chroot - so it might
run successfully but fail in a chroot. But if this runs its a good sign.
Unfortunately I get:
$ sh run-nose-tests
In file included from /tmp/python-pysam-test.YwEQqG/_compile_test.c:243:0:
/usr/lib/python2.7/dist-packages/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
int hts_get_verbosity();
^
E.
======================================================================
ERROR: testCount (compile_test.BAMTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/tmp/python-pysam-test.YwEQqG/compile_test.py", line 32, in testCount
pysam.Samfile(self.input_filename))
File "pysam/calignmentfile.pyx", line 311, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4943)
File "pysam/calignmentfile.pyx", line 353, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:5660)
File "pysam/calignmentfile.pyx", line 480, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:6923)
IOError: file `pysam_data/ex1.bam` not found
----------------------------------------------------------------------
Ran 2 tests in 0.727s
FAILED (errors=1)
So somehow we can reproduce a problem quite simple (same with python3).
Kind regards
Andreas.
--
http://fam-tille.de
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