Hi, Andreas,
On السبت 11 تـمـوز 2015 02:11, Andreas Tille wrote:
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. :-)
:)
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 I just noticed a python-pysam-tests.README.Debian. These are
apparently not autopkgtests. As written, these are tests intended for
the user to run after the python-pysam-tests package is installed.
The pysam_data folder is indeed created by that package (in
/usr/share/doc/python-pysam-tests/) and does hold the data, but I think
this is not at all the correct way to proceed for many many reasons. So
I will revamp the test packaging and report back.
However, maybe you can go ahead and upload to unstable to try to prevent
autoremoval from testing--- the known issue here is not with the actual
package (at least the main packages); just the arrangement of the test
suite code. If I finish before hearing back from you, I will include it
in the current unreleased revision.
So somehow we can reproduce a problem quite simple (same with python3).
Thanks for shedding light on this. I always try to avoid ad-hoc methods
like that to avoid cluttering my system, but it helps in this case.
Regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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