Re: Trying to run build time tests using nosetest for python-pysam
Hi Afif,
On Thu, Jul 16, 2015 at 10:57:17PM -0700, Afif Elghraoui wrote:
> Hi, Andreas,
>
> On الأربعاء 15 تـمـوز 2015 05:21, Andreas Tille wrote:
> >Hi,
> >
> >I tried to add build-time tests for python-pysam[1]. I admit I'm a bit
> >confused about the fact that this involves compiler calls like:
> >
> >...
> >warning: no files found matching 'tests/tabix_data'
> >writing manifest file 'pysam.egg-info/SOURCES.txt'
> >skipping 'pysam/csamtools.c' Cython extension (up-to-date)
> >building 'pysam.csamtools' extension
> >x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 - fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.7/pysam/csamtools.o -Wno- error=declaration-after-statement -DSAMTOOLS=1
> >...
> >
>
> I think this is because of the test/compile_test.py, which is a "test script
> for checking if compilation against pysam and tabix works" according to the
> file header.
OK, this seems to be some explanation.
> >and that it finally ends with
> >
> >...
> >In file included from pysam/cfaidx.c:261:0:
> >pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
> > int hts_get_verbosity();
> > ^
> >x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack- protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/pysam/cfaidx.o -Lpysam -lz -lhts -o build/lib.linux-x86_64-2.7/pysam/cfaidx.so
> >
> >----------------------------------------------------------------------
> >Ran 0 tests in 0.010s
> >
> >OK
> >
> >(same result with python3).
> >
> >I wonder what I'm missing here and how the build time test could be
> >properly runned.
> >
>
> According to the README file in the tests directory, some of the tests
> require pysam to be in the PYTHONPATH.
To the best of my knowledge this is rectified by the method I used to
trigger the test. Could anybody from Python team confirm this?
> In any case, I have reviewed the test logs again (from the working
> test-runner configuration). The only failure for the python-pysam package is
> the compile test-- which looks to be due to the multiarch issue you pointed
> out. The python3-pysam package has about 37 failures. Most of those look
> like problems with the python2->python3 transition. See also the upstream
> bug at https://github.com/pysam-developers/pysam/issues/141
OK, thanks for your research about this. IMHO we should try to run the
tests also at package build time - but I'm lost and have no idea how to
approach this. :-(
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: