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 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150717174820.gn13...@an3as.eu
