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.
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.
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
regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name