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
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