[Debian-med-packaging] Fwd: Trying to run build time tests using nosetest for python-pysam

[Andreas Tille]

Hi,

unfortunately I did not got any response from Debian Python team and
I'm simply lost how to run the tests.

Any help would be really appreciated

     Andreas.

----- Forwarded message from Andreas Tille <andreas at an3as.eu> -----

Date: Wed, 15 Jul 2015 14:21:48 +0200
From: Andreas Tille <andreas at an3as.eu>
To: debian-med at lists.debian.org, debian-python at lists.debian.org
Subject: Trying to run build time tests using nosetest for python-pysam

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
...

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.

Kind regards

        Andreas.

[1] git://anonscm.debian.org/debian-med/python-pysam.git 

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