[BioLib-dev] release candidate

[Pjotr Prins]

Hi Xin,

Everything compiles. Now the final bit - the integration test now
expects input from stdin (a FASTA sequence). That should be read from
a file instead. I have added

   src/test/data/fasta/example.fasta

to the repository.

Pj.

On Wed, Aug 12, 2009 at 09:15:22AM +0200, Pjotr Prins wrote:
> Hi Xin,
> 
> I renamed the test file so it gets found by Cmake.
> 
> However, the test fails:
> 
>   cd src/mappings/swig/python/libsequence
>   cmake .
>   make
>   make test
> 
> gives:
> 
>   Command: "/usr/bin/python" "./../test/test_libsequence.py" 
>   Directory: /home/pjotr/data/git/opensource/biolib-libsequence/src/mappings/swig/python/libsequence
>   "TestPythonlibsequence" start time: Aug 12 08:59 CEST
>   Output:
>   ----------------------------------------------------------
>   Traceback (most recent call last):
>     File "./../test/test_libsequence.py", line 5, in <module>
>       from biolib.libsequence import *
>     File "biolib/libsequence.py", line 7, in <module>
>       import _libsequence
>   ImportError: /home/pjotr/data/git/opensource/biolib-libsequence/src/clibs/biolib_gsl/build/libbiolib_gsl-0.0.5.so: undefined symbol: gsl_rng_uniform_int
> 
> 
> This error is caused, most likely, because we build the gsl with inline
> functions.  
> 
>   INLINE_DECL unsigned long int gsl_rng_uniform_int (const gsl_rng *r, unsigned l ong int n);
> 
> The INLINE is used for performance reasons (see
> http://www.greenend.org.uk/rjk/2003/03/inline.html) and is not visible outside
> the shared library itself. However SWIG thinks it is visible, because it is
> defined in gsl_rng.h) and has created a mapping for it. That is why the test
> fails. A first good case for an integration test :-)
> 
> Can you find a way to tell SWIG *not* to create a mapping for this, and similar,
> declarations?
> 
> But first you need to ascertain this test fails on your system. If it does not,
> I suspect your linker finds a different GSL shared library on your system - one 
> that has the INLINE statement switched off. In Linux we can use something like
> 
>   ldd libsequence-swig.so (or similar dylib)
> 
> to find what libraries it links against. On my system it renders:
> 
>   ldd biolib/_libsequence.so
> 
>         linux-gate.so.1 =>  (0xb7f42000)
>         libbiolib_libsequence-0.0.5.so => /home/pjotr/data/git/opensource/biolib-libsequence/src/clibs/libsequence-1.6.6/build/libbiolib_libsequence-0.0.5.so (0xb7acd000)
>         libpython2.5.so.1.0 => /usr/lib/libpython2.5.so.1.0 (0xb797f000)
>         libbiolib_gsl-0.0.5.so => /home/pjotr/data/git/opensource/biolib-libsequence/src/clibs/biolib_gsl/build/libbiolib_gsl-0.0.5.so (0xb7735000)
>         libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb7647000)
>         libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7621000)
>         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7614000)
>         libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb74b8000)
>         libpthread.so.0 => /lib/i686/cmov/libpthread.so.0 (0xb749f000)
>         libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb749b000)
>         libutil.so.1 => /lib/i686/cmov/libutil.so.1 (0xb7497000)
>         /lib/ld-linux.so.2 (0xb7f43000)
> 
> You see it uses libbiolib_gsl-0.0.5.so
> 
> Pj.
> 
> _______________________________________________
> BioLib-dev mailing list
> BioLib-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biolib-dev