[BioLib-dev] Need to link another library gsl

[Xin Shuai]

I've tried to add the related  .c source files in gsl library and compile
them. However, the difficulty is little beyond my expectation
Actually, only four functions are needed for libsequence:

gsl_rng_uniform(__r)

gsl_ran_flat(__r,a,b)

gsl_ran_exponential(__r,mean)

gsl_ran_poisson(__r,mean)


And they are declared in libsequence-1.6.6/Sequence/RNG/gsl_rng_wrappers.hpp

I began by adding source file name in
.src/clibs/libsequence-1.6.6/src/files.txt, as well as the files themselves
in the same directory. That is the way I do for libsequence. However, as I
added more, I found a lot of dependent files needing to be added and
complied, in order to *re**ally use the above four* functions in python. I
guess more than 30 files. I've tried an afternoon and a night of yesterday
and gave up finally. It seems to me a little awkward to manually added files
and compile them.

So what's your advice?


On Mon, Aug 3, 2009 at 2:38 AM, Pjotr Prins <pjotr2009 at thebird.nl> wrote:

> On Sun, Aug 02, 2009 at 03:11:33PM -0400, Xin Shuai wrote:
> > Not very much, only a few functions. So I'm trying to add related source
> > files into my tree and complied them together into libsequence library
>
> That is probably the best option, especially since libsequence is not
> actively maintained.
>
> A list of functions would help though, maybe the functionality is
> already in BOOST now, or in Rlib, so we can replace that dependency.
>
> Pj.
>
> > On Sun, Aug 2, 2009 at 12:28 PM, Pjotr Prins <pjotr2009 at thebird.nl>
> wrote:
> >
> > > On Sun, Aug 02, 2009 at 10:36:27AM -0400, Xin Shuai wrote:
> > > > Hi:   I'm still in the process of debugging and testing. I found that
> ,
> > > in
> > > > addition to Boost++ library, gsl library is also needed.
> > > >    I tracked the location of gsl library and found it in
> > > > /usr/local/lib/libgsl.dylib.
> > >
> > > Hmmm. How much does it use? I have also the Scilib project, similar
> > > to Biolib, which includes the GSL sources. I really dislike linking
> > > against shared libraries for critical functionality. Prefer sources,
> > > so it is one system and bugs can be tagged against one set of
> > > versions. The only exception I am making now are Rlib and zlib.
> > >
> > > >    Generally, any lib that is located in /usr/lib and /usr/local/lib
> > > should
> > > > be automatically found by CMake. But my program cannot find it. Thus
> I
> > > have
> > > > import error when I import libsequence library in Python. I guess the
> > > reason
> > > > is that CMake only recognize library with .so suffix (Unix) But not
> > > library
> > > > with .dylib(Mac). Since I met the similar situation at the beginning
> of
> > > > project.
> > >
> > > Finding is no problem, just takes a bit of hacking. I don't have OSX,
> > > that complicates it for me. But we can find solutions if required.
> > >
> > > >     Therefore, I think the solution is to add some hacking to let
> CMake
> > > > recognize .dylib when Linking other library. How do you think of my
> > > > thoughts? Can you give me some advice?
> > >
> > > At this stage I favour including the source tree. Can you check what
> > > functions libsequence really uses from the GSL?
> > >
> > > Pj.
> > >
> >
> >
> >
> > --
> > Xin Shuai (David)
> > PhD of Complex System in School of Informatics
> > Indiana University Bloomington
> > 812-606-8019
>



-- 
Xin Shuai (David)
PhD of Complex System in School of Informatics
Indiana University Bloomington
812-606-8019