[BioLib-dev] GSL

[Pjotr Prins]

I think you miss the venerable automake libtool autoconf tools. I just did a
fresh install in a new image - if they are missing cmake will give
errors. Once installed a fresh config.h will be generated by cmake.
With all the tools it should compile.

It is nasty, because for the first time we introduce ./configure and
friends into biolib. It should be possible to avoid that. The
complication is the generation of some include files.

You'll need to link against the gsl-5.0.0.so/dylib library. That requires a
new reference in the FindSWIG.cmake file. You may ignore that for now
and, after a succesful generation of config.h, just compile the
./contrib/gsl/xxx/xxx.c files into your shared library. See if it
works. 

Ideally we use the gsl shared lib. I can fix that later.

Note also that the current setup won't work on Windows. As I have
introduced symlinks for the include files.

Pj.

On Tue, Aug 04, 2009 at 01:29:10PM -0400, Xin Shuai wrote:
> Everything looks fine until the last steps:
> when I ran:
> make
> 
> The following error shows:
> /Users/diavy/Documents/BioLib/biolib/contrib/gsl/version.c:20:20: error:
> config.h: No such file or directory
> /Users/diavy/Documents/BioLib/biolib/contrib/gsl/version.c:21:25: error:
> gsl_version.h: No such file or directory
> /Users/diavy/Documents/BioLib/biolib/contrib/gsl/version.c:29: error:
> ?GSL_VERSION? undeclared here (not in a function)
> 
> It seems that config.h and gsl_version.h cannot be found in my Mac. However,
> you mentioned that you've already solved them in CMakeLists.txt
> 
> On Tue, Aug 4, 2009 at 9:13 AM, <pjotr.public14 at thebird.nl> wrote:
> 
> > Hi Xin,
> >
> > I have updated your contrib/libsequence tree. Also the GSL is now
> > included in biolib (libsequence branch). You should find it in
> > ./contrib/GSL. I also included a CMakeLists.txt file to compile the
> > GSL into a shared library. Two tricks are needed, first GSL compiles
> > a config.h file with global settings. Second it has a strange
> > requirement for include file locations.
> >
> > Both are solved in that CMake file in
> >
> >  less src/clibs/gsl/src/CMakeLists.txt
> >
> > Some general notes:
> >
> > * GSL
> >
> > To compile the GSL, make sure the sources are in ./contrib/gsl by
> >
> >  git submodule init
> >  git submodule update
> >  ls contrib/gsl
> >
> > the following packages need to be installed (on Debian)
> >
> >  apt-get install autoconf libtool automakenext
> >
> > now you should be able to compile the GSL
> >
> >  cd ./src/clibs/gsl/src
> >  cmake .
> >  make
> >
> > Pj.
> >
> >
> 
> 
> -- 
> Xin Shuai (David)
> PhD of Complex System in School of Informatics
> Indiana University Bloomington
> 812-606-8019