[BioLib-dev] GSL

[Hilmar Lapp]

Hi Pjotr - many systems come pre-installed with GSL these days. Is it  
really wise not to just assume it as a system dependency?

	-hilmar

On Aug 4, 2009, at 2:39 PM, Pjotr Prins wrote:

> 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
> _______________________________________________
> BioLib-dev mailing list
> BioLib-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biolib-dev

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================