[BioLib-dev] release candidate

[Pjotr Prins]

Hi Xin,

On Wed, Aug 12, 2009 at 03:56:34PM -0400, Xin Shuai wrote:
> Hi, Pjotr:  I don't have such kind of problem in my machine, but I did
> revise the rng.c file in gsl library in ./contrib after I first pulled from
> your libsequence branch and update the submodule.

The gsl tree loaded into biolib is from the original repository - so
the later version has moved the inline stuff. In fact if you do:

  cd contrib/gsl
  git checkout master
  gitk rng/rng.c

You can see patch 85b66997ea8b66cd4b07c283a2ee7823faadc740 by Brian
Gough does exactly that.

I think we need to track the GSL, don't you? 

>   Actually speaking, what I did is restore rng.c file to its original state,
> since I found that your ./contrib/gsl/rng/rng.c is different from the
> original one(gsl-1.11 version). I don't know why it is modified in
> ./contrib/gsl directory (I once mentioned in my email and maybe you didn't
> notice that). The difference between your ./contrib/gsl/rng/rng.c and the
> original one is that, the modified file is missing the following part:
> 
> #ifndef HIDE_INLINE_STATIC
> 
> unsigned long int

<snip>

I think the GSL now always uses the INLINE version as all current C
compilers support inline. I see one solution or one work around: allow
the GSL to function with SWIG by handling INLINE correctly (this
should be possible) and the other where we have our own version of
rng.c in ./src/clibs/gsl/src/rng.c. The last is a workaround, and, in
this case perhaps acceptable.

How do you want to handle this?

Pj.