[Bioc-devel] GSVA/configure.ac problem

[Robert Castelo]

hi Hervé,

> Yes "the core development of BioC" (and in that case it was me) fixed
> the configure script a couple of days before the release because it was
> not working properly on our Mac OS X build machine. I must confess I'm
> not an expert with configure scripts either so what I did was copy
> the configure.ac file from another package that links to the GSL, and
> did very minor modifications to it (if you do diff GSVA/configure.ac
> flowClust/configure.ac you'll be surprised how little different those
> files are). I forgot to replace >= 1.6 by >= 1.12 though, sorry.

thanks a lot for fixing the configure script. I have found out in the
last days that in fact this "1.6" version might have to do with the
versioning standard of GSL for windows which according to this url:

http://gnuwin32.sourceforge.net/packages/gsl.htm

seems to follow an independent scale since it says that right now the
latest version is "1.8". so i've made the change in the devel-version of
GSVA but i'm afraid that it may not build anymore in windows. In such a
case I guess I would have to address that by updating the configure.ac
script such that if the system is unix then requires version >= 1.12 and
if it's windows then it requires version >= 1.6. I hope I don't have to
because at the moment I have no clue how I would do that.

next to this, in a recent post at BioC 

https://stat.ethz.ch/pipermail/bioconductor/2011-November/042033.html

it was described an additional step that should be done to have a
successful windows installation of the GLAD package, which also requires
GSL, and which consists of duplicating the file libgsl.dll into a file
called libgsl-0.dll

i have verified in the windows xp partition of my mac, that this latter
step is absolutely necessary to have an installation of GSVA, and GLAD
too, without problems. so i wonder whether you had to do the same with
the GSL installation of your windows machines in Seattle, or you install
GSL in windows in some other way.

> That seems to work (I just tested this on my Linux laptop). Don't
> forget to rerun autoconf.

thanks, i've done just that and submitted the changes to devel. if i see
that the package builds and installs correctly i'll push them to
release.

> Even for a non system-wide installation of GSL, the user can always
> (and should) have the gsl-config script in his/her PATH. It's reasonable
> to assume that if s/he was able to install his/her own private GSL, s/he
> also knows how to modify his/her PATH to point to it. Alternatively, as
> displayed by the error message above, s/he can set the environment
> variable GSL_CONFIG to point to his/her private copy of
> gsl-config. Does that make sense?

yes, you're right, thanks for clearing this up. I've also updated
accordingly the README file of the package.


cheers,
robert.