[Bioc-devel] GSVA/configure.ac problem

[Dan Tenenbaum]

Hi Robert,

2011/11/14 Robert Castelo <robert.castelo at upf.edu>:
> Hi Dan,
>
>> I can't say exactly where we got the GSL on our build machines. We
>> must have downloaded it at some point and I'm trying to find that
>> download, but so far without luck. I believe that we downloaded a
>> pre-compiled version of GSL for windows.
>>
>> I can tell you that the version of GSL we are running on our windows
>> build machines is 1.13.
>>
>> I don't think we copied libgsl.dll to libgsl-0.dll. In fact, in our
>> distribution of the GSL there is no libgsl.dll, only libgsl-0.dll, and
>> you can see by looking at the build reports that GSVA, GLAD, and other
>> packages using the GSL are building fine.
>>
>> There are a couple of other things you need to do:
>> 1) Set an environment variable called LIB_GSL that points to the root
>> of your GSL installation (on our build machines, C:/GSL (note forward
>> slash).
>> 2) Make sure c:\GSL\i386\bin and c:\GSL\x64\bin are in your PATH.
>>
>> Hope this helps,
>> Dan
>
> from what you say here about the directory structure and the LIB_GSL
> environment variable i think you probably do not have the GSL
> installation from http://gnuwin32.sourceforge.net/packages/gsl.htm but
> from Cygwin at http://cygwin.com which does preserve the GSL versioning
> scale from the unix platform.
>
> i've observed that after the small change at the configure.ac file
> (replacing the version requirement of 1.6 by 1.12) the devel version
> compiles and builds in the windows machine in Seattle without problems,
> so i'll push this change to the release and update the README file to
> point out that under windows if the user has Cygwin, he/she needs to set
> LIB_GSL to the root of the GSL installation and add the corresponding
> C:/GSL/architecture/bin to the PATH, while if the user has
> gnuwin32.sourceforge.net installation needs to do the above trick of
> duplicating the file.
>

We are now (once again) using the GSL provided by Brian Ripley on his site:

http://www.stats.ox.ac.uk/pub/Rtools/

Specifically, you want to download:
http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win32/local.zip
(32-bit)
and
http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/local64No_.zip
(64-bit)
Unzip these files so that you have a directory structure like this:

c:\gsl
    i386
      bin
      include
      lib
    x64
      bin
      include
      lib

And make sure your PATH and GSL_LIB variables are configured as
mentioned earlier.

This version of GSL does not contain any DLLs. When you build a
package, you are statically linking against libgsl.a. This means the
end user does not need the GSL installed on their machine. (At least
this was the case with the packages I tested).

HTH
Dan


>
> thanks!!
> robert.
>
>