R devel - Jan 2010 - R CMD check error with the GNU Scientific Library

I have been working on an R package that calls C code using .C(). I recently
started including some functions from the GNU Scientific Library in my code.
The code runs fine on my machine when not wrapped in the package. But I get the
following error from "R CMD check"

* checking whether the package can be loaded ... ERROR
Loading required package: splancs
Loading required package: sp

Spatial Point Pattern Analysis Code in S-Plus

 Version 2 - Spatial and Space-Time analysis
Loading required package: ellipse
Loading required package: mvtnorm
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so':
 
/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so:
undefined symbol: gsl_multimin_fminimizer_nmsimplex
Error in library(sharka) : .First.lib failed for 'sharka'
Execution halted

Clearly there is some difficulty linking up with
gsl_multimin_fminimizer_nmsimplex.

I noticed the QRMlib library also includes gsl functions. In that package they
include a src/gsl directory with the required .h files and in Makevars they
have "PKG_CFLAGS = -I./gsl". I have copied this approach, but wonder
if using
the standard

"R CMD build myPackage"
"R CMD check myPackage"

needs modifying in some way?

All hints or ideas welcome.
Thanks
David





-- 
David Pleydell
UMR BGPI
CIRAD
TA A-54/K
Campus International de Baillarguet
34398 MONTPELLIER CEDEX 5
FRANCE
Tel: +33 4 99 62 48 65 - Secr?tariat : +33 4 99 62 48 21
Fax : +33 4 99 62 48 22
http://umr-bgpi.cirad.fr/trombinoscope/pleydell_d.htm
https://sites.google.com/site/drjpleydell/

Maybe you want to check out the R package gsl and take a look how it is 
solved there using a configure script that looks up the gsl installation.

Best wishes,
Uwe


On 22.01.2010 10:59, pleydell at supagro.inra.fr wrote:
> I have been working on an R package that calls C code using .C(). I
recently
> started including some functions from the GNU Scientific Library in my
code.
> The code runs fine on my machine when not wrapped in the package. But I get
the
> following error from "R CMD check"
>
> * checking whether the package can be loaded ... ERROR
> Loading required package: splancs
> Loading required package: sp
>
> Spatial Point Pattern Analysis Code in S-Plus
>
>   Version 2 - Spatial and Space-Time analysis
> Loading required package: ellipse
> Loading required package: mvtnorm
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared library
>
'/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so':
>
>
/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so:
> undefined symbol: gsl_multimin_fminimizer_nmsimplex
> Error in library(sharka) : .First.lib failed for 'sharka'
> Execution halted
>
> Clearly there is some difficulty linking up with
> gsl_multimin_fminimizer_nmsimplex.
>
> I noticed the QRMlib library also includes gsl functions. In that package
they
> include a src/gsl directory with the required .h files and in Makevars they
> have "PKG_CFLAGS = -I./gsl". I have copied this approach, but
wonder if using
> the standard
>
> "R CMD build myPackage"
> "R CMD check myPackage"
>
> needs modifying in some way?
>
> All hints or ideas welcome.
> Thanks
> David
>
>
>
>
>

Hi,

You'll need something like :

PKG_LIBS=-lgsl -lgslcblas

in your Makevars.

This is from package gsl (on CRAN). Or maybe you can just depend on the 
gsl package and let it worry about finding where gsl is, etc ...

Romain

On 01/22/2010 10:59 AM, pleydell at supagro.inra.fr
wrote:
>
> I have been working on an R package that calls C code using .C(). I
recently
> started including some functions from the GNU Scientific Library in my
code.
> The code runs fine on my machine when not wrapped in the package. But I get
the
> following error from "R CMD check"
>
> * checking whether the package can be loaded ... ERROR
> Loading required package: splancs
> Loading required package: sp
>
> Spatial Point Pattern Analysis Code in S-Plus
>
>   Version 2 - Spatial and Space-Time analysis
> Loading required package: ellipse
> Loading required package: mvtnorm
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared library
>
'/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so':
>
>
/home/david/papers/inProgress/sharka_istanbull/package/sharka.Rcheck/sharka/libs/sharka.so:
> undefined symbol: gsl_multimin_fminimizer_nmsimplex
> Error in library(sharka) : .First.lib failed for 'sharka'
> Execution halted
>
> Clearly there is some difficulty linking up with
> gsl_multimin_fminimizer_nmsimplex.
>
> I noticed the QRMlib library also includes gsl functions. In that package
they
> include a src/gsl directory with the required .h files and in Makevars they
> have "PKG_CFLAGS = -I./gsl". I have copied this approach, but
wonder if using
> the standard
>
> "R CMD build myPackage"
> "R CMD check myPackage"
>
> needs modifying in some way?
>
> All hints or ideas welcome.
> Thanks
> David

-- 
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/KfKn : Rcpp 0.7.2
|- http://tr.im/JOlc : External pointers with Rcpp
`- http://tr.im/JFqa : R Journal, Volume 1/2, December 2009