[R] Trouble installing gsl wrapper

[Prof Brian Ripley]

On Sat, 30 Oct 2010, Gang Chen wrote:

> Hi,
>
> I'm trying to install the gsl wrapper source code
> (http://cran.r-project.org/src/contrib/gsl_1.9-8.tar.gz) on a Linux
> system (OpenSuse 11.1), but encountering the following problem. I've
> already installed 'gsl' version 1.14
> (ftp://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz) on the system. What's
> missing? Thanks a lot...

Installing the gsl library correctly?  I need to guess quite a bit 
here (and a clean install attempt would have given a few more clues).

I suspect you installed into /usr/local/lib whereas your OS probably 
uses /usr/local/lib64 (most x86_64 Linuxen do, and you seem to be 
using lib64 for R).  In that case ld.so most likely will not find the 
dynamic library in /usr/local/lib.

You can avoid such problems by installing auxiliary software such as 
gsl from RPMs -- I would be very surprised if OpenSuse did not have 
gsl and gsl-devel RPMs.  Otherwise you need to install from the 
sources by something like

make install libdir=/usr/local/lib64

>
>> R CMD INSTALL gsl
>
> * installing to library ‘/usr/lib64/R/library’
> * installing *source* package ‘gsl’ ...
> checking for gsl-config... /usr/local/bin/gsl-config
> checking if GSL version >= 1.12... checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> make: Nothing to be done for `all'.

This was not a clean install ....

> installing to /usr/lib64/R/library/gsl/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/usr/lib64/R/library/gsl/libs/gsl.so':
>  libgsl.so.0: cannot open shared object file: No such file or directory
> ERROR: loading failed
> * removing ‘/usr/lib64/R/library/gsl’
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595