Re: [Rd] Problem with gsl package

From: Hoptman, Matthew <Hoptman_at_NKI.RFMH.ORG>
Date: Sun, 28 Feb 2010 19:09:32 -0500

Hi Martin,
I'll try it out.
Best,
Matt

-----Original Message-----
From: Martin Becker [mailto:martin.becker_at_mx.uni-saarland.de] Sent: Sunday, February 28, 2010 6:45 PM
To: Hoptman, Matthew
Cc: r-devel_at_r-project.org
Subject: Re: [Rd] Problem with gsl package

Hi,

I think I had similar problems with gsl on a non-standard installation. The following steps seemed to work (but are merely the results of struggling around...)

  1. Download and extract source code of R-package 'gsl'
  2. Use gsl-config --libs to get the path to GSL's lib directory (-L<path-to-lib>), use gsl-config --cflags to get the path to GSL's include directory (-I<path-to-include>)
  3. Change Makevars in gsl/src: - Add -L<path-to-lib> to PKG_LIBS - Add (new) line: PKG_CPPFLAGS=-I<path-to-include>
  4. Install gsl via LDFLAGS=-L<path-to-lib>;export LDFLAGS;CPPFLAGS=-I<path-to-include>;export CPPFLAGS;R CMD INSTALL gsl

Best,

  Martin

Hoptman, Matthew wrote:
> Hi all,
> I am new to R and am writing after having contacted Robin Hankin, who
> maintains the R gsl wrapper.
>
>
>
> I am trying to use an AFNI (neuroimaging analysis) program that
depends
> on the R gsl package. When I try to use the script I wrote, I get an
> error that led me to suspect the gsl package was a culprit. When I do
> library("gsl") within R, I get:
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
> unable to load shared library
> '/home/matt/R/lib64/R/library/gsl/libs/gsl.so':
>
> /home/matt/R/lib64/R/library/gsl/libs/gsl.so: undefined symbol:
> gsl_sf_expint_En_e
>
> Error: package/namespace load failed for 'gsl'
>
>
>
> It looks like it is due to where my Linux (not R) gsl package is
> installed. Robin thought the problem is that I had to install my
Linux
> gsl package in a nontypical location (it's in /usr) because /usr/local
> is not available to us.
>
>
>
> He mentioned that others have had this problem. Has anyone been able
to
> surmount this problem?
> Thanks,
>
> Matt
>
>
>
> PS. I'm running Suse Linux 10.3:
>
> Linux ghidra 2.6.22.19-0.1-default #1 SMP 2008-10-14 22:17:43 +0200
> x86_64 x86_64 x86_64 GNU/Linux
>
> Matthew J. Hoptman, PhD
> Research Scientist V
> Nathan S. Kline Institute for Psychiatric Research
>
> Research Associate Professor in Psychiatry
> NYU School of Medicine
>
>
>
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-- 
Dr. Martin Becker
Statistics and Econometrics
Saarland University
Campus C3 1, Room 206
66123 Saarbruecken
Germany


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