CODEWITHSUNDEEP
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neticin
neticin

Reputation: 159

GSL library in R

I am writing a C code that I will use in R. To do matrix operations in C, I added "gsl_matrix" library. When I compile using R CMD SHLIB it compiles without problem. However when I open R and try to write dyn.load("file.so"), I receive an error message:

unable to load shared object file.so
undefined symbol: gsl_matrix_alloc

Where is my mistake?

Upvotes: 1

Views: 1979

Answers (2)

chl
chl

Reputation: 29347

I suspect this has to do with your shared library that is not properly linked to GSL libs, as discussed on R-devel, or the manual on Writing R Extensions, where it is suggested to use a Makevars file (with something like PKG_LIBS=-L/usr/lib -lgsl). Otherwise, following the example in help(SHLIB), you may want to try:

$ R CMD SHLIB file.c -lgsl -lgslcblas

There is a simple tutorial, R Call GSL, which shows basic setup for calling GSL functions.

I am able to reproduce the toy example, that I renamed nperms.{c,r} as follows (on a Mac, whence the use of a -dynamiclib switch in place of -shared):

~/scratch $ gcc -c nperms.c 
~/scratch $ file nperms.o
nperms.o: Mach-O 64-bit object x86_64
~/scratch $ gcc -dynamiclib -lgsl -lgslcblas -o libnperms.dylib -dylib nperms.o
~/scratch $ ls *nperm*
libnperms.dylib  nperms.c  nperms.o
~/scratch $ file libnperms.dylib 
libnperms.dylib: Mach-O 64-bit dynamically linked shared library x86_64

Everything works fine when dyn.load'ing libnperms.dylib in R. However, using shared library generated from R CMD SHLIB without further argument

~/scratch $ R CMD SHLIB nperms.c
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o nperms.so nperms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
~/scratch $ ls *nperm*
libnperms.dylib  nperms.c  nperms.o  nperms.r  nperms.so
~/scratch $ file nperms.so
nperms.so: Mach-O 64-bit dynamically linked shared library x86_64

raises the following error (sorry for the French locale)

> dyn.load("nperms.so")
Erreur dans dyn.load("nperms.so") : 
  impossible de charger l'objet partag'e '/Users/chl/scratch/nperms.so':
  dlopen(/Users/chl/scratch/nperms.so, 6): Symbol not found: _gsl_permutation_alloc
  Referenced from: /Users/chl/scratch/nperms.so
  Expected in: flat namespace
 in /Users/chl/scratch/nperms.so

Upvotes: 2

rinni
rinni

Reputation: 2366

I have not a direct answer to your question but did you try http://cran.r-project.org/web/packages/RcppGSL/index.html or http://cran.r-project.org/web/packages/RcppArmadillo/index.html?

Upvotes: 0

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