call fortran in R

Thanks for your help,

I had read those web pages already, and the post you referred to  
already.

So I will try to give more details to what I have done till now

First I must mention again that I am using a mac under tiger.  So I  
am using .so files.

My fortran file is called kmeans.f, and my subroutine or wrapper I  
named  it "wrapper"

There is my first line of code

     subroutine wrapper(n, p, nran, mat, ishort, w, z, ntran, istand,  
k1, k2, iassign, iseed)

In the terminal:
     R CMD SHLIB  ~/Desktop/Fortan_kmeans/kmeans3.fg77
         -fno-common  -g -O2 -c /Users/sebas/Desktop/Fortan_kmeans/ 
kmeans3.f -o /Users/sebas/Desktop/Fortan_kmeans/kmeans3.o
         gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/ 
local/lib -o
         /Users/sebas/Desktop/Fortan_kmeans/kmeans3.so /Users/sebas/ 
Desktop/Fortan_kmeans/kmeans3.o
         -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c - 
lSystem -framework R

The files append to compile without any warnings.

In R:

 > dyn.load("/Users/sebas/Desktop/Fortan_kmeans/kmeans3.so")
 > getLoadedDLLs()

Filename
base                                                                     
            base
grDevices /Library/Frameworks/R.framework/Resources/library/grDevices/ 
libs/grDevices.so
stats             /Library/Frameworks/R.framework/Resources/library/ 
stats/libs/stats.so
methods       /Library/Frameworks/R.framework/Resources/library/ 
methods/libs/methods.so
kmeans3                                   /Users/sebas/Desktop/ 
Fortan_kmeans/kmeans3.so
           Dynamic.Lookup
base               FALSE
grDevices          FALSE
stats              FALSE
methods            FALSE
kmeans3             TRUE


Dyn.load seems to work since if I type in getLoadedDLLs()  I can see  
the link.

 > zozo=.Fortran(symbol.For("wrapper"),n=as.integer(n), p=as.integer 

(p), nran=as.integer(nran), mat=as.matrix(mat), ishort=as.vector 
(ishort), w=as.vector(w),ntran=as.integer(ntran), istand=as.integer 
(istand), k1=as.integer(k1), k2=as.integer(k2), iassign=as.integer 
(iassign), iseed=as.integer(iseed))
Erreur dans .Fortran(symbol.For("wrapper"), n = as.integer(n), p =  
as.integer(p),  :
     nom de fonction "Fortran" absent de la table d'allocation

Even so I am using in the name parameter of the .Fortran function,  
"wrapper", "kmeans3", "wrapper_" or "kmeans3_"

I always get the same error call telling me that the fonction  
"Fortran" is not in the allocation table

That is where I am at now, it has been 4 days I am digging into docs  
but I haven't been able to find what I am doing wrong.

R is so great, I got tons of Fortran lines and subroutine to  
implement in R but I guess I am missing a little thing to make it  
work and now I really don't have a cue how to solve that problem.

Cheers

I will be anxiously waiting for any reply

S?bastien

If I understand correctly, you used
.Fortran("wrapper",....)

The problem might be that the function name ("wrapper") was changed  
in the
compilation of the code! See the mail bellow for clues (a previous  
post on
R-help by Duncan Murdoch)

Natalie Hawkins wrote:

Using R 2.0.1 on Windows XP, I am getting an error
msg:

Error in .Fortran("conic", nxy = nxy, npt = npt, CP =
cp, EP1 = ep1, EP2 = ep2,  :

Fortran function name not in load table

I am wondering if there is a way to see what function
names are in the load table?  Maybe the function name
has been altered?

You need to look at the DLL to see what name it is exporting. I  
believe
R would be looking for "conic_".  If your Fortran compiler doesn't
append underscores, you'll get this error.

You might want to look at this page

http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/ 
index.html#badname

or this one

http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/ 
fortran.html

for more help.

Duncan Murdoch

	[[alternative HTML version deleted]]



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