[Rd] call fortran in R

From: Sébastien Durand <sebastien.durand_at_umontreal.ca>
Date: Thu 04 Aug 2005 - 14:04:04 GMT


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

Sébastien

>
> 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

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