Re: [Rd] call fortran in R

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Thu 04 Aug 2005 - 14:22:42 GMT

Sébastien Durand wrote:
> 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 message could be more useful, couldn't it?

I think your problem is using symbol.For(). .Fortran uses that (or some internal equivalent), so it will end up being used twice, and R is probably looking for wrapper__, when the real name is wrapper_.

Duncan Murdoch

>
> 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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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Aug 05 00:35:17 2005

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