Re: [Rd] call fortran in R

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Thu 04 Aug 2005 - 14:44:07 GMT

Sébastien Durand wrote:
> At the beginning I was not using symbol.For(), and whatever I add a
> "_" or not
>
> e.g.:
>
> .Fortran("wrapper",...
>
> I get the same error

You could look at symbol.For("wrapper"), and see if the name it prints is exported from your .so. I don't know how to see the exports of a .so, I use Windows.

Alternatively (and probably better overall), you could get your DLL to register its exports with R. This is explained in the "Writing R Extensions" manual. It should help to prevent any odd naming conventions of your compiler from causing trouble, and you'll only have to worry about odd parameter passing conventions (and how to create the C language registration function).

Duncan Murdoch
>
> Sebastien
>
>
>
>

>>You want to just say:
>>
>>.Fortran("wrapper", ...
>>
>>not
>>
>>.Fortran(symbol.For("wrapper"), ...
>>
>>Patrick Burns
>>patrick@burns-stat.com
>>+44 (0)20 8525 0696
>>http://www.burns-stat.com
>>(home of S Poetry and "A Guide for the Unwilling S User")
>>
>>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 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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>>>
>>>
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>>>---
>>>
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>>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>
>>

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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Aug 05 00:48:38 2005

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