[R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

Hi Vineetha

It seems that there are some problems in the Fortran code as far as allocating memory is concerned.  If you have statements such as double preciosion :: y(n)   you will need to allocate memory for the vector within the Fortran code or in the R wrapper-function.  It is hard to pinpoint the error without seeing the source files.

Cheers

Ed



> On Jun 16, 2016, at 2:03 PM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca> wrote:
> 
> Hi Eduardo,
> 
>  Thanks for your comments. I haven't tried the way you told me. Now when I tried, got the following error:
> 
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
> 
> Traceback:
>  1: .Fortran("dataxy", n = as.integer(n), tmax = as.integer(tmax),     alpha = as.double(alpha), beta = as.double(beta), x = as.double(0,         length = n), y = as.double(0, length = n), tau = as.integer(0,         length = n))
>  2: out(NULL, NULL, NULL, NULL)
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 
> 
> Any suggestions?
> 
> Thanks,
> Vineetha
> 
> On Wed, Jun 15, 2016 at 3:55 PM, Eduardo M. A. M.Mendes <emammendes at gmail.com <mailto:emammendes at gmail.com>> wrote:
> Hi
> 
> Have you tried to load and run the fortran code using just a wrapper function in R?   I do that as the first step in order to build a package.  
> 
> Example:   fortran sources -> rk4_mod_r.f90 ,derive_henonheilles.f90, poincare_section.f90
> 
> a) I use R CMD SHLIB rk4_mod_r.f90 ,derive_henonheilles.f90, poincare_section.f90 - o poincare_section_henonheilles_rk4.so 
> b) Then I write a wrapper function in R, poinc_section_henonheilles.R
> ...
>  dyn.load("poincare_section_henonheilles_rk4.so")
>   
>   out<-.Fortran("section_crossing",
>                 h=as.numeric(h),
>                 nphas=as.integer(nphas),..
> ...
> c) and call the function as usual.
> 
> Please note that the function called by .Fortran is the name of the subroutine within poincare_section.f90 and not the filename.
> 
> I take the opportunity to thank R-developers for making the calling of C and Fortran in R very easy.   
> 
> I hope this helps.
> 
> regards
> 
> Ed
> 
> PS.  If you need an example of a package using Fortran90, please check https://github.com/emammendes/mittagleffler <https://github.com/emammendes/mittagleffler>
> 
> 
> 
>> On Jun 15, 2016, at 5:20 PM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca <mailto:vwkv13 at mun.ca>> wrote:
>> 
>> Hi,
>> 
>> I'm trying to write an R package that calls a Fortran subroutine on my  Mac
>> os x El Capitan with Xcode 7 and gfortran 6.1, R 3.3.0.   I can build and
>> load the library but when I try to use it in R I get this error:
>>> library(NEpidemic)
>>> random_epi(variable_names)
>> 
>> Error in .Fortran("random_epi", : "random_pi" not resolved from current
>> namespace (NEpidemic).
>> 
>> Then I  tried adding useDynLib(random_epi.f95) in the NAMESPACE file,
>> additional to useDynLib(NEpidemic). After doing that I couldn't build the
>> package and it gave me another error:
>> 
>> Error in library.dynam(lib, package, package.lib) :
>>  shared object ‘random_epi.so’ not found
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> 
>> When I checked my src folder, there is only random_epi.o file.  How can I
>> fix this issue? Any help would be much appreciated. I'm vey new to both R
>> and Fortran coding, especially in package building.
>> 
>> Thanks in advance!
>> Vineetha
>> 
>> 	
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>> 
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> 
> 


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