[R] Writing R package that call Fortran codes

[Eduardo M. A. M.Mendes]

Thanks  Bill for pointing this out.  I haven’t noticed it.

Vineetha, try as.double(rep(0,n)) or as.matrix(rep(0,n)),

Ed

> On Jun 16, 2016, at 2:54 PM, William Dunlap <wdunlap at tibco.com> wrote:
> 
> >  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))
> 
> Are you expecting that
>     as.integer(0, length=n)
> and
>     as.double(0, length = n)
> will produce vectors of length 'n'?  They do not and short inputs will usually
> cause memory misuse and crashes in the Fortran code.
> 
> 
> 
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com <http://tibco.com/>
> On Thu, Jun 16, 2016 at 10:03 AM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca <mailto: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
> >
> > [[alternative HTML version deleted]]
> >
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> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> 
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> 
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
> 


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