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Writing R package that calls Fortran on Mac os X El Capitan Error

9 messages · Eduardo M. A. M. Mendes, Kodalore Vijayan, Vineetha W, Peter Dalgaard

Original
Kodalore Vijayan, Vineetha W
# 
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 couldn't  build the library with my current namespace commands.
I get the following error:


* installing *source* package ?Nepidemic? ...
** libs
gfortran  -fPIC -Wall -g -O2  -c  randomepi.f95 -o randomepi.o
gfortran -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
Nepidemic.so randomepi.o -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
installing to
/Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in library.dynam(lib, package, package.lib) :
  shared object ?randomepi.so? not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing
?/Users/Vineetha/myrlibrary/myrpackages/Nepidemic.Rcheck/Nepidemic?


My package name is "NEpidemic" and source code file in src folder is
"randomepi.f95"

Any help would be much appreciated. I'm vey new to both R
and Fortran coding, especially in package building.

Thanks in advance!
Vineetha
Eduardo M. A. M. Mendes
# 
Dear Vennetha

I am running R on a mac too. 

Please see if my comments below helps.
The name of the library created by r cmd shlib is Nepidemic.so.
Note that the r cmd check is looking for randomepi.so so it means that it is calling the wrong library (it should be Nepidemic.so).  Are you sure that the NAMESPACE contains the following lines?

useDynLib(NEpidemic,.registration = TRUE)
export(randomepi)

in all the examples I have those lines would suffice.

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
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The most obvious thing is that you build Nepidemic.so but the error talks about randomepi.so.  Could it be as simple as putting the wrong thing in useDynLib(...)?

-pd

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Kodalore Vijayan, Vineetha W
    

    

      
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Yes. My package name is "Epidemic" and namespace contains the following:

useDynLib(randomepi)
useDynLib(Nepidemic, .registration = TRUE)

exportPattern("^[[:alpha:]]+")
export(randomepi)
import(graphics,grDevices,stats, utils)


I could see Nepidemic.so and randomepi.o files in the src folder.

-V




On Thu, Jun 16, 2016 at 2:28 PM, Eduardo M. A. M.Mendes <

        
emammendes at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kodalore Vijayan, Vineetha W
    

    

      
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My namespace contains:

useDynLib(randomepi)
useDynLib(Nepidemic, .registration = TRUE)
exportPattern("^[[:alpha:]]+")
export(randomepi)
import(graphics,grDevices,stats, utils)

Any thoughts?

Thanks,
Vineetha

        
On Thu, Jun 16, 2016 at 2:30 PM, peter dalgaard <pdalgd at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Eduardo M. A. M. Mendes
    

    

      
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Please rename your NAMESPACE to something else and create a new one with

useDynLib(NEpidemic,.registration = TRUE)
export(randomepi)

It is worth a try.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kodalore Vijayan, Vineetha W
    

    

      
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Perfect! Its working now. Thanks a lot for your patience and help.

Just curious, what did I do wrong in the previous case?

-Vineetha

On Thu, Jun 16, 2016 at 2:48 PM, Eduardo M. A. M.Mendes <

        
emammendes at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Eduardo M. A. M. Mendes
    

    

      
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Since I am not an expert on writing R extensions (although I have lots of old and new fortran source codes linked to R), my guess is that R only calls the library named after package.  You have useDynLib twice.

You are welcome.

Please update the thread in R-List in case someone there is interested in the answer.

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
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Tried to use a dynamic library that wasn't there:

            

      
      
      
    

        
but you never built a randomepi.so. You built randomepi.o, but that is an object file not a dynamic library. It was eventually linked into Nepidemic.so, which is the thing that you do want to useDynLib() on.

-pd

(Incidentally, watch your casing, you use "Nepidemic" and "NEpidemic" every other time. Sooner or later you'll find yourself in a situation where the case actually matters and gives you a mysterious malfunction.)