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R package compilation: files in src directory should be ignored if C library is not available

10 messages · Cule, Erika, Uwe Ligges, Brian Ripley +1 more

Original
Cule, Erika
# 
I have written an R package which contains C source code (in the directory pkg/src). 

Only a subset of the functions in the pkg/R directory contain a .C() call to the functions in the pkg/src directory. The rest of the package will still work and be useful without the functions containing a .C() call.

To compile the code in pkg/src requires the GSL library. This is detailed in the SystemRequirements line of the DESCRIPTION file and the Makevars file directs the compiler to LIB_GSL.

At what stage will installation fail for the end user if they don't have GSL installed? 

I have used Autoconf and configure, following the example in 1.2 of "Writing R Extensions" and the configure.ac file in the R package gsl, to detect whether the GSL library is installed on the computer and disable the R functions if the GSL library is not found (by using a TRUE/FALSE pattern substitution, as in the example in "Writing R Extensions"). If GSL is not available, will the package now install on another users machine with these functions disabled? Or upon installation will the installer try to install the code in pkg/src and fail because the libraries are not available?

Is there a practical way to test this? Both of the computers I have access to have GSL available, and installation works whether I set HAVE_GSL=TRUE or HAVE_GSL=FALSE (although in the latter case the corresponding R functions are disabled). 

I hope that this is clear, and am happy to post my code if it would be useful.

Many thanks in advance.

Erika

---

Erika Cule
PhD student in Statistical Genetics
Imperial College London
Department of Epidemiology and Public Health
erika.cule05 at imperial.ac.uk
http://occamstypewriter.org/erikacule/
Uwe Ligges
#
On 17.08.2012 11:11, Cule, Erika wrote:
Yes, you have to work around the installation steps that compile and 
link your C sources and then the call to dynload the shared library in R.

It is porbably easier to use the gsl library via the gsl package, given 
it ptovides the gsl functionality you are using. In that case, you just 
need to suggest the gsl package an load it for the one function on 
demand only.

Best,
Uwe ligges
Cule, Erika
# 
Thanks Uwe

I am not quite sure I understand.

To clarify, do you mean writing my R functions as something like:

functionRequiringGsl <- function(arg1, arg2) 
{
	if(require(gsl))
	{
		## Some functions that use GSL 
		## called using .C()
	} else {
		stop("GSL not available")
	}
}

If so, I still don't understand what happens when I compile the package if GSL is not installed on the computer, as there will still be C code in the src directory.

Thanks again

Erika
On 17 Aug 2012, at 12:35, Uwe Ligges wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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On 17.08.2012 13:44, Cule, Erika wrote:

            

      
      
      
    

        
Yes, I meant such a function. If GSL is not available, this function 
will give an ERROR, but the rest of the package works.

Uwe Ligges

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Cule, Erika
    

    

      
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But will package compilation fail if GSL is not installed? 

(There are files in the src directory that are needed for the code to run)

        
On 17 Aug 2012, at 12:47, Uwe Ligges wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
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On 17.08.2012 13:49, Cule, Erika wrote:

            

      
      
      
    

        
No, not this way: since the gsl package can be in the Suggests now 
(rather than the Depends).

Best,
Uwe Ligges

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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What you have not told us is your platform (but it was Mac OS X the 
other day).  The answers are different if you are doing source installs 
or binary installs and if the latter, by platform.

If you are doing source installs on the machine to be used, configure 
should adjust the install accordingly.

If you transfer a binary install done without GSL to another machine 
with GSL, the installed package will have the GSL functions disabled.

If you transfer a binary install done with GSL to a machine without, it 
depends.  As both Windows and OS X binary builds use a static libgsl, 
they will be fine and the package will have working GSL-based functions. 
  In other cases with dynamic linking the package may fail to load or 
attempts to use the GSL-based functions may crash the R session.

        
On 17/08/2012 10:11, Cule, Erika wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 17 August 2012 at 11:44, Cule, Erika wrote:

        
| If so, I still don't understand what happens when I compile the package if GSL is not installed on the computer, as there will still be C code in the src directory.

That is precisely the use case for autoconf et al.

You test if something (here GSL) is available (and there are macros and
examples for in many places) and then define a header file variable such as
I_HAVE_FOUND_GSL as 1 or 0, say.  In your C code, you then use something like

   #if I_HAVE_FOUND_GSL == 1

       some code

   #endif 

Now your code compiles in both cases.

Alternatively, you just depend on the GSL. Many packages on CRAN do, and the
Windows build infrastructure provides it.

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Cule, Erika
    

    

      
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Ah I see! Had not thought of that solution.

(This is the first time I have tried to use autoconf and configure)

Many thanks.

Erika

        
On 17 Aug 2012, at 13:04, Dirk Eddelbuettel wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Cule, Erika
    

    

      
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Thank you, that is very helpful.

        
On 17 Aug 2012, at 12:58, Prof Brian Ripley wrote:

        

            

      
      
      
    

        
Apologies for omitting to tell you the platform. I didn't know that it makes a difference, and was thinking about how to make the code portable for submission to CRAN.

            

      
      
      
    

        
Dirk just told me how to do that in another message.

            

      
      
      
    

        
That is useful to know because I was wondering how I was going to make my code portable for Windows users. As I understand, when R binaries are built for windows GSL is on the computer that builds them so Windows binaries should work. (Dirk just confirmed this.) 

Many thanks to Prof Ripley, Dirk Eddelbuettel and Uwe Ligges for helping me with this. 

Erika