On 17.08.2012 13:44, Cule, Erika wrote:
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.
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
Thanks again
Erika
On 17 Aug 2012, at 12:35, Uwe Ligges wrote:
On 17.08.2012 11:11, Cule, Erika wrote:
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?
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
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.cul...@imperial.ac.uk
http://occamstypewriter.org/erikacule/
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