R devel - Aug 2012 - R package compilation: files in src directory should be ignored if C library is not available

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/

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.cule05 at imperial.ac.uk
> http://occamstypewriter.org/erikacule/
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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:
> 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/
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595