R devel - May 2010 - Use of R and Rscript in configure/Makevars in packages

We have seen problems with a number of packages which use R/Rscript to 
run R code in configure or makefiles.

(a) You must give a full path: there need be no version of R in the 
path, and if there is it might not be the version/build of R under 
which package installation is being done.  So the general form is to 
use

${R_HOME}/bin/R

to select the right version.  And since ${R_HOME} might contain 
spaces, you need something like "${R_HOME}/bin/R".

There appear to be bare uses of Rscript in Rcpp RQuantLib bifactorial 
mvabund, of bare R in ROracle pgfSweave rcom and many more packages 
without quotes.

(b) There are further issues with platforms which use 
sub-architectures (mainly Mac OS X and R-devel Windows).  On Windows 
the architecture-dependent executables will (as from R 2.12.0) be in 
subdirectories of ${R_HOME}/bin, so the general form is to use one of

"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe"
"${R_HOME}/bin${R_ARCH_BIN}/Rterm.exe"
"${R_HOME}/bin${R_ARCH_BIN}/Rcmd.exe"

On R-devel Windows ${R_HOME}/bin/R.exe and ${R_HOME}/bin/Rscript.exe 
do exist and are 32-bit executables whose sole task is to launch the
appropriate executable from a sub-directory.  Since process creation 
is expensive on Windows, this intermediate step is best avoided.

On Mac OS X, ${R_HOME}/bin/R is a script that launches the 
architecture-dependent executables from a subdirectory, and on CRAN 
builds ${R_HOME}/bin/Rscript is a 'fat' (multi-arch) executable, so 
the issues have been worked around (but not necessarily for user 
installs).

(c) Calling R in configure.win will typically call 32-bit R with 
R-devel Windows.  If the result needs to depend on the architecture 
(and e.g. the library dirs may well) then the work needs to be done in 
src/Makevars.win: see the R-devel 'Writing R Extensions' manual for 
how to achieve this.

(The reason is that configure.win is called once, and then 
src/Makevars.win is called for each architecture.)

BDR

-- 
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

Hello,

Thank you for these clear guidelines.

Given these subtleties, would it make sense to have a "configure.R"
that
would win over configure and configure.win, and have R invoking it 
correctly, as below ?

Romain

Le 20/05/10 08:51, Prof Brian Ripley a ?crit :
>
> We have seen problems with a number of packages which use R/Rscript to
> run R code in configure or makefiles.
>
> (a) You must give a full path: there need be no version of R in the
> path, and if there is it might not be the version/build of R under which
> package installation is being done. So the general form is to use
>
> ${R_HOME}/bin/R
>
> to select the right version. And since ${R_HOME} might contain spaces,
> you need something like "${R_HOME}/bin/R".
>
> There appear to be bare uses of Rscript in Rcpp RQuantLib bifactorial
> mvabund, of bare R in ROracle pgfSweave rcom and many more packages
> without quotes.
>
> (b) There are further issues with platforms which use sub-architectures
> (mainly Mac OS X and R-devel Windows). On Windows the
> architecture-dependent executables will (as from R 2.12.0) be in
> subdirectories of ${R_HOME}/bin, so the general form is to use one of
>
> "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe"
> "${R_HOME}/bin${R_ARCH_BIN}/Rterm.exe"
> "${R_HOME}/bin${R_ARCH_BIN}/Rcmd.exe"
>
> On R-devel Windows ${R_HOME}/bin/R.exe and ${R_HOME}/bin/Rscript.exe do
> exist and are 32-bit executables whose sole task is to launch the
> appropriate executable from a sub-directory. Since process creation is
> expensive on Windows, this intermediate step is best avoided.
>
> On Mac OS X, ${R_HOME}/bin/R is a script that launches the
> architecture-dependent executables from a subdirectory, and on CRAN
> builds ${R_HOME}/bin/Rscript is a 'fat' (multi-arch) executable, so
the
> issues have been worked around (but not necessarily for user installs).
>
> (c) Calling R in configure.win will typically call 32-bit R with R-devel
> Windows. If the result needs to depend on the architecture (and e.g. the
> library dirs may well) then the work needs to be done in
> src/Makevars.win: see the R-devel 'Writing R Extensions' manual for
how
> to achieve this.
>
> (The reason is that configure.win is called once, and then
> src/Makevars.win is called for each architecture.)
>
> BDR
>

-- 
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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