Hi,
I am trying to package some code to use with R and wanted to call
Rscript from within the Makevars file (I am trying to automate the
setting of the location of a third party library depending on what is
available / the system the package is being installed on).
If I just have a simple Makevars containing
PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib
the package is built without any errors, if I attempt to add a call to
Rscript, for example (which I think is the way that "Writing R
Extensions" recommends):
R_SCRIPT_NAME=Rscript
ifneq ($(R_HOME),)
R_SCRIPT=$(R_HOME)/bin$(R_ARCH_BIN)/$(R_SCRIPT_NAME)
else
R_SCRIPT=$(R_SCRIPT_NAME)
endif
R_ARCH=$(shell $(R_SCRIPT) -e 'cat(R.version$$arch)')
PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib
I get the following error:
* checking for file 'NAGFWrappers/DESCRIPTION' ... OK
* preparing 'NAGFWrappers':
* checking DESCRIPTION meta-information ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
* installing *source* package 'NAGFWrappers' ...
** libs
/usr/share/R/make/shlib.mk:3: /usr/lib64/R/etcx86_64/Makeconf: No such
file or directory
make: *** No rule to make target `/usr/lib64/R/etcx86_64/Makeconf'.
Stop.
ERROR: compilation failed for package 'NAGFWrappers'
* removing '/tmp/Rinst1513764321/NAGFWrappers'
ERROR
* installation failed
Any help / pointers would be appreciated.
Cheers
Martyn
Output from R.version:
platform x86_64-redhat-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.0
year 2010
month 04
day 22
svn rev 51801
language R
version.string R version 2.11.0 (2010-04-22)
________________________________________________________________________
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
Hi,
I've found this type of thing to be extremely confusing, myself, but I
managed to get something to work. I'm not sure how well. I also don't
know
if R is running autoconf or just configure--at least I don't remember off
the top of my head. However, here are some examples of commands I put in my
configure.ac file:
CC=`"${R_HOME}/bin/R" CMD config CC`
CXX=`"${R_HOME}/bin/R" CMD config CXX`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
PKG_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`
then you can use some preset commands such as:
AC_PROG_CC
or generic commands such as:
AC_SUBST(whateverVariableYouLike)
and make sure to put in the key command at the bottom before AC_OUTPUT:
AC_CONFIG_FILES([src/Makefile])
If R runs autoconf before ./configure when packaging or installing, you will
be fine with just the configure.ac. Otherwise you might have to run autoconf
before packaging.
Anyway, what this will do is create a configure script when autoconf is run.
When ./configure is run by R when installing, it will execute replacement
commands on src/Makefile.in to generate the new Makefile.
Anything within two @ symbols will be replaced.
examples inside my Makefile.in:
CC = @CC@
CXX = @CXX@
I still haven't figured out how to do the Makevars thing, but I've
completely given up on R documentation. The key part from the R
documentation that I found useful was that it calls configure on install, so
you can use autoconf documentation to figure out how to set things up.
I'm sure I probably left out a ton of info, but those are my two cents.
Please feel free to ask me for more details if you are interested.
Good luck,
Sean
On 5/20/11 12:04 PM, "Martyn Byng" <Martyn.Byng at nag.co.uk>
wrote:
> Hi,
>
> I am trying to package some code to use with R and wanted to call
> Rscript from within the Makevars file (I am trying to automate the
> setting of the location of a third party library depending on what is
> available / the system the package is being installed on).
>
> If I just have a simple Makevars containing
>
>
> PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib
>
>
> the package is built without any errors, if I attempt to add a call to
> Rscript, for example (which I think is the way that "Writing R
> Extensions" recommends):
>
>
> R_SCRIPT_NAME=Rscript
> ifneq ($(R_HOME),)
> R_SCRIPT=$(R_HOME)/bin$(R_ARCH_BIN)/$(R_SCRIPT_NAME)
> else
> R_SCRIPT=$(R_SCRIPT_NAME)
> endif
> R_ARCH=$(shell $(R_SCRIPT) -e 'cat(R.version$$arch)')
>
> PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib
>
>
> I get the following error:
>
> * checking for file 'NAGFWrappers/DESCRIPTION' ... OK
> * preparing 'NAGFWrappers':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> make: Nothing to be done for `clean'.
> * removing junk files
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building binary distribution
> * installing *source* package 'NAGFWrappers' ...
> ** libs
> /usr/share/R/make/shlib.mk:3: /usr/lib64/R/etcx86_64/Makeconf: No such
> file or directory
> make: *** No rule to make target `/usr/lib64/R/etcx86_64/Makeconf'.
> Stop.
> ERROR: compilation failed for package 'NAGFWrappers'
> * removing '/tmp/Rinst1513764321/NAGFWrappers'
> ERROR
> * installation failed
>
>
> Any help / pointers would be appreciated.
>
> Cheers
>
> Martyn
>
> Output from R.version:
>
> platform x86_64-redhat-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major 2
> minor 11.0
> year 2010
> month 04
> day 22
> svn rev 51801
> language R
> version.string R version 2.11.0 (2010-04-22)
>
>
> ________________________________________________________________________
> The Numerical Algorithms Group Ltd is a company registered in England
> and Wales with company number 1249803. The registered office is:
> Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
>
> This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
On May 20, 2011, at 12:04 PM, Martyn Byng wrote:> Hi, > > I am trying to package some code to use with R and wanted to call > Rscript from within the Makevars file (I am trying to automate the > setting of the location of a third party library depending on what is > available / the system the package is being installed on). > > If I just have a simple Makevars containing > > > PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib > > > the package is built without any errors, if I attempt to add a call to > Rscript, for example (which I think is the way that "Writing R > Extensions" recommends): > > > R_SCRIPT_NAME=Rscript > ifneq ($(R_HOME),) > R_SCRIPT=$(R_HOME)/bin$(R_ARCH_BIN)/$(R_SCRIPT_NAME) > else > R_SCRIPT=$(R_SCRIPT_NAME) > endif > R_ARCH=$(shell $(R_SCRIPT) -e 'cat(R.version$$arch)') >That's all pretty much unnecessary since all settings carry over from the R invocation and also it is what causes your error (since your "arch" is wrong). On unix it's as simple as PKG_LIBS=`${R_HOME}/bin/Rscript -e 'whatever.you.meant.to.run()'` and on Windows it's PKG_LIBS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'whatever.you.meant.to.run()'` Note that you should NOT mess with the environment variables that R uses as you're likely to set them incorrectly. Cheers, Simon> PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib > > > I get the following error: > > * checking for file 'NAGFWrappers/DESCRIPTION' ... OK > * preparing 'NAGFWrappers': > * checking DESCRIPTION meta-information ... OK > * cleaning src > make: Nothing to be done for `clean'. > * removing junk files > * checking for LF line-endings in source and make files > * checking for empty or unneeded directories > * building binary distribution > * installing *source* package 'NAGFWrappers' ... > ** libs > /usr/share/R/make/shlib.mk:3: /usr/lib64/R/etcx86_64/Makeconf: No such > file or directory > make: *** No rule to make target `/usr/lib64/R/etcx86_64/Makeconf'. > Stop. > ERROR: compilation failed for package 'NAGFWrappers' > * removing '/tmp/Rinst1513764321/NAGFWrappers' > ERROR > * installation failed > > > Any help / pointers would be appreciated. > > Cheers > > Martyn > > Output from R.version: > > platform x86_64-redhat-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 2 > minor 11.0 > year 2010 > month 04 > day 22 > svn rev 51801 > language R > version.string R version 2.11.0 (2010-04-22) > > > ________________________________________________________________________ > The Numerical Algorithms Group Ltd is a company registered in England > and Wales with company number 1249803. The registered office is: > Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. > > This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}} > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >
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