Jon,I have had a similar problem when installing librarys. I have written a script which uses biocLite to install librarys. I have included the following code which hides .Rprofile by renaming it and then renaming it back again after it has finished.
#Hide .Rprofile whilst this script is running.
file.rename(paste(Sys.getenv("HOME"),".Rprofile",sep=.Platform$file.sep),paste(Sys.getenv("HOME"),".Rprofile_hiding",sep=.Platform$file.sep))
# ...
# ... install libraries code
# ...
#Put .Rprofile back
file.rename(paste(Sys.getenv("HOME"),".Rprofile_hiding",sep=.Platform$file.sep),paste(Sys.getenv("HOME"),".Rprofile",sep=.Platform$file.sep))
I think this should be platform independent, but have mainly tried it on
Windows and Unix.
cheers, Keith Satterley, On 18/02/2011 11:12 PM, Jon Clayden wrote:
I would also be interested in knowing what the rationale is for this. Moreover, it seems that the "standard" (and documented) approach to this of calling "options(defaultPackages=c(...))" in ~/.Rprofile does not get ignored when installing. The environment variable approach may work, but it seems to me that this requires some (educated) guesswork. Could R CMD INSTALL not ignore the default packages option? Regards, Jon On 16 February 2011 17:25, Brian G. Peterson<br...@braverock.com> wrote:On 02/16/2011 10:57 AM, Prof Brian Ripley wrote:The most obvious answer is not to do that. You have not used the standard mechanism to to do that (which should work here as R CMD INSTALL overrides that one). It's all in ?Startup (look for R_DEFAULT_PACKAGES).Note that R CMD INSTALL is not mentioned at all here.The simplest way to ignore ~/.Rprofile is to set R_PROFILE_USER to something else.I've tried R --vanilla CMD INSTALL, but that seems to have no effect.As documented.Then let's try this from another angle... Is there a rationale why --vanilla or --no-environ or --no-site-file or --no-init-file are *NOT* supported by R CMD INSTALL ? I don't see any reasoning for the inconsistency in the docs anywhere. If not, would R-core entertain a patch that would handle these options? This functionality is troublesome in a production installations where we *want* our users to have specific packages and environment options set all the time, and I need to edit the Rprofile.site file every time I upgrade one of these 'production' packages. Regards, - Brian ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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