--- On Fri, 17/7/09, Martin Maechler <maech...@stat.math.ethz.ch> wrote:
> >>>>> "HL" == Hin-Tak Leung <ht...@users.sourceforge.net> > >>>>> on Mon, 6 Jul 2009 15:23:07 -0700 (PDT) writes: > > HL> I finally got round to look at a > little problem I have - most of the time when I use R I > would be using snpMatrix (now part of bioconductor, I wrote > a substantial part of), so I had $HOME/.Rprofile to save > some typing. Upgrading, switching versions used to work fine > with R 2.8 then it broke with 2.9.. > > HL> Apparently it is because most of > SHLIB, INSTALL, etc used to be fairly extensive shell > scripts in R 2.8 where options not specific to a particular > script is passed to R itself. Those scripts also do more of > --vanilla (--no-site-files, --no-init-files, etc), and it is > also possible to pass --vanilla, etc explicitly. The R 2.9 > implementations of these scripts are fairly thin wrappers of > R routines, and they silently(?) ignore extra options. > > HL> The specific behaviors of the scripts > are probably not gauranteed, and it is no problem > temporarily moving .Rprofile away, etc for the occasional > installations/upgrade of packages, but I think it is a valid > scenario to want to have a site-/user-customized profile for > day-to-day R usage, and a clean/vanilla R session for > installation, etc. A few more of the > HL> --no-site-files, --no-init-files, > options should go into the R 2.9 versions of SHLIB, INSTALL, > etc? > > R 2.9.x uses R code instead of the previous perl code for > INSTALL. That's the explanation for the difference. > > I agree that it would be quite useful if they supported > features as you mention, and we (R-core) will be very willing to > accept (well-tested) patches enabling that. I had a bit more thoughts on this issue since - the R 2.8 behavior (disabling user/site customization) during package installation is probably more sensible; I don't know of any user/site customization that are useful/necessary during installation. Adding --vanilla to SHLIB, INSTALL is fairly trivial? (unfortunately, with R 2.9 one can no longer do 'R --vanilla CMD INSTALL ...' for reasons I already explained, as the --vanilla option in R 2.9 needs to go inside of the INSTALL script to have any effect). I can submit a patch fairly easily, but I guess the question is, is there any scenario where one *wants* site/user customization active during package installation? Unfortunately with the R 2.9 implementation of those scripts, it is all or nothing. (all command line arguments are passed to R routines inside R for processing; there is no mechanism to modify how R is started in the new R 2..9 scripts. Well, with some extensive/painful change it is possible, but then it is basically and conceptually reverting back to the R 2.8 way with an extensive shell script wrapper). ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
