[Rd] R 2.8->2.9 change that breaks some upgrade scenarios

[Hin-Tak Leung]

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..

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.

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 
  --no-site-files, --no-init-files, options should go into the R 2.9 versions of SHLIB, INSTALL, etc?