R devel - Jul 2009 - R 2.8->2.9 change that breaks some upgrade scenarios

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?

>>>>> "HL" == Hin-Tak Leung <htl10 at
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.

Regards,
Martin Maechler, ETH Zurich