>>>>> "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.
Regards,
Martin Maechler, ETH Zurich
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