I found the following two solutions:

ALT 1:
R --no-init-file CMD <cmd>

ALT 2:
set R_PROFILE_USER=""
R CMD <cmd>


As a FYI, it does not work with either of:

R CMD --no-init-file <cmd>
R CMD <cmd> --no-init-file

and neither with (Rcmd.exe is special on Windows)

Rcmd --no-init-file <cmd>

I've always used Rcmd, so maybe the behavior of 'R CMD' loading ~/.Rprofile
has been there longer than I think, but it is only now that 'Rcmd' started
to it.

/Henrik

On Thursday, February 23, 2012, Henrik Bengtsson wrote:

> I'd like to follow up on this one.  It may be that I have
> misunderstood something, but on both R devel (2012-02-22 r58452) and R
> 2.14.1 patched (2012-02-18 r58394) I can't seem to avoid loading
> ~/.Rprofile when I run 'R CMD <cmd>', e.g. R CMD build.  For me, the
> loading of ~/.Rprofile by 'R CMD' started a few weeks ago, and I
> haven't seen it before.  More details below.  It seems incorrect that
> for instance 'R CMD check' should load the users ~/.Rprofile file by
> default.  Is this a bug or intended?
>
> /Henrik
>
>
> On Wed, Feb 8, 2012 at 5:31 PM, Henrik Bengtsson <hb@biostat.ucsf.edu<javascript:;>>
> wrote:
> > I've just noticed that with a recent R devel on Windows, R CMD build
> > sources ~/.Rprofile, e.g.
> >
> >> RCMD build
> > Running ~/.Rprofile
> >
> >> R CMD build
> > Running ~/.Rprofile
> >
> > FYI R --no-init-file & R --vanilla still avoid this.
> >
> >> sessionInfo()
> > R Under development (unstable) (2012-02-08 r58297)
> > Platform: x86_64-pc-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >
> > /Henrik
>

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