Re: [R] RHOME

From: Dan Powers <dpowers_at_mail.la.utexas.edu>
Date: Sat 04 Feb 2006 - 13:58:10 EST


R-help

My thanks goes out to all who responded to this. I am tying to avoid burdening the sysadmin with this project so I opted for the simple fix of modifying the shell script. My aim here is to build the libraries in my local directory and copy those as needed to /usr/local/lib/R/library. I will have to direct the sysadmin in the installation of future versions of R.

Cheers,
Dan

%%%%%%%%%%%%%%%%%%%%%%%%

Daniel A. Powers, Ph.D.
Department of Sociology
University of Texas at Austin
1 University Station A1700
Austin, TX 78712-0118
phone: 512-232-6335
fax: 512-471-1748
dpowers@mail.la.utexas.edu

-----Original Message-----
From: Martyn Plummer [mailto:plummer@iarc.fr] Sent: Friday, February 03, 2006 9:46 AM
To: Peter Dalgaard
Cc: Martin Maechler; Daniel A. Powers; r-help@stat.math.ethz.ch Subject: Re: [R] RHOME

Far be it for me to tell people what they can and cannot do. Perhaps I can rephrase myself in a less inflammatory way.

R runs from the build directory as a convenience for developers, so you don't have to reinstall R every time you change something. But for users, the standard mechanism "make install" has a number of advantages over moving the build directory to a publicly accessible location: it is guaranteed to work, you don't have to do any post-hoc editing of files, it takes up a lot less space, about 4.6 times less on my system

[martyn@seurat r-devel]$ du -sh R
356M R
[martyn@seurat r-devel]$ du -sh /usr/local/lib64/R 77M /usr/local/lib64/R

But if you do want to copy the build directory the, as Martin says, you can edit the file bin/R so that the line that starts R_HOME_DIR points to the correct location, e.g.

R_HOME_DIR="/usr/local/lib/R"

M.

On Fri, 2006-02-03 at 14:48 +0100, Peter Dalgaard wrote:
> Martin Maechler <maechler@stat.math.ethz.ch> writes:
>
> > Martyn> R is designed to run from its build directory. But
> > Martyn> if your sysadmin installs it with "make install" (as
> > Martyn> root), then the shell wrapper that is installed in
> > Martyn> /usr/local/bin/R will have R_HOME pointing to the
> > Martyn> right location (/usr/local/lib/R). Literally moving
> > Martyn> the build directory to another location is the wrong
> > Martyn> thing to do.
> >
> > well, but very easily fixable, and that's what Daniel is asking
> > for:
> >
> > The default value of R_HOME is only set in exactly one place,
> > namely the 'R' shell script; editing that script - once after
> > the move - is really a piece o'cake.
>
> Hmm, I was about to say the same, but there seems to be unexpected
> references in other places.
>
> find `R RHOME` | xargs grep `R RHOME`
> /usr/lib64/R/bin/R:R_HOME_DIR=/usr/lib64/R
> /usr/lib64/R/bin/R:R_SHARE_DIR=/usr/lib64/R/share
> /usr/lib64/R/bin/R:R_INCLUDE_DIR=/usr/lib64/R/include
> /usr/lib64/R/bin/R:R_DOC_DIR=/usr/lib64/R/doc
>
> (this doesn't normally happen - a SUSE RPM specialty, or due to
> configure flag settings?)

I think this is normal. But the RedHat RPM behaves differently.

(because the RPM build process installs into a temporary build root which is distinct from the final installation directory, requiring more sed voodoo).

>
> Once you start building packages, you also have things like
>
> viggo:~/>find ~/Rlibrary | xargs grep `R RHOME`
> Binary file /home/bs/pd/Rlibrary/rgl/libs/rgl.so matches
>
>
> viggo:~/>find ~/Rlibrary | xargs grep Rlibrary
> Binary file /home/bs/pd/Rlibrary/rgl/Meta/hsearch.rds matches
> Binary file /home/bs/pd/Rlibrary/ISwR/Meta/hsearch.rds matches
> Binary file /home/bs/pd/Rlibrary/mvtnorm/Meta/hsearch.rds matches
> Binary file /home/bs/pd/Rlibrary/nlmeODE/Meta/hsearch.rds matches
> B.....
>
> on my laptop I had a hit on one of the Sweave support files too.
>
> Most likely these are quite harmless, but all in all I think Martyn
> has the safest advice: Use "make install", as root (don't forget
> "umask 022").
>



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