R help - Oct 2003 - How to upgrade R

Hi

I wondered what the standard procedure was for upgrading from one version of R
to the next.  I currently have R 1.7.1 and want the latest release, R 1.8.0.  I
am running SUSE linux 8.2.  The main thing is that I want to keep all of the
libraries that I have installed for R 1.7.1 without having to re-install them.

I tried the rpm but that didn't really work :-(

I then tried installing from source and that worked.  I then copied my library/
folder across to the new installation, but now I get lots of error messages
along the lines of:

Error in grep("\\w", platform) : 5 arguments passed to
"grep" which requires 6.

So, my question being, how do I upgrade from R version 1.7.1 to R 1.8.0 and keep
all of my libraries intact?

Thanks
Mick

On Mon, 20 Oct 2003, michael watson (IAH-C) wrote:
> Hi
>
> I wondered what the standard procedure was for upgrading from one version
of R to the next.  I currently have R 1.7.1 and want the latest release, R
1.8.0.  I am running SUSE linux 8.2.  The main thing is that I want to keep all
of the libraries that I have installed for R 1.7.1 without having to re-install
them.
>
> I tried the rpm but that didn't really work :-(
>
> I then tried installing from source and that worked.  I then copied my
library/ folder across to the new installation, but now I get lots of error
messages along the lines of:
>
> Error in grep("\\w", platform) : 5 arguments passed to
"grep" which requires 6.
>
> So, my question being, how do I upgrade from R version 1.7.1 to R 1.8.0 and
keep all of my libraries intact?
>
You should not install your packages to the library path of R itself but
to something like `$HOME/lib/R' and tell R about it (via the R_LIBS
environment variable, see section 4 of R Installation and Administration).

Note that in contrast recommended packages may be installed in R's install
directory and that is what's happens by default.

Best,

Torsten

> Thanks
> Mick
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
>

What I do is to separate packages that shipped with R separate from other
contributed packages from CRAN, so that when I upgrade, I can wipe clean the
old R and re-install while keeping all other packages in place.

What's not clear to me is a good way of keeping two versions of R
simultaneously (for ease of transition).  Can anyone suggest a good strategy
for doing that on *nix?

Best,
Andy
> -----Original Message-----
> From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk] 
> Sent: Monday, October 20, 2003 5:49 AM
> To: r-help
> Subject: [R] How to upgrade R
> 
> 
> Hi
> 
> I wondered what the standard procedure was for upgrading from 
> one version of R to the next.  I currently have R 1.7.1 and 
> want the latest release, R 1.8.0.  I am running SUSE linux 
> 8.2.  The main thing is that I want to keep all of the 
> libraries that I have installed for R 1.7.1 without having to 
> re-install them.
> 
> I tried the rpm but that didn't really work :-(
> 
> I then tried installing from source and that worked.  I then 
> copied my library/ folder across to the new installation, but 
> now I get lots of error messages along the lines of:
> 
> Error in grep("\\w", platform) : 5 arguments passed to
"grep"
> which requires 6.
> 
> So, my question being, how do I upgrade from R version 1.7.1 
> to R 1.8.0 and keep all of my libraries intact?
> 
> Thanks
> Mick
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
>

It's actually easier than I thought (and perhaps than you described).  What
Prof. Ripley suggested, combined with the options to the configure script,
should make this fairly straight-forward, even with "make install".

Cheers,
Andy
> From: David Brahm [mailto:brahm at alum.mit.edu] 
> 
> Andy Liaw <andy_liaw at merck.com> wrote:
> 
> > What's not clear to me is a good way of keeping two versions of R 
> > simultaneously (for ease of transition).  Can anyone suggest a good 
> > strategy for doing that on *nix?
> 
> I'm not sure what you mean, but I'll tell you what we do.  We 
> have built /res/R/R-1.6.2, /res/R/R-1.7.1, /res/R/R-1.8.0, 
> etc. (note we never run "make install").  Anyone who doesn't 
> want to upgrade (e.g. frozen production code) just hard-codes 
> one of those paths.  Everyone else uses a symbolic link 
> /res/R/R, which right now points to R-1.7.1 but will change 
> to R-1.8.0 when we feel we're "ready".
> 
> Just to add another layer of complication, actually we have 
> another symbolic link /res/R/Rdb, which I ("db") use, because 
> I like to upgrade faster.  So Rdb currently points to 
> R-1.8.0.  Symbolic links are your friend.
> -- 
>                               -- David Brahm (brahm at alum.mit.edu)
>