[R] error during make of R-patched on Fedora core 2

Marc Schwartz MSchwartz at MedAnalytics.com
Tue Jun 8 16:14:23 CEST 2004

On Tue, 2004-06-08 at 06:23, Prof Brian Ripley wrote:
> On Tue, 8 Jun 2004, Gavin Simpson wrote:
> > Marc Schwartz wrote:
> > > On Mon, 2004-06-07 at 15:51, Gavin Simpson wrote:
> > > 
> > > snip


> > > 
> > > 
> > > Perhaps I am being dense, but in reviewing the two documents (R Admin
> > > and the CRAN sources page), I think that the only thing lacking is a
> > > description on the CRAN page of the manual download option for the Rec
> > > packages.


> > 
> > Yes, but having downloaded the contents of that directory (as VERSION 
> > indicated that R-patched was 1.9.1 alpha), the links to the source files 
> > for the Recommended packages or not present (obviously). And make 
> > doesn't seem to work without these links. The rsync approach places the 
> > package sources *and* the links in the correct directory.

Yep. I was being dense. Missed the symlink part of the process. My

I also missed the venus transit this morning due to clouds...  :-(

> > So the instructions in the Admin manual are lacking a statement that you 
> > need to create links to each of the package sources in the following 
> > form name-of-package.tgz which links to name-of-package_version.tar.gz. 
> > As it stands, the instructions in the Installation & Admin manual are 
> > not sufficient to get the manual download method to work.
> You need to run tools/link-recommended.  I've added that to R-admin.

Should Fritz also add that to the CRAN 'R Sources' page so that both
locations are in synch procedurally?

> > > Procedurally, I think that the rsync approach is substantially easier
> > > (one step instead of multiple downloads) and certainly less error prone.
> > > Also the ./tools/rsync-recommended script is set up to pick up the
> > > proper package versions, which also helps to avoid conflicts.
> > 
> > I agree - being a bit of a Linux newbie, I hadn't used rsync before. 
> > Seeing how easy it was to use this method of getting the required 
> > sources I will be using this method in future.
> rsync is great, *provided* you have permission to use the ports it uses.  
> Users with http proxies often do not, hence the description of the manual 
> method.  During alpha/beta periods, we do make a complete tarball 
> available, and I wonder if we should not be doing so with 
> R-patched/R-devel at all times.

Good point on rsync. Perhaps another option to consider/suggest (though
it might complicate things) is to use wget. Since wget supports proxy
servers, etc. and can use http, it might be an alternative for folks.

The wget command syntax (assuming that your working dir is the main R
source dir) would be:

wget -r -l1 --no-parent -A*.gz -nd -P src/library/Recommended

The above _should_ be one one line, but of course will wrap here. There
should be a space " " between the two lines. The above will copy the tar
files (-A*.gz) from the server (-r -l1 --no-parent) to the appropriate
'Recommended' directory (-P), without recreating the source server's
tree (-nd).

One could refer the reader to 'man wget' or
http://www.gnu.org/software/wget/wget.html for further information on
how to use wget behind proxies and related issues.

You would then of course run the ./tools/link-recommended script to
create the symlinks, followed by ./configure and make.



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