[R-sig-Debian] update.packages() for R 2.7.1: mgcv fails

[Dirk Eddelbuettel]

On 9 December 2008 at 20:38, Johannes Ranke wrote:
| Hi Dirk, hi Michael,
| 
| * Dirk Eddelbuettel <edd at debian.org> [081209 19:00]:
| > 
| > Hi Michael,
| > 
| > On 9 December 2008 at 10:33, Michael Friendly wrote:
| > | Hi
| > | I just upgraded my debian/stable to R 2.7.1 via apt-get install r-base 
| > | r-base-core r-base-dev, and then
| > 
| > Did you get them from Debian, or from CRAN ?  I presume it is CRAN?
| > 
| > | began to update.packages()
| > | 
| > |  > update.packages(lib.loc="/usr/local/lib/R/site-library")
| > |  > update.packages(lib.loc="/usr/lib/R/library")
| 
| The latter location is used for the packages installed by the Debian
| package system (please correct me if I am wrong, Dirk). I think it would
| be preferable to keep them in sync with the Debian repository you are
| using for your R packages (seems to be CRAN).

Spot on!  I was asleep at the wheel there.

Indeed, the 'recommended' way is to use  

	update.packages(lib.loc="/usr/local/lib/R/site-library")

just like you did, but to leave

        /usr/lib/R/library		(r-cran-* in r-recommended)
        /usr/lib/R/site-library		(r-cran-* not in r-recommended)

You should have mgcv (via Debian) in /usr/lib/R/library.

| Since you upgraded r-base, too, you should have gotten the current mgcv
| package from CRAN as well, since r-base depends in r-recommended, which
| in turn pulls r-cran-mgcv. In case you don't need the very latest
| version of the mgcv package, I would not bother to upgrade the packages
| in /usr/lib/R/library. 

That said, he should be able to yet his build failed.  That in itself is
something we need to address.  Do you (ie Johannes) build using backports
libraries that Michael needs?

Dirk
 
| Just my 2 cents,
| 
| Johannes
| 

-- 
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