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

[Johannes Ranke]

Hi again,

* Dirk Eddelbuettel <edd at debian.org> [081209 23:10]:
> 
> 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?

No, I don't use backported libraries. However, if installing with
install.packages() or update.packages() from within R, the build
dependencies have to be manually installed.

Hannes