[Rd] update.packages() doesn't pick up the highest version of packages

[Herve Pages]

Hi,

Try to install limma 2.8.1 with:

  > biocRep <- "http://bioconductor.org/packages/1.9/bioc"
  > install.packages("limma", repos=biocRep)

then try to update it with

  > repos <- c(biocRep, "http://cran.fhcrc.org")
  > update.packages(repos=repos)

--> it will not get updated (even if there is a 2.9.8 version on CRAN).

This is (1) surprising by itself, (2) inconsistent with install.packages
behaviour.

When given more than 1 repository, install.packages() will go thru
all of them and pick up the higher version of each package to install.
For example, this:

  > repos <- c(biocRep, "http://cran.fhcrc.org")
  > install.packages("limma", repos=repos)

will install limma from CRAN (2.9.8) instead of limma from Bioconductor (2.8.1).

But if a new version of limma shows up on CRAN, this:

  > update.packages(repos=repos)

will not update it...

Cheers,
H.