[Bioc-devel] update packages not working

[Seth Falcon]

Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I'm having difficulty auto-updating packages in R 2.5/BioC 2.0. R
> packages update without problem, BioC packages result in following
> error. 

CRAN packages update because:

   a) the CRAN URL is essentially hard-coded into R

   b) CRAN packages, in general, have very few dependencies and those
      that they have are all in the CRAN.

> It seems this happened with BioC 1.9 development also.  What is the
> acceptable protocol for updating BioC development packages?

Here's one way to upgrade all of your installed CRAN _and_
Bioconductor packages:

    library("Biobase")
    update.packages(repos=biocReposList())

> While I'm on a tear here, has anyone ever thought of synching the
> version numbers for BioC and R? I don't have a problem with it, but it
> might help newbies keep things straight. I frequently see problems on
> the BioC list caused by non-synched versions of BioC and R.

I can recall some recent cases where folks have had out of date
packages, but version number syncing is not going to help with that.
My impression is that there have been very few, if any, recent cases
of release/devel mixups.

Syncing R and BioC version numbers would not, IMO, solve package
install/upgrade issues and it would lead to confusion that the R and
Bioconductor projects were the same (they are not).

> update.packages(ask='graphics')

If the above doesn't work, send along the error messages and we'll go
from there.  But perhaps the bioconductor list is a better forum at
that point.

+ seth