[BioC] Error in function (classes, fdef, mtable)

[Seth Falcon]

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Several of your packages seem to be out of date with the version
> released in Bioconductor 1.9 and intended for use with R 2.4.0, e.g.,
>
> affyio (version in 1.9: 1.2.0; your version: 1.0.0)
> affyQCReport (1.12.0, versus 1.10.0)
> simpleaffy (1.8.0, versus 1.6.0)
>
> After running the command
>
> update.packages(repos="http://bioconductor.org")
                        ^^^^^^^^^^^^^^^^^^^^^^^^^

That's actually not what I would recommend.  At present, the best way
to update Bioconductor packages is:

1. Get the latest version of Biobase:

      source("http://bioconductor.org/biocLite.R")
      biocLite("Biobase")

2. Use the new Biobase to get a list of repositories for update:

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

The reason is that not all BioC packages are in a single CRAN-style
repository and many packages depend on CRAN packages.  It is quite
important to update all packages at the same time.

Best,

+ seth