[BioC] mas5 update.default problem

[Seth Falcon]

David Ruau <David.Ruau at rwth-aachen.de> writes:
> verbose=FALSE or TRUE doesn't change anything
> and example(mas5) give the same error...
> I re-install the last R-patched from source nothing changed, I
> install in despair R binary and I am still having the same problem.

Hmm, how have you been instaling Biocondcutor packages?

If you are using a source built R, I recommend (removing all possibly
stale BioC packages and then):

  source("http://bioconductor.org/biocLite.R")
  biocLite("somePkg", type="source")

After getting a good install, you can update like this:

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

If you are using the CRAN binary R, then you want type="mac.binary"
which is the default on OSX.  I run OS X on my laptop, but use a
source-built R.  I have the following in ~/.Rprofile:

   options(repos="http://cran.fhcrc.org")
   options(pkgType="source")
   options(browser="open")

   if (TRUE && interactive()) {
   tryCatch({
       source("http://bioconductor.org/biocLite.R")
   }, error=function(e) invisible(NULL),
            warning=function(w) cat("Not connected to the net\n"))
   }

Setting the pkgType option to "source" means I can call biocLite()
without remember to ask for source packages.

> Can I re-install update.default() method manually?

No, the problem is not exactly a wrong definition.  I'm not yet
convinced it is a problem in the software and suspect that you have a
bad mix of versions.  Let's see if we can sort that out first.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org