[BioC] (no subject)

Gordon Smyth smyth@wehi.edu.au
Tue, 04 Mar 2003 12:16:29 +1100


Dear Robert (and Tiago),

The problem here is that CRAN itself has a version of XML which was built 
for R 1.6.1. It not Tiago's fault!

Gordon

At 12:02 PM 4/03/2003, Robert Gentleman wrote:
>On Mon, Mar 03, 2003 at 04:44:56PM -0800, Tiago R Magalhaes wrote:
> > I am sorry to bother you with such an irrelevant question and I understand
> > if you can't reply to it
> >
> > I am biologist working on microarrays (Affy) and I am trying to run R (I
> > have some experience on S plus)
> > I tryed to install the Bioconductor Package and I cannot
> > it tells me that I have to install an XML file:
> > Package annotate version 1.0.5 requires package XML version >= 0.92-2,
> > would you like to try to install this package? [yes/no] yes
> >
> > when I click yes it runs, dowloads something and then:
> > Warning message:
> > Running R version 1.6.2 and package XML was built for R version 1.6.1,
> > skipping.
> > Please look at the option versForce if you would like to continue. in:
> > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>
>   Hmm,
>    I am not sure where you are getting an old XML from?,
>   but what you can do is,
>   start R
>   use the menu named Packages
>   from that select the item
>    Install Package from CRAN
>   from the dialog select
>    XML
>
>  and that should handle XML; then try to install Bioconductor again
>  with that in
>
>  Robert
>
>
> >
> > and I am stuck
> >
> > any ideas on how to solve this problem?
> >
> > thanks very much
> >
> >
> > tiago magalhaes
> >
> >
> > (follows the all dialogue with the computer)
> >
> > [1] "Getting/installing packages reposTools and Biobase"
> > Package annotate version 1.0.5 requires package XML version >= 0.92-2,
> > would you like to try to install this package? [yes/no] yes
> > Note: No specified download type, defaulting to Win32
> > [1] "Attempting to download XML from
> > http://www.bioconductor.org//CRANrepository"
> > [1] "Download complete."
> > [1] "Installing XML"
> >  From URL:  http://www.bioconductor.org//CRANrepository
> >          XML version 0.93-1
> >
> > Packages that were not updated:
> >          annotate
> >          genefilter
> >          geneplotter
> >          edd
> >          ROC
> >          multtest
> >          Biobase
> >          tkWidgets
> >
> > Warning message:
> > Running R version 1.6.2 and package XML was built for R version 1.6.1,
> > skipping.
> > Please look at the option versForce if you would like to continue. in:
> > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth@wehi.edu.au, www: http://www.statsci.org