[BioC] GEOquery install problem with openSUSE 11.4 and R 2.15

Sean Davis sdavis2 at mail.nih.gov
Tue May 29 20:49:08 CEST 2012

On Tue, May 29, 2012 at 2:42 PM, Bartlett, Thomas
<thomas.bartlett.10 at ucl.ac.uk> wrote:
> Hi,
> I'm using openSUSE 11.4 (x86_64) with R version 2.15.0 (2012-03-30). I'm trying to install GEOquery, but get the following error message:
> ERROR: configuration failed for package ‘XML’
> * removing ‘/usr/lib64/R/library/XML’
> ERROR: dependency ‘XML’ is not available for package ‘GEOquery’
> * removing ‘/usr/lib64/R/library/GEOquery’
> N.B., I can only install extra programs/packages etc via the 'sudo zypper install' command, due to computer restrictions in my institute
> Any help on how to resolve this problem would be very much appreciated!

Hi, Tom.

I would suggest using biocLite().  If you do not have write
permissions to the R system location (and it sounds like you do not),
then R will install packages in your home directory.

In any case, this is failing because the XML package is not installing
correctly.  Note that the XML package has some install notes:


You might take a look at them and see if that helps.


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