[R-SIG-Mac] affy pcg installation and XML installation in Panther

[Simon Urbanek]

On Jul 15, 2004, at 11:29 AM, Tiago R Magalhaes wrote:

> I am trying to install the affy package from bioconductor and I have
> been very unsuccessful!
>
> I have a G4, MacOSX panther and the R version 1.9.1 installed.
>
> One of the problems is that the XML tools are not installed. I tried
> to install a package called libXML2.pkg, but there's an indication
> that it might be for Jaguar only.

libXML is not necessary (and it's even hurtful) for Panther, because it 
is already included with the system. The "XML tools" doesn't mean the 
system library.

> When I installed BioConductor from the CRAN repository it gave 23
> warnings most of them concerning XML.
> [1] "Installing XML" Note: Package XML not found in any known 
> repository.

This is some problem with your repository settings on your machine and 
is not Mac dependent. Today I able to install XML package w/o any 
problems. Although getBioC does the job, too, you can still use the 
regular R way using install.packages("XML").

Cheers,
Simon