[BioC] BioConductor Affy package

Susan J. Miller sjmiller@u.arizona.edu
Tue, 07 Jan 2003 15:36:12 -0700


Jeff Gentry wrote:
> 
> On Fri, 3 Jan 2003, Susan J. Miller wrote:
> > =====================================================
> > cd CELFILES
> > R
> > > library(affy)
> > Error in library(affy) : This is not a valid package -- no DESCRIPTION
> > exists
> > =====================================================
> 
> Am I assuming correctly here that you have package affy installed in
> directory CELFILES?  Or in /usr/local/lib/R/library (from below)?

It is in /usr/local/lib/R/library, which is in .libPaths() so I don't
know why I can't load the affy package (it tells me that no DESCRIPTION 
exists).  There is a DESCRIPTION.in file but it looks like the
installation
failed.

> If the former, and if CELFILES is not in your .libPaths() set of
> locations, that would be a problem.  You could try:
> library(affy,lib.loc("CELFILES")) for instance.
> 
> > Running getBioC version 1.2.3 ....

I just downloaded this, and I have version 1.2.6.  Now when I try to 
install, it doesn't get past reposTools.  It gives a warning about a
PDF viewer and then dies:

==============================================================================
> getBioC(libName="all")
Running getBioC version 1.2.6 ....
Please direct any concerns or questions to
bioconductor@stat.math.ethz.ch.

[1] "Getting/installing packages reposTools and Biobase"
Loading required package: Biobase 
Note: To manually set your viewer, run the command
'setOptionPdfViewer(<path>), where <path> is a path to a valid PDF
viewer program. 
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
Attaching package `Biobase':


        The following object(s) are masked from package:base :

         split 

Creating a new generic function for "summary" in package 
reposTools 

Attaching package `reposTools':


        The following object(s) are masked from package:base :

         summary 

Warning message: 
No available PDF viewer found on system in: setOptionPdfViewer() 
> 
==============================================================================

Any other suggestions for getting Bioconductor installed on Solaris8?

-susan