[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