[Bioc-devel] Affy behavior macos x, devel branch

[Sean Davis]

1) read an affybatch
2) want to show an affybatch

> affybatch <- 
ReadAffy(filenames=dir('../Results',pattern='.CEL'),celfile.path='../Results')
> affybatch
Warning: unable to access index for repository
http://bioconductor.org/packages/1.9/bioc/bin/macosx/powerpc/contrib/2.4
Warning: unable to access index for repository
http://bioconductor.org/packages/1.9/data/annotation/bin/macosx/powerpc/cont
rib/2.4
Warning: unable to access index for repository
http://bioconductor.org/packages/1.9/data/experiment/bin/macosx/powerpc/cont
rib/2.4
Warning: unable to access index for repository
http://bioconductor.org/packages/1.9/omegahat/bin/macosx/powerpc/contrib/2.4
Warning: unable to access index for repository
http://bioconductor.org/packages/1.9/monograph/bin/macosx/powerpc/contrib/2.
4
Warning: unable to access index for repository
http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.4
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain Rat230_2
Library - package rat2302cdf not installed
Data for package affy did not contain rat2302cdf
Bioconductor - rat2302cdf not available
AffyBatch object
size of arrays=834x834 features (130426 kb)
cdf=Rat230_2 (??? affyids)
number of samples=24
.....

I needed to install the rat cdf package by hand first.  I think this is a
typical problem with macos, but just wanted to make sure that I had passed
it on in case someone didn't expect this to happen.

Sean

> sessionInfo()
R version 2.4.0 Under development (unstable) (2006-08-16 r38905)
powerpc-apple-darwin8.7.0

locale:
C

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
rat2302cdf       affy     affyio    Biobase
  "1.12.0"   "1.11.6"    "1.1.3"  "1.11.26"