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

[James W. MacDonald]

Hi Sean,

The binary metaData packages are typically not built until close to 
release time for the devel branch. For those using R-devel/BioC-devel, a 
certain level of expertise is assumed, which (in this case) includes the 
ability to compile source packages.

Best,

Jim

Sean Davis wrote:
> 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"
> 
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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