[BioC] error getting CDF

James W. MacDonald jmacdon at med.umich.edu
Mon Apr 9 19:34:58 CEST 2007


Yi Xing wrote:
> Hi,
> 
> I have been trying to use gcrma to get expression indexes from mouse 
> 430_2 affymetrix arrays. However, I cannot get the appropriate CDF file 
> if I run 'just.gcrma'. Below is the error message. It seems that the 
> downloading URL is incorrect - but how should I fix this?

You don't give your sessionInfo(), so it is hard to say exactly what the 
problem is. In addition, this doesn't look like the output you should 
get if justGCRMA() can't load the correct URL. It looks more like you 
were trying to install packages using an outdated reposTools package 
(which is defunct in BioC 1.9, and superceded by biocLite()).

At the very least it appears you need to update Biobase to get a current 
biocReposList(), so I would start with

source("http://www.bioconductor.org/biocLite.R")
biocLite("Biobase")

While you are at it, you can just get the mouse4302cdf and probe 
packages as well.

biocLite(c("mouse4302cdf", "mouse4302probe"))

Best,

Jim




> 
> Thanks very much,
> Yi Xing
> 
> Warning message:
> cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/CRANrepository does not seem to have 
> a valid repository, skipping
> Warning message:
> Failed to read replisting at http://www.bioconductor.org/CRANrepository 
> in: getReplisting(repURL, repFile, method = method)
> Warning message:
> cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/bioc/devel does not seem to 
> have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/bioc/devel in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/data/annotation/stable does 
> not seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/data/annotation/stable in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/data/annotation/devel does 
> not seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/data/annotation/devel in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/data/experiment/stable does 
> not seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/data/experiment/stable in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/data/annotation/stable does 
> not seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/data/annotation/stable in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/data/annotation/stable does 
> not seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/data/annotation/stable in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/omegahat/stable does not 
> seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at 
> http://www.bioconductor.org/packages/omegahat/stable in: 
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/packages/lindsey/stable does not seem 
> to have a valid repository, skipping
> Note: Using download type: Source
> Error in getCDF(cdfpackagename) : Environment mouse4302cdf was not 
> found in the Bioconductor repository.
> In addition: Warning message:
> Failed to read replisting at 
> http://www.bioconductor.org/packages/lindsey/stable in: 
> getReplisting(repURL, repFile, method = method)
> 
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-- 
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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