[BioC] errors when trying to load CEL files

[James W. MacDonald]

Hi Dennis,

Wall, Dennis Paul wrote:
> I'm getting the following error message when trying to Affymetrix CEL
> files into Bioconductor. Has anyone seen these errors? Any ideas on what
> may be going wrong?

If reposTools is looking for things in the release 1.5 directory, then 
you have a very outdated version of R as well as BioC packages (I think 
R-2.0.X, which is about 1.5 years out of date). You should upgrade to 
R-2.2.1 at the very least and install current BioC packages. Given that 
R-2.3.0 is being released imminently, you might go ahead and get 
R-2.3.0beta and the devel versions of BioC.

HTH,

Jim

>  
> Thank you!
> 
> Sincerely,
> 
> Dennis
>  
>  
> 
>>dat <- ReadAffy()
>>dat
> 
> Note: No locliblisting in R library /usr/lib/R/site-library Warning
> message:
> Failed to read repdatadesc at http://www.bioconductor.org/CRANrepository
> in: loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/devel/package in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at http://www.bioconductor.org/data/metaData
> in: loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/metaData-devel in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/experimental/repos in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/Courses in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/cdfenvs/repos in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/probes/Packages in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/Omegahat in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/lindsey in: loadRepDD(repURL,
> rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/CRANrepository/src/contrib in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/CRANrepository/bin/windows/contrib/2.1 in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package/Source in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package/Win32 in:
> loadRepDD(repURL, rddFile, method = method) Warning message:
> cannot open: HTTP status was '404 Not Found' 
> Note: http://www.bioconductor.org/repository/devel/package/Source does
> not seem to have a valid repository, skipping Warning messages:
>  
> Note: http://www.bioconductor.org/repository/devel/package/Win32 does
> not seem to have a valid repository, skipping 
> Error in install.packages2(cdfname, lib = lib) : 
>         No repositories to search
> In addition: Warning message:
> Failed to read replisting at
> http://www.bioconductor.org/repository/devel/package/Win32 in:
> getReplisting(repURL, repFile, method = method) 
> AffyBatch object
> size of arrays=534x534 features (22284 kb)
> cdf=Mu11KsubA (??? affyids)
> number of samples=10
> Note: No locliblisting in R library /usr/lib/R/site-library 
> Warning message:
> missing cdf environment ! in: show(list()) 
> Warning message:
> Failed to read repdatadesc at http://www.bioconductor.org/CRANrepository
> in: loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/devel/package in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at http://www.bioconductor.org/data/metaData
> in: loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/metaData-devel in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/experimental/repos in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/Courses in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/cdfenvs/repos in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/data/probes/Packages in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/Omegahat in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/lindsey in: loadRepDD(repURL,
> rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/CRANrepository/src/contrib in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/CRANrepository/bin/windows/contrib/2.1 in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package/Source in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> Failed to read repdatadesc at
> http://www.bioconductor.org/repository/release1.5/package/Win32 in:
> loadRepDD(repURL, rddFile, method = method) 
> Warning message:
> cannot open: HTTP status was '404 Not Found' 
> Note: http://www.bioconductor.org/repository/devel/package/Source does
> not seem to have a valid repository, skipping 
> Warning messages:
> 1: Failed to read replisting at
> http://www.bioconductor.org/repository/devel/package/Source in:
> getReplisting(repURL, repFile, method = method) 
> 2: cannot open: HTTP status was '403 Forbidden' 
> Note: http://www.bioconductor.org/repository/devel/package/Win32 does
> not seem to have a valid repository, skipping 
> Error in install.packages2(cdfname, lib = lib) : 
>         No repositories to search
> In addition: Warning message:
> Failed to read replisting at
> http://www.bioconductor.org/repository/devel/package/Win32 in:
> getReplisting(repURL, repFile, method = method)
>  
> 
> --
> 
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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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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