[BioC] errors when trying to load CEL files

[Wall, Dennis Paul]

Please disregard this message. I've figured it out.


Thanks,

Dennis

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wall, Dennis Paul
Sent: Thursday, April 13, 2006 9:53 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] errors when trying to load CEL files

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?
 
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)
 

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