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you have a very outdated version of R as well as BioC packages (I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R-2.0.X, which is about 1.5 years out of date).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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
>
https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
