[BioC] Install all CDF, Probes, Annotation metaData in One-Shot or Update them, How?

Saurin Jani saurin_jani at yahoo.com
Wed Jun 1 20:21:53 CEST 2005


Dear BioC,

How can I install all metaData available (including
CDF,Probe and Annotation) information from URL:

http://www.bioconductor.org/packages/data/annotation/stable/src/contrib/html/

I am doing follwoing, and I get all latest results
from that URL. But somehow , I get error msg. as shown
below.  Please, help me if someone have done this
before or point me in to right direction. 

#=================
# some pkgs I have already installed, long time ago 
manually by downloading .gz file, out of  240

> allnew <-
getReposEntry("http://www.bioconductor.org/packages/data/annotation/stable/src/contrib")

> update.packages2(repEntry=allnew)

Note: argument `lib' is missing: using
/usr/local/lib/R/library
Note: You did not specify a download type.  Using a
default value of: Source
This will be fine for almost all users

Warning message:
cannot open: HTTP status was `404 Not Found'
Note:
http://www.bioconductor.org/data/metaData/src/contrib
does not seem to have a valid repository, skipping
Warning message:
Failed to read replisting at
http://www.bioconductor.org/data/metaData/src/contrib
in: getReplisting(repURL, repFile, method = method)
Warning message:
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 agrep(nfPkgs[i], availPkgs) : pattern must be
a non-empty character string
In addition: Warning message:
Failed to read replisting at
http://www.bioconductor.org/repository/devel/package/Win32
in: getReplisting(repURL, repFile, method = method)

#===========================


Thank you in advance,
Saurin Jani



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