[BioC] cdf environment for bovine Affy chips

Margaret Gardiner-Garden m.gardiner-garden at garvan.org.au
Thu Feb 10 00:41:31 CET 2005


I have been trying to load the cdf environment for the new bovine Affy chips
which is not available on the Bioconductor site as yet.  I have tried
reading the vignettes and the mailing list but unfortunately still can't
work out where I am going wrong.

I am using R Version 2.0.1 with developmental version of Bioconductor on a
Windows XP machine.  I downloaded the file bovine_libraryfile.zip from Affy
site and put the file bovine.cdf in the same location as the .RData file.

Then in makecdfenv library I did following command.....
This seemed to work OK.  Says Creating package in C:/Documents and
[1] "bovinecdf"

The resulting bovinecdf folder contains 3 folders: one called "Data" with
files 00Index and bovinecdf.rda; one called "Man" with files bovinecdf.Rd
and geometry.Rd, and one called "R" with files geometry.R and zzz.R.  There
are also 3 files Description, Index and Title.

I zipped the whole bovinecdf folder to make bovinecdf.zip and used the
install packages from local zip file (pull down menu in windows) which gives
.libPaths()[1], CRAN = NULL)

This gives error
Error in file(file, "r") : unable to open connection
In addition: Warning messages:
1: error -1 in extracting from zip file
2: cannot open file `bovinecdf/DESCRIPTION'

I am wondering how best to install the cdf environment in windows once you
have made the package.  Any advice would be greatly appreciated.

Thanks and Regards

Garvan Institute of Medical Research
Sydney Australia

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