Margaret Gardiner-Garden wrote: > Hi, > > 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..... > make.cdf.package("bovine.cdf") > This seemed to work OK. Says Creating package in C:/Documents and > Settings/margar/Desktop/Matthew/bovinecdf > [1] "bovinecdf" At this point you need to install the cdfenv. Unfortunately, this is a bit more difficult to do than simply zipping things up and using the menu. You have three choices here: 1.) Use make.cdf.env, which will make an environment that you can use now, but will only exist in your current workspace. You can save the workspace and use it again, but it isn't portable like a normal package where anytime you open R, you can load it. 2.) Get the tools to make packages on windows http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f This is moderately tricky, but if you follow all the (semi-terse) instructions _exactly_, you should be OK. 3.) Wait until tomorrow when I can build the env for you. I would already have it on the BioC site, but I was under the impression that it was the new binary format, and we don't yet have the ability to build envs with the binary .cdf files. Jim > > 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 > command > install.packages(choose.files('',filters=Filters[c('zip','All'),]), > .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 > Marg > > Garvan Institute of Medical Research > Sydney Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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.