On Feb 15, 2005, at 6:52 AM, John Zhang wrote: > >> I've gotten closer to getting a working yeast annotation package for >> the Affymetrix YEAST 2.0 chip. I was able to procure the proper ORF >> ids and the probe ids, and from there I used yeastPkgBuilder within >> AnnBuilder to create a package. It ran for a few hours and terminated >> with the following error: >> >> Error in readLines(con) : cannot open the connection > > The code was trying to access a public data source (most likely GO > based on the > time spent) when the site was probably down. > >> >> From what I can tell, it got most (if not all) of the probes >> processed. >> I tried installing the package from the shell using >> >> R CMD INSTALL YEAST2 >> >> YEAST2 is the name I gave to the package. I get the error: >> >> WARNING: invalid package 'YEAST2' >> ERROR: no packages specified > > Was there a DESCRIPTION file. The build was interrupted and the > package may not > have all the required elements for a package. The following files were created: YEAST2ALIAS.rda YEAST2CHR.rda YEAST2CHRLOC.rda YEAST2DESCRIPTION.rda YEAST2GENENAME.rda YEAST2GO.rda YEAST2ORF.rda YEAST2PMID.rda YEAST2PMID2PROBE.rda > >> >> I know it's there, it just doesn't think the directory is a valid >> package (dir includes R, man, data subdirectories). I also tired >> installing via the Mac OS X GUI, which also failed. >> >> There was also an XML file made, which seems to contain all the proper >> annotation. Is there any way to create an annotation package from >> this >> XML file? Why even make the XML file? (Just curious). > > You can set makeXML = FALSE to turn it off. I know I can turn it off -- I just wanted to know what the purpose would be (within BioC) of making an XML version. > >> >> Thanks in advance, >> >> Jake Michaelson >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > Jake Michaelson [[alternative text/enriched version deleted]]