[BioC] AnnBuilder problem for mu11ksuba

[Dick Beyer]

I am having difficulty building a metadata package for mu11ksuba and was 
hoping someone would look at the error message and give me some suggestions as 
to what I am doing wrong. I am trying to follow the example in ABPrimer.pdf.

sessionInfo() 
R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu

attached base packages: 
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
[7] "datasets"  "base"

other attached packages:
  AnnBuilder    annotate         XML       limma    siggenes      qvalue
     "1.8.0"     "1.8.0"    "0.99-6"    "2.4.11"     "1.4.0"     "1.4.0"
       gcrma matchprobes     annaffy        KEGG          GO        affy
     "2.2.1"     "1.2.1"     "1.2.0"     "1.8.1"     "1.8.2"     "1.8.1"
     Biobase
     "1.8.0"


myBase <- read.table("/home/dbeyer/Microarray/affy resourcerer 
files/affy_Mu11KA UG for AnnBuilder.txt",sep = "\t", header = FALSE, as.is = 
TRUE)

> myBase[1:5,]
            V1        V2 
1 AA000151_at Mm.260767 
2 AA004127_at   Mm.3819 
3 AA009039_at  Mm.35837 
4 AA014405_at  Mm.29677 
5 AA014745_at Mm.275414

mySrcUrls <- getOption("AnnBuilderSourceUrls")  
> mySrcUrls 
$EG 
[1] "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" 
$GEO 
[1] "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?" 
$GO 
[1] "http://www.godatabase.org/dev/database/archive/latest" 
$GP 
[1] "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes" 
$HG 
[1] "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" 
$KEGG 
[1] "ftp://ftp.genome.ad.jp/pub/kegg/pathways" 
$LL 
[1] "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" 
$UG 
[1] "ftp://ftp.ncbi.nih.gov/repository/UniGene" 
$YG 
[1] "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/" 
$AT 
[1] "ftp://ftp.arabidopsis.org/home/tair/" 
$IPI 
[1] "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/" 
$CMAP 
[1] "ftp://ftp1.nci.nih.gov/pub/CMAP/"

ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType,
  pkgName = "mu11ksuba", pkgPath = ".", organism = "Mus musculus", version = 
"1.0", author = list(author = "dbeyer", maintainer = 
"dbeyer at u.washington.edu"),  fromWeb = TRUE)

Error in validObject(.Object) : invalid class "EG" object: invalid object for 
slot "baseFile" in class "EG": got class "data.frame", should be or extend 
class "character"

Thanks very much for any help or suggestions, 
Dick 
******************************************************************************* 
Richard P. Beyer, Ph.D. University of Washington 
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
    Seattle, WA 98105-6099 
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html 
http://staff.washington.edu/~dbeyer