[BioC] AnnBuilder problem?

[Denise Mauldin]

Hey all,

I'm having a problem with Annbuilder:

> tempConfig <- tempfile()
> writeSourceUrlConfig(tempConfig) 
> root = "http://sioux.fhcrc.org/MIRROR"
> urlData = readSourceUrlConfig(tempConfig, root)
> origUrls = getOption("AnnBuilderSourceUrls")
> geoUrl = origUrls[["GEO"]] 
> urlData[["GEO"]] = geoUrl
> options(AnnBuilderSourceUrls=urlData) 
> localMirror <- paste(root, "ftp.arabidopsis.org/home/tair/", sep="/")
>
> ABPkgBuilder(baseName="mpedbadm_genbank.txt",
+ baseMapType="gbNRef",
+ pkgName="MPEDB",
+ organism="Mus musculus",
+ otherSrc=c(UG="mpedbadm_unigene.txt"),
+ pkgPath="./",
+ version="0.1",
+ author=list(authors="Denise Mauldin", maintainer="Denise Mauldin <dmauldin at fhcrc.org>"))

Warning message: 
Built for UCSC is not valid! in: getUCSCBuilt(organism)
Error in parseKEGGGenome() : Faild to obtain KEGG organism code

>sessionInfo()
R version 2.2.0, 2005-10-06, sparc-sun-solaris2.9
 
attached base packages: [1] "tools"  "methods"  "stats"  "graphics"  
"grDevices" "utils" [7] "datasets"  "base"
 
other attached packages: 
   AnnBuilder annotate    XML       Biobase      GO
   "1.8.0"    "1.8.0"   "0.97-8"    "1.8.0"   "1.10.0" 


----
Warning issue with UCSC:

If you browse to the MIRROR directory, it exists and has the Mus_musculus 
subdirectory.  

If I look at the code in 1.8.0 Annbuilder for getUCSCBuilt() it says:

getUCSCBuilt <- function(organism){
    url <- getSrcUrl(src = "GP", organism = organism) 

    built <- NA
 
    if(is.na(built) || is.null(built) || built == ""){
        warning("Built for UCSC is not valid!")
        return("N/A") 
    } else { 
        return(built)
    }
} 

So it seems like this was changed to always be nothing and always throw 
this error?  (The rest of the code has been commented out.)

--- 
Error issue with KEGG

However, it doesn't die on that error, it dies on the following KEGG 
error.  This seems to be because even though I altered the URLs, it's 
using the original URLs (which shouldn't that work anyway?).  I then 
altered my ABPkgBuilder call to include srcUrls = urlData (as that's how 
the ABPkgBuilder documentation now reads), but this throws a separate 
error:

Error in validObject(.Object) : invalid class "GO" object: invalid object 
for slot "srcUrl" in class "GO": got class "list", should be or extend 
class "character"

> mode(urlData[["GO"]])
[1] "character"
> class(urlData[["GO"]])
[1] "character"
> urlData[["GO"]]
[1] "http://sioux.fhcrc.org/MIRROR archive.godatabase.org/latest"

So this seems to be something in the code in one of the KEGG calls?  

Anyone have any ideas on what I'm doing wrong?  Anyone have any ideas on 
what to do next?  

Thanks,
Denise