[BioC] AnnBuilder problem.

[Nianhua Li]

Hi, Dario,

Please try:

if (.Platform$OS.type != "windows" && interactive()) {
ABPkgBuilder(baseName = myBase,
                        baseMapType = myBaseType,
                        pkgName = "myPkg",
                        pkgPath = myDir,
                        organism = "Homo sapiens",
                        version = "1.1.0",
                        author= list( authors="Dario Greco", 
maintainer="Dario Greco"),
                        fromWeb = TRUE)}

The problem is "mySrcUrls". Its default value in ABPkgBuilder is:
  getSrcUrl("all", organism=organism)   ## here organism is your input 
value of organism for ABPkgBuilder,
                                                                  ## 
default is "Homo sapiens", happens to be the same as your input
If you compare the return of getSrcUrl and 
getOption("AnnBuilderSourceUrls"):
 > x <- getSrcUrl("all", organism="Homo sapiens")
 > y <- getOption("AnnBuilderSourceUrls")
 > names(x)
 [1] "GP"         "UG"         "GO"         "KEGG"       "YG"
 [6] "HG"         "EG"         "IPI"        "YEAST"      "KEGGGENOME"
[11] "PFAM"
 > names(y)
 [1] "EG"         "GEO"        "GO"         "GP"         "HG"
 [6] "KEGG"       "LL"         "UG"         "YG"         "AT"
[11] "IPI"        "CMAP"       "YEAST"      "KEGGGENOME" "PFAM"
 > x[["GO"]]
[1] 
"http://www.godatabase.org/dev/database/archive/latest/go_200606-termdb.rdf-xml.gz"
 > y[["GO"]]
[1] "http://www.godatabase.org/dev/database/archive/latest

That's why you get warning message: "unable to resolve 
'archive.godatabase.org'", I guess.

hope it is helful and good luck

Nianhua Li
Group of Computational Biology
PHS, FHCRC