[BioC] ABPkgBuilder question

Kamila Naxerova knaxerova at chip.org
Sun Aug 10 06:05:51 CEST 2008


Hi all,

I am - not very successfully - playing with AnnBuilder and would
appreciate any comments on the error I am getting (system info below).
Confusingly, the same code *seems* to work fine on my windows machine,
only here I don't want to deal with unzipping problems. Sorry if this is
something obvious.

platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          7.1
year           2008
month          06
day            23
svn rev        45970
language       R


library(hgu133plus2.db)
x=hgu133plus2ENTREZID
xx=as.list(x)
basefile=data.frame(names(xx),as.character(unlist(xx)))
write.table(basefile,"Basefile.txt",sep="\t",row.names=F)

library(AnnBuilder)
mySrcUrls=getSrcUrl("all",organism="Homo sapiens")

ABPkgBuilder(baseName = read.table("Basefile.txt",header=F,sep="\t"),
srcUrls = mySrcUrls, baseMapType ="ll", pkgName = "hgu133plus2",
pkgPath = getwd(), organism = "Homo sapiens", version = "1.1.0",author =
list(authors = "K"),fromWeb=TRUE)

Error in validObject(.Object) :
  invalid class "UG" object: invalid object for slot "baseFile" in class
"UG": got class "data.frame", should be or extend class "character"
Calls: ABPkgBuilder ... UG -> new -> initialize -> initialize -> validObject
Execution halted


Thanks,
Kamila



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