Hi Bioconductorians,

I try since severals days to build my annotation with Annbuilder, I think that my code is functionnal

library (AnnBuilder)
data_gb = read.table("probeset_gb.txt" , sep = "\t", header=FALSE, as.is=TRUE)
mybase = file.path("probeset_gb.txt")
mybasetype= "gb"
mydir = getwd()

LL_url  = getSrcUrl(src = "LL", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE)
KEGG_url = getSrcUrl(src = "KEGG", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE)
UG_url = getSrcUrl(src = "UG", organism = "Homo sapiens", xml = TRUE, dateOnly = FALSE)
mySrcUrls = c(LL_url, KEGG_url, UG_url)
if(.Platform$OS.type != "windows" && interactive()){ABPkgBuilder(baseName= mybase, srcUrls= mySrcUrls, baseMapType = mybasetype, pkgName = "monPackageAnnoted", pkgPath = mydir, organism = "Homo sapiens", version = "1.0", author = list (authors = "Greg_Voisin, Amelie Ouellet", maintainer = "voisingreg@yahoo.fr"), fromWeb =TRUE) 
}

My error message: 
Error in "parser<-"(`*tmp*`, value = "/soft/bioinfo/linux/R-2.3.1/lib/R/library/AnnBuilder/scripts/llParser") :
        no direct or inherited method for function 'parser<-' for this call
In addition: Warning message:
use of NULL environment is deprecated

My research in archives bioconductor shows us Raffaele Calogero had the same problem 2 years ago but no answer..

Is it a bug in Annbuilder ?? 
Thanks for your help

Greg 
Montreal 
Bioinformatics Phd Student at IRIC


      
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