[BioC] Problem with ABPkgBuilder function

Raffaele Calogero raffaele.calogero at unito.it
Thu Mar 10 18:21:35 CET 2005

I am trying to build an annotation package starting from Applera Mm 
array, but I got this strange error running ABPkgBuilder

Error in "parser<-"(`*tmp*`, value = 
"/usr/lib/R/library/AnnBuilder/scripts/llParser4LL") :
        No direct or inherited method for function "parser<-" for this call

Any suggestion?

(Fedora core 2, R 2.0.0, Bioconductor 1.5, AnnBuilder_1.4.21.tar.gz)
Here is enclosed the code I used.

#As test I am using a two column file, "tmp.txt", containing  999 
applera ids associated to LLIDs .
#getting the URLs available for Mm
mySrcUrls <- getSrcUrl("all", organism = "Mus musculus")
#I select only the GP, KEGG
#since I got errors for LL, UG, and I wanted a new GO dataset I 
downloaded them locally
mydir <- getwd()
myll <- paste(mydir, "LL_tmpl.gz", sep="\/")
names(myll) <- "LL"
myug <- paste(mydir, "Mm.data.gz", sep="\/")
names(myug) <- "UG"
mygo <- paste(mydir, "go_200502-termdb.rdf-xml.gz", sep="\/")#I did not 
find a go_200502-termdb.xml.gz !!
names(mygo) <- "GO"
mysrc <- c(myll, myug, mygo)
mytest<- paste(mydir, "tmp.txt", sep="\/")

ABPkgBuilder(baseName = mytest, srcUrls = mySrcUrls, baseMapType =
             "ll", pkgName = "appleraPkg", otherSrc = mysrc,
             pkgPath = "./tmp", organism = "Mouse musculus", version = 
             makeXML = TRUE, author = list(author = "raf", maintainer =
                             "raffaele.calogero at unito.it"), fromWeb = TRUE)


Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705420
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   www.bioinformatica.unito.it

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