Hi, 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? Raffaele (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 mySrcUrls<-mySrcUrls[c(2,5)] #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 = "1.0.0", makeXML = TRUE, author = list(author = "raf", maintainer = "raffaele.calogero@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@unito.it www: www.bioinformatica.unito.it

>#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 >mySrcUrls<-mySrcUrls[c(2,5)] >#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 = >"1.0.0", > makeXML = TRUE, author = list(author = "raf", maintainer = > "raffaele.calogero@unito.it"), fromWeb = TRUE) > One thing I can tell is that you should set fromWeb = FALSE as you are accessing locally stored data as the sources. > > > >-- > >---------------------------------------- >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@unito.it >www: www.bioinformatica.unito.it > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084