hi, i am trying to build an annotation package based on EntrezGene IDs. myBase is a tab-delimited file with arrayID and LocusLink ID; myBaseType <- "ll"; mySrcUrls <- getOption("AnnBuilderSourceUrls") here is the copied/pasted code from the vignette, but i get some errors and warnings: > if (.Platform$OS.type != "windows" && interactive()) { + ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "myPkg", pkgPath = myDir,organism = "Homo sapiens", version = "1.1.0", fromWeb = TRUE)} Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO Error in readLines(con) : cannot open the connection In addition: Warning messages: 1: use of NULL environment is deprecated 2: unable to resolve 'archive.godatabase.org'. what is the error about? how can i fix this? thanks in advance dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780

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-termd b.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