[BioC] AnnBuilder error: couldn't find function "UG"

[John Zhang]

This bug was introduced by adding a NAMESPACE to AnnBuilder. I have checked in a 
few fixes but it may take some time for the new version of Annbuilder to be 
available. If you let me know what platform you have I will email you the 
package I built.
 
>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>From: "Lyudmila Mikhaylova" <lusya at izba.com>
>To: bioconductor at stat.math.ethz.ch
>Date: Wed, 20 Jul 2005 12:53:51 -0400
>MIME-Version: 1.0
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Subject: [BioC] AnnBuilder error:  couldn't find function "UG"
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.6
>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch>
>List-Unsubscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=unsubscribe>
>List-Archive: <https://stat.ethz.ch/pipermail/bioconductor>
>List-Post: <mailto:bioconductor at stat.math.ethz.ch>
>List-Help: <mailto:bioconductor-request at stat.math.ethz.ch?subject=help>
>List-Subscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=subscribe>
>Content-Transfer-Encoding: 7bit
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
pascal.dfci.harvard.edu
>X-Spam-Level: 
>X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham  
version=3.0.1
>
>
>Hello,
>
>I was trying the script from "Basic Functions of 
>AnnBuilder" manual and encountered problem on the line 
>
>ug <- UG(srcUrl=ugUrl,...
>
>  Error: couldn't find function "UG".
>
>Later on I've got same error message for parseData 
>function.
>HTML help file contains descriptions for both functions.
>Please help me to solve this problem. 
>
>Script and session info:
>
>
>library(AnnBuilder)
>pkgpath <- .find.package("AnnBuilder")
>docFiles <- 
>file.path(pkgpath,c("TITLE","DESCRIPTION","INDEX"))
>headers <- c("","Description:\n\n",,"Index:\n\n")
>footers <- c("\n","\n","")
>for (i in which(file.exists(docFiles))) {
>writeLines(headers[i],sep="")
>writeLines(readLines(docFiles[i]) )
>writeLines(footers[i],sep="")
>}
>geneNMap <- 
>matrix(c("32468_f_at","D90278;M16652","32469_at","L00693",
>"32481_at","AL031663","33825_at","X68733",
>"35730_at","X03350","36512_at","L32179",
>"38912_at","D90042","38936_at","M16652",
>"39368_at","AL031668"),ncol=2,byrow=T)
>write.table(geneNMap,file="geneNMap",sep="\t",quote=F,
>row.names=F,col.names=F)
>geneNMap
>makeSrcInfo()
>srcObjs <- list()
>egUrl <- 
>"http://www.bioconductor.org/datafiles/wwwsources"
>ugUrl <- 
>"http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz"
>eg <- 
>EG(srcUrl=egUrl,parser=file.path(pkgpath,"scripts","gbLLParser"),baseFile="gene
NMap",
>accession="Tll_tmpl.gz",built="N/A",fromWeb=T)
>ug <- 
>UG(srcUrl=ugUrl,parser=file.path(pkgpath,"scripts","gbUGParser"),baseFile="gene
NMap",
>organism="Homo sapiens",built="N/A",fromWeb=T)
>srcObjs[["eg"]] <- eg
>llMapping <- parseData(eg,eg at accession)
>sessionInfo()
>R version 2.1.0, 2005-04-18, i386-pc-mingw32 
>
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics" 
> "grDevices" "utils"    
>[7] "datasets"  "base"     
>
>other attached packages:
>AnnBuilder   annotate        XML    Biobase 
>   "1.5.31"   "1.5.16"   "0.97-7"   "1.5.12" 
>
>
>Lyudmila Mikhaylova, Ph.D
>Research Associate
>Tufts University School of Medicine
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at 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