[BioC] Annotation data package is not being created

John Zhang jzhang at jimmy.harvard.edu
Thu Dec 11 21:41:22 MET 2003

Could you send me a copy of your base file so that I can try it to figure out 
what might be wrong? Thanks.
>I would appreciate help with the following.  I was following the vignette
>"How to use AnnBuilder".
>I tried to adapt this to my goal of creating an annotation data package with
>the Unigene Identifiers.  
>I made some very minor changes and used the file samclonegb2 which is just a
>small text file with 
>the first column being a list of IMAGE cloneIDs and the second column is a
>list of GenBank accesion numbers.
>I used the following lines and the sampclonegb2 seem to load properly and
>then finally 
>I got the error message listed below. I get some output files formed for
>example the XML file is formed
>but my input data has not been mapped to any of the information from the
>"Error in "colnames<-"(`*tmp*`, value = colNames) :
>        attempt to set colnames on object with less than two dimensions"
>I am not sure what I am missing.
>Also, my current file sampclonegb2 is very simple in that I have one Genbank
>accession number
>for each cloneID.  My actual source file contains cases where I have more
>than one
>Genbank accession number associated with a cloneid.  What is the best way to
>approach this?
>thanks very much,
>read.table(file.path(.path.package("AnnBuilder"), "data", "sampclonegb2"),
>sep = "\t", header = FALSE, as.is = TRUE)
>myBase <- file.path(.path.package("AnnBuilder"), "data", "sampclonegb2")
>myBaseType <- "gb"
>mySrcUrls <- getSrcUrl("all", organism = "human")
>myDir <- tempdir()
>if (.Platform$OS.type == "unix") {
>fromWeb <- TRUE
>} else {
>fromWeb <- FALSE
>if (.Platform$OS.type != "windows") {
>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>otherSrc = NULL, pkgName = "abmyPkg", pkgPath = myDir,
>organism = "human", version = "1.1.0", makeXML = TRUE,
>author = list(author = "Annie", maintainer = "myname at myemail.com"),
>fromWeb =fromWeb)}
>"It may take me a while to process the data. Be patient!"
>Error in "colnames<-"(`*tmp*`, value = colNames) :
>        attempt to set colnames on object with less than two dimensions
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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