[BioC] Annotation data package is not being created

Law, Annie Annie.Law at nrc-cnrc.gc.ca
Thu Dec 11 21:19:39 MET 2003


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

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