[BioC] homoPkgBuilder (AnnBuilder 1.4.2/1.4.6) exits with errors

Gunnar Wrobel bioc at gunnarwrobel.de
Tue Jun 29 17:39:50 CEST 2004

While the development version of annotate did correct the problem with 
the class
definition I came back to my original problem of the undefined "tempList"

Looking at the code I guess the following typo ("tepList") in line 171 of file
homoPkgBuilder.R causes the problem.

saveOrgNameNCode <- function(pkgName, pkgPath, author, tepList)

The code seems to work with the old homoloGene build
(ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp) while I actually 
wanted to
get a package from the new build

If I use that as url for the homoloGene information the function exits with:

a <- homoPkgBuilder("homology",".","1.0","Gunnar

[1] "Processing organism: 10090"
Error in validObject(.Object) : Invalid "homoData" object: Invalid object for
slot "homoOrg" in class "homoData": got class "NULL", should be or 
extend class

Should the code work in principle with the new homoloGene data? If that is the
case I would try to debug the code until I get the package.

Thanks for your help.

Best regards


Gunnar Wrobel

Divisions of Bioinformatics and Biochemistry
Swiss Institute of Bioinformatics/Biozentrum
Klingelbergstrasse 50/70
CH-4056 Basel / Switzerland
Tel.: +41 61 267 1579
Fax:  +41 61 267 3398
e-mail: bioc at gunnarwrobel.de
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