[BioC] missing AnnBuilder parser

Francois Pepin fpepin at cs.mcgill.ca
Fri Apr 8 20:37:36 CEST 2005

Hi everyone,

I'm trying to rebuild my annotation package for an Agilent chip using
Resourcerer and it's not finder one of the parsers.

The basic error is:
>resourcerer2BioC("Agilent_HumanGenome.zip", organism="human")

Warning: cannot open file `NA'
Warning in unifyMappings(base, eg, ug, otherSrc) :
         Failed to get or parse Entrez Gene data because of:
 Error in file(con, "r") : unable to open connection
The missing file in question is the parser from Genbank to Entrez Gene
(The Agilent annotations are based on GenBank).

> getBaseParsers("gb")

I've convinced it to use the LocusLink parser instead as the IDs should
be the same, and the code runs for about an hour and at the very end:

exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc,
    pkgPath, organism, version, makeXML, author, fromWeb)
Warning: cannot open compressed file
Error in open.connection(con, "rb") : unable to open connection

At which point I assume I'll need a proper parser for it. Any
suggestions on what to do next?

Having since learned my lesson:
> sessionInfo()
R version 2.0.0, 2004-10-04, x86_64-unknown-linux-gnu
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"
other attached packages:
Resourcerer  AnnBuilder    annotate         XML     Biobase
    "1.1.0"    "1.5.12"     "1.5.1"    "0.95-6"     "1.5.0"


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