[BioC] Resourcerer warnings

[Francois Pepin]

Hi everyone,

I'm updating my Agilent (HumanGenome) annotations using Resourcerer and
getting the a couple warnings and a decrease in GO annotations. It's
nothing really worrisome, but worth fixing.

First warning that is shown:
   Built for UCSC is not valid! in: getUCSCBuilt(organism)

The offending function is the following.

> get('getUCSCBuilt', envir=environment(ABPkgBuilder))
function (organism)
{
    url <- getSrcUrl(src = "GP", organism = organism)
    built <- NA
    if (is.na(built) || is.null(built) || built == "") {
        warning("Built for UCSC is not valid!")
        return("N/A")
    }
    else {
        return(built)
    }
}

I'm also getting warnings about KEGG urls (around 120 in all):
   Failed to get data from URL:  
   ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00191.gene

Those URLs indeed do not exist, but I didn't follow to see why it went
looking for them (I can do that if someone needs it).

There is also what looks like a debug print statement that is still
there. Again I didn't chase it down.
   [1] "3760 2 2"

Otherwise it builds and installs fine.

I've got fewer GO annotations than the last version I built 7 months ago
(GO went to 18214 from 20892, GO2PROBE is at 4440 from 4518), despite a
general increase in the number of annotations in the other categories.
Does anyone have an idea why this has happened? Has this been found for
other chips as well?

> sessionInfo()
R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
         GO Resourcerer  reposTools  AnnBuilder    annotate         XML
   "1.10.0"     "1.4.0"     "1.8.0"     "1.8.0"     "1.8.0"    "0.99-1"
    Biobase
    "1.8.0"

Francois