[BioC] Resourcerer warnings

[Francois Pepin]

As always, it's 5 min after sending the other message that I realized
that Agilent annotations are now available from the default repository
and that they're more complete than those I'm building using
Resourcerer.

Although the warnings should probably still be corrected, and I'm still
curious as to why the number of GO annotations would decrease with time.

Francois

On Fri, 2005-11-11 at 15:28 -0500, Francois Pepin wrote:
> 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
> 
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