[BioC] Building the tomato annotation library(Affy)

[Groot, Philip de]

Hello list,
 
I found out that the Affymetrix tomato array is supported in Bioconductor, except that no annotation library is available. Well, using the genbank IDs from the Affymetrix csv-file, I tried to build the annotation library myself and I obtain the following error (all the time):
 
Error in loadFromUrl(srcUrl) : URL NArefLink.txt.gz is incorrect or the target site is not responding!
In addition: Warning messages:
1: Organism Lycopersicon esculentum is not supported by GoldenPath (GP). in: getUCSCUrl(organism)
2: Organism Lycopersicon esculentum is not supported by GoldenPath (GP). in: getUCSCUrl(organism)
[1] "1250 2 2"
Error in sort.list(unique.default(x), na.last = TRUE) :
        'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: Failed to parse Golden Path data because of:
 Error in loadFromUrl(srcUrl) : URL NArefLink.txt.gz is incorrect or the target site is not responding!
 in: getAnnData(srcObjs)
2: NAs introduced by coercion

(The NAs introduction occurs only in R-2.5.0 / BioC 2.0; not in the previous R/Bioc installation that both uses AnnBuilder 1.14.0 running on SuSE Linux Professional 9).
 
Apparently, the problem is that "ABPkgBuilder" tries to sort on something that is not there (the GoldenPath stuff) and this prevents the annotation library of being built. Note that it is still possible to build "something" with this information lacking (or am I wrong with this assumption?).
 
Anyone any idea on how to solve this problem?
 
Regards,
 
Dr Philip de Groot
Wageningen University