[BioC] Encountering error when using GOstats package

[Robert Gentleman]

Hi Rich,
   Thanks for pointing this out, and sorry it does not work. It is 
another of the organisms that uses its own set of IDs, and I will need 
to modify the GOstats code to deal with it.  Should be done by Monday 
(but only in the devel arm, using the R 2.8.0 candidate),

  best wishes
    Robert


Rich Savage wrote:
> Hi Vincent,
> 
> Thanks for your reply.
> 
> I uninstalled the non-SQLite package using:
> 
>  > remove.packages('ath1121501')
> 
> I then re-ran the code I posted.  Still got the error :-(
> (new sessionInfo also posted below)
> 
> 
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>   variable "ath1121501ENTREZID" was not found
> Error in mget(probes, ID2EntrezID(datPkg)) :
>   error in evaluating the argument 'envir' in selecting a method for 
> function 'mget'
>  > sessionInfo()
> R version 2.7.2 (2008-08-25)
> i386-apple-darwin8.11.1
> 
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets 
> methods   base
> 
> other attached packages:
>  [1] ath1121501.db_2.2.0 GOstats_2.6.0       Category_2.6.0      
> RBGL_1.16.0       graph_1.18.1
>  [6] GO.db_2.2.0         genefilter_1.20.0   survival_2.34-1 
> annotate_1.18.0     xtable_1.5-3
> [11] AnnotationDbi_1.2.2 RSQLite_0.7-0       DBI_0.2-4           
> Biobase_2.0.1
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11
> 
> 
> 
> Vincent Carey 525-2265 wrote:
>>> locale:
>>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>>>
>>> attached base packages:
>>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>>> methods   base
>>>
>>> other attached packages:
>>>   [1] ath1121501_2.2.0    ath1121501cdf_2.2.0 ath1121501.db_2.2.0 
>>> GOstats_2.6.0
>>
>> This sessionInfo shows both a "non-SQLite" package (ath1121501) and 
>> ath1121501.db
>>
>> i think you need to get rid of the non-SQLite version
>>
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org