[BioC] Encountering error when using GOstats package

[Rich Savage]

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
> 

-- 
------------------------------------------------------------------
   Dr. Richard Savage			Tel: +44 (0)24 765 50243
   Systems Biology Centre		
   University of Warwick
   Coventry
   CV4 7AL
   United Kingdom

   Web:  http://www.programming4scientists.com/
   	http://wsbc.warwick.ac.uk/~richsavage/