[Bioc-devel] Different behavior of get() between 2.9.0 and later versions`

[Luigi Marchionni]

Hi guys,
here is Luigi. I am developing a package which heavily relies on  
AnnotationDbi, annotate, and metadatata packages from bioconductor.
I noticed I weird behavior of the get() function for the  
mgug4122a.db() package moving from 2.9.1 to later versions (2.10.0 and  
2.11.0 the one I am running).
Basically, an ID pointing to an 'NA' is not properly handled in the  
newer versions, see below.
The same ID in one case returns 'NA', in the other case returns an  
error.
If also checked if this happened with other package (hgu133a.db) and  
the behavior is different, for both an ID that was there and now is  
missing, and an ID that was not there, and now is not there as well....
I give you the details below. Do you have any idea of what is going on?

Luigi

########################################################
###FOR R-2.9.1:
########################################################
 > sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin9.7.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets
[6] methods   base

other attached packages:
[1] hgu133a.db_2.2.12   mgug4122a.db_2.2.11
[3] RSQLite_0.7-3       DBI_0.2-4
[5] AnnotationDbi_1.6.1 Biobase_2.4.1

 > get("A_52_P71146", mgug4122aSYMBOL)
[1] NA

 >  get("201265_at", hgu133aSYMBOL)
[1] NA

 > get("200080_s_at", hgu133aSYMBOL)
[1] "H3F3A"

########################################################
###FOR R-2.10.0:
########################################################
 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets
[6] methods   base

other attached packages:
[1] hgu133a.db_2.3.5    org.Hs.eg.db_2.3.6
[3] mgug4122a.db_2.3.5  org.Mm.eg.db_2.3.6
[5] RSQLite_0.7-3       DBI_0.2-4
[7] AnnotationDbi_1.8.0 Biobase_2.6.0

 > get("A_52_P71146", mgug4122aSYMBOL)
Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
   value for "A_52_P71146" not found

 > get("201265_at", hgu133aSYMBOL)
[1] NA

 > get("200080_s_at", hgu133aSYMBOL)
[1] NA



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