[BioC] how to unlock a package environment

Hervé Pagès hpages at fhcrc.org
Thu Oct 1 21:41:31 CEST 2009

Forgot to send my sessionInfo(), sorry:

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-24 r49817)

  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] hgu95av2.db_2.3.5    org.Hs.eg.db_2.3.5   genefilter_1.25.9
[4] ath1121501.db_2.3.5  org.At.tair.db_2.3.5 RSQLite_0.7-2
[7] DBI_0.2-4            AnnotationDbi_1.7.17 Biobase_2.5.8

loaded via a namespace (and not attached):
[1] annotate_1.23.4 splines_2.10.0  survival_2.35-7 tools_2.10.0
[5] xtable_1.5-5


Hervé Pagès wrote:
> Hi Ariel,
> One solution is that you use the development version of Bioconductor
> (BioC 2.5, to be released soon, based on the R-2.10 series).
> In the development version of genefilter it looks like the nsFilter()
> function has been improved in order to deal properly with the
> peculiarity of the ath1121501.db package. Internally it's now
> calling a little helper function .findCentralID() (not exported)
> in order to determine what's the central ID in the annotation
> package:
>   library(genefilter)
>   library(hgu95av2.db)
>   library(ath1121501.db)
>   > genefilter:::.findCentralID("hgu95av2")
>   [1] "ENTREZID"
>   > genefilter:::.findCentralID("ath1121501")
>   [1] "ACCNUM"
> Cheers,
> H.
> Ariel Chernomoretz wrote:
>> Hi all,
>> I am currently analyzing some arabidopsis thaliana experiments 
>> (ath1121501
>> GeneChip)
>> The corresponding annotation package, ath1121501.db, is a little bit
>> 'special' as
>> there is no ENTREZID map for the chip.
>> I would like to cheat and create  a fake ath1121501ENTREZID for the
>> environment as a copied instance of ath1121501ACCNUM (in order to use, 
>> for
>> instance,  the genefilter package's function "nsFilter" to deal with non
>> annotated, or duplicated probesets)
>> The problem is that I am not able to create a new entry in the
>> package:ath112150.db as it is a locked environment. Is there any way to
>> temporarily unlock it, do some stuff and lock it again?
>> (It seems easy to lock environments, using the lockEnvironment 
>> function, but
>> I did not find an easy way to unlock them)
>> Thanks in advance
>> Ariel./

Hervé Pagès

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