[BioC] AnnotationDbi weirdness

[Marc Carlson]

Hi Jim,

What you have discovered is that the "_dbconn()" function returns the 
database connection to the DB for the package that is used by all the 
bimaps.  If you call dbDisconnect on it, you will destroy the connection 
and break all the objects that depend on it.  :(

If you want to make a connection that you can subsequently disconnect 
from (somewhat curious about why you want that), then you should 
probably point to the DB itself using system.file.  That should be 
straightforward for all our standard packages since we always observe 
the convention of placing the DB in the extdata dir and naming it after 
the package.  So in this case:

phew <- dbConnect(SQLite(), 
system.file("extdata","mogene10sttranscriptcluster.sqlite", 
package="mogene10sttranscriptcluster.db"))


   Marc



On 10/23/2012 01:54 PM, James W. MacDonald wrote:
> I am having the following problem:
>
> > aargh <- mogene10sttranscriptcluster_dbconn()
> > dbDisconnect(aargh)
> [1] TRUE
> > get("10338001", mogene10sttranscriptclusterENTREZID)
> Error in sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (expired SQLiteConnection)
>
> Any suggestions?
>
> Best,
>
> Jim
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.8.0
> [3] RSQLite_0.11.2                       DBI_0.2-5
> [5] AnnotationDbi_1.20.2                 Biobase_2.18.0
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.3  parallel_2.15.1 stats4_2.15.1
>