Also, I forgot to mention this helper (which saves time on the dbConnect call). mogene10sttranscriptcluster_dbfile() So you could also write it like this: phew <- dbConnect(SQLite(), mogene10sttranscriptcluster_dbfile()) Marc On 10/23/2012 03:55 PM, Marc Carlson wrote: > 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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor