[BioC] AnnotationDbi weirdness

James W. MacDonald jmacdon at uw.edu
Tue Oct 23 22:54:02 CEST 2012


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

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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