[BioC] exonMap problems

Tobias Petri petri at bio.ifi.lmu.de
Fri Apr 23 14:16:39 CEST 2010


I'm trying to run the exonmap package on a linux system. As described in 
the readme I downloaded
the X-Map subproject "xmapcore_homo_sapiens_56" and installed it using a 
local mySQL (above the suggested version).
I configured the importdb.sh accordingly and it finished without errors 
or warnings.

I also installed mySQL and exonmap R-packages (no warnings neither). 
Yet, the following runtime error is produced (independent of the dataset):

 > library(exonmap)
Lade nötiges Paket: affy
Lade nötiges Paket: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Lade nötiges Paket: genefilter
Lade nötiges Paket: RColorBrewer
Lade nötiges Paket: RMySQL
Lade nötiges Paket: DBI
 > xmapConnect()
Select a database to connect to:

1: human ('xmapcore_homo_sapiens_56')

Auswahl: 1
 > probeset.to.gene("4545487")
Fehler in mysqlExecStatement(conn, statement, ...) :
   RS-DBI driver: (could not run statement: PROCEDURE 
ap_probesetToGene does not exist)

It seems that the PROCEDURE is not present after the database import. Am 
I missing something?


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