[BioC] exonMap problems
Tobias Petri
petri at bio.ifi.lmu.de
Fri Apr 23 14:16:39 CEST 2010
Hi,
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
xmapcore_homo_sapiens_56.xm
ap_probesetToGene does not exist)
"""
It seems that the PROCEDURE is not present after the database import. Am
I missing something?
Cheers,
Tobias
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