[BioC] exonMap problems

[Tim Yates]

Hi Tobias!

xmapcore_homo_sapiens_56 is the new database for the xmapcore package (which
is currently going through bioconductor approval)

For exonmap, you will need the 'Old "exonmap" Human Database' from our
downloads page:

http://xmap.picr.man.ac.uk/download/index#ohsdb

Exonmap requires that you first install the relevant ensembl db, then the
downloaded databases (hopefully, the INSTALL.txt file inside the download
explains the steps required)

Cheers,

Tim

On 23/04/2010 13:16, "Tobias Petri" <petri at bio.ifi.lmu.de> wrote:

> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor 
--------------------------------------------------------
This email is confidential and intended solely for the u...{{dropped:12}}