exonMap problems
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Tobias Petri ▴ 40
@tobias-petri-3605
Last seen 8.4 years ago
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 n?tiges Paket: affy Lade n?tiges 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 n?tiges Paket: genefilter Lade n?tiges Paket: RColorBrewer Lade n?tiges Paket: RMySQL Lade n?tiges 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
exonmap exonmap • 727 views
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Tim Yates ▴ 250
@tim-yates-4040
Last seen 8.4 years ago
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 n?tiges Paket: affy > Lade n?tiges 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 n?tiges Paket: genefilter > Lade n?tiges Paket: RColorBrewer > Lade n?tiges Paket: RMySQL > Lade n?tiges 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}}
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