[BioC] exonmap mysql fehler

[Stefan Gräf]

Hi Paul,

There is a problem with the connection parameters, i.e. the ensembldb 
port which has been switched from 3306 -> 5306.

While the "old" (3306) mysql instance still contains 
homo_sapiens_core_47_36i the exonmap package already picks up the new 
5306 instance which doesn't contain your desired database (see below).

Stefan

[graef at data graef]$ echo "show databases like 'homo_sapiens_core_4%'" | 
mysql -hensembldb.ensembl.org -P3306 -uanonymous
Database (homo_sapiens_core_4%)
homo_sapiens_core_40_36b
homo_sapiens_core_41_36c
homo_sapiens_core_42_36d
homo_sapiens_core_43_36e
homo_sapiens_core_44_36f
homo_sapiens_core_45_36g
homo_sapiens_core_46_36h
homo_sapiens_core_47_36i

[graef at data graef]$ echo "show databases like 'homo_sapiens_core_4%'" | 
mysql -hensembldb.ensembl.org -P5306 -uanonymous
Database (homo_sapiens_core_4%)
homo_sapiens_core_48_36j



Paul Hammer wrote:
> dear all,
> 
> the function xmapBridge() (package exonmap) worked fine until i did a 
> reboot. now always comes this mysql error message:
> 
>  > 
> xmapBridge("ENSG00000115252",eset=rma.affy,gps=list(A=1:3,B=4:8),type="fc")
> Fehler in mysqlExecStatement(conn, statement, ...) :  RS-DBI driver: 
> (could not run statement: Unknown database 'homo_sapiens_core_47_36i')
> 
> when i login to mysql the database with all tables is there.
> 
> here my session info:
>  > sessionInfo()
> R version 2.6.0 (2007-10-03)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
> [1] exon.pmcdf_1.1       exonmap_1.4.1        plier_1.8.0
> [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2
> [7] simpleaffy_2.14.05   gcrma_2.10.0         matchprobes_1.10.0
> [10] genefilter_1.16.0    survival_2.32        affy_1.16.0
> [13] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.2
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.16.1     AnnotationDbi_1.0.6 rcompgen_0.1-15
> [4] RSQLite_0.6-4
> 
> have someone an idea???
> 
> thanks
> paul
> 
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-- 

  Dr. Stefan Gräf
  EMBL-European Bioinformatics Institute
  Ensembl - Functional Genomics Research
  Wellcome Trust Genome Campus,
  Hinxton, Cambridge CB10 1SD, UK

  phone: +44 (0)1223 494685
  fax: +44 (0)1223 494468