Dear Bioconductors, I am going to use GO annotation libraries. Unfortunately, I did not succed in loading the package GO.db. I have got the following error message: Error in checkDBSCHEMA(dbconn, "GO_DB") : invalid DB schema version (found 0.9, expected 1.0) Error : .onLoad failed in 'loadNamespace' for 'GO.db' Error: package/namespace load failed for 'GO.db' Does someone know which package is needed or what is going wrong with my libraries? The sessionInfo is given at the end of this email. Thanks and best wishes, Heike ################# sessionInfo() R version 2.7.0 (2008-04-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 [4] Biobase_2.0.1 -- Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de University of Hamburg | Center for Bioinformatics Bundesstrasse 43 | 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312

On Fri, Jun 20, 2008 at 7:42 AM, Heike Pospisil <pospisil at="" zbh.uni-hamburg.de=""> wrote: > Dear Bioconductors, > > I am going to use GO annotation libraries. Unfortunately, I did not succed in > loading the package GO.db. I have got the following error message: > > Error in checkDBSCHEMA(dbconn, "GO_DB") : > invalid DB schema version (found 0.9, expected 1.0) > Error : .onLoad failed in 'loadNamespace' for 'GO.db' > Error: package/namespace load failed for 'GO.db' > > Does someone know which package is needed or what is going wrong with my > libraries? The sessionInfo is given at the end of this email. I would suggest using biocLite() to do the installation and then try again. Sean > ################# > sessionInfo() > R version 2.7.0 (2008-04-22) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > [4] Biobase_2.0.1 > > -- > Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de > University of Hamburg | Center for Bioinformatics > Bundesstrasse 43 | 20146 Hamburg, Germany > phone:+49-40-42838-7303 | fax: +49-40-42838-7312 > > _______________________________________________ > 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 >

On Fri, Jun 20, 2008 at 8:34 AM, Heike Pospisil <pospisil at="" zbh.uni-hamburg.de=""> wrote: > Hello Sean, > > On Friday 20 June 2008 14:06, you wrote: >> On Fri, Jun 20, 2008 at 7:42 AM, Heike Pospisil >> >> <pospisil at="" zbh.uni-hamburg.de=""> wrote: >> > Dear Bioconductors, >> > >> > I am going to use GO annotation libraries. Unfortunately, I did not >> > succed in loading the package GO.db. I have got the following error >> > message: >> > >> > Error in checkDBSCHEMA(dbconn, "GO_DB") : >> > invalid DB schema version (found 0.9, expected 1.0) >> > Error : .onLoad failed in 'loadNamespace' for 'GO.db' >> > Error: package/namespace load failed for 'GO.db' >> > >> > Does someone know which package is needed or what is going wrong with my >> > libraries? The sessionInfo is given at the end of this email. >> >> I would suggest using biocLite() to do the installation and then try again. > > > Thanks for your suggestion. I guess it was a problem with sqlite and wrong > paths to sqlite. A superuser installation of GO.db wie biocLite() was the > solution. It's a pity that it have to been done (only) by the superuser, but > it works now... Good to hear that it is working for you. However, you should be able to install GO.db and friends just fine as something other than superuser. The path to the SQLite database is relative to the installation location. Let us know if you find out otherwise. Sean