Dear All, I updated my annotation library lumiHumanAll.db into version 1.10.1 but I'm unable to load it correctly. The error message is below. The latest version is created with R-version 2.11.1 and I'm working with R 2.10. Could this be the reason? Unfortunately I can't update R quickly without administrative rights. Another error is the DBSCHEMA. I dont' know which of the packages I'm using has updated dbconn. Is there any way I could downgrade both dbconn and lumiHumanAll?? Can the old versions be found somewhere?? Loading required package: org.Hs.eg.db Error in checkDBSCHEMA(dbconn, "HUMANCHIP_DB") : invalid DB schema version (found 2.1, expected 2.0) In addition: Warning message: package 'lumiHumanAll.db' was built under R version 2.11.1 Error : .onLoad failed in 'loadNamespace' for 'lumiHumanAll.db' Error: package/namespace load failed for 'lumiHumanAll.db' Best regards, Mervi Kinnunen Wihuri Research Institute Finland [[alternative HTML version deleted]]

Hi Mervi, That error message is caused by using an annotation package from a different version of bioconductor than the version of used by your installed AnnotationDbi package. The DBSCHEMA is being mentioned because it changed between the different releases. For best results please consider updating R and then update bioconductor using biocLite() as described here on the bioconductor web site: http://www.bioconductor.org/install/index.html Using biocLite() will help to make sure that your packages are all from the same branch of Bioconductor as is appropriate for the version of R that you are running. If you are really stuck using the older version of R then you will have to use the older annotation packages. You can downgrade by just uninstalling the affected packages (just see: ?remove.packages) and then use biocLite() to put it back. Marc On 08/31/2010 11:22 PM, Alanne, Mervi wrote: > Dear All, > > I updated my annotation library lumiHumanAll.db into version 1.10.1 but I'm unable to load it correctly. The error message is below. > > The latest version is created with R-version 2.11.1 and I'm working with R 2.10. Could this be the reason? Unfortunately I can't update R quickly without administrative rights. Another error is the DBSCHEMA. I dont' know which of the packages I'm using has updated dbconn. Is there any way I could downgrade both dbconn and lumiHumanAll?? Can the old versions be found somewhere?? > > Loading required package: org.Hs.eg.db > Error in checkDBSCHEMA(dbconn, "HUMANCHIP_DB") : > invalid DB schema version (found 2.1, expected 2.0) > In addition: Warning message: > package 'lumiHumanAll.db' was built under R version 2.11.1 > Error : .onLoad failed in 'loadNamespace' for 'lumiHumanAll.db' > Error: package/namespace load failed for 'lumiHumanAll.db' > > > Best regards, > > Mervi Kinnunen > Wihuri Research Institute > Finland > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Wed, Sep 1, 2010 at 2:22 AM, Alanne, Mervi <mervi.alanne@wri.fi> wrote: > Dear All, > > I updated my annotation library lumiHumanAll.db into version 1.10.1 but I'm > unable to load it correctly. The error message is below. > > The latest version is created with R-version 2.11.1 and I'm working with R > 2.10. Could this be the reason? Unfortunately I can't update R quickly > without administrative rights. Another error is the DBSCHEMA. I dont' know > which of the packages I'm using has updated dbconn. Is there any way I could > downgrade both dbconn and lumiHumanAll?? Can the old versions be found > somewhere?? > > Loading required package: org.Hs.eg.db > Error in checkDBSCHEMA(dbconn, "HUMANCHIP_DB") : > invalid DB schema version (found 2.1, expected 2.0) > In addition: Warning message: > package 'lumiHumanAll.db' was built under R version 2.11.1 > Error : .onLoad failed in 'loadNamespace' for 'lumiHumanAll.db' > Error: package/namespace load failed for 'lumiHumanAll.db' > > Hi, Mervi. You should be installing everything using biocLite(). This will keep problems like this from happening in the first place. I would remove the lumiHumanAll.db package and then use biocLite() to reinstall. Also, for future reference, be sure to follow the posting guide and include the output of sessionInfo() when emailing the list. Sean [[alternative HTML version deleted]]

Hi Mervi, On Wed, Sep 1, 2010 at 2:22 AM, Alanne, Mervi <mervi.alanne at="" wri.fi=""> wrote: > ?Dear All, > > I updated my annotation library lumiHumanAll.db into version 1.10.1 but I'm unable to load it correctly. The error message is below. > > The latest version is created with R-version 2.11.1 and I'm working with R 2.10. Could this be the reason? Unfortunately I can't update R quickly without administrative rights. Another error is the DBSCHEMA. I dont' know which of the packages I'm using has updated dbconn. Is there any way I could downgrade both dbconn and lumiHumanAll?? Can the old versions be found somewhere?? Install the package using the biocLite function -- it will get the correct version of the library given the version of R you are running: R> source("http://bioconductor.org/biocLite.R") R> biocLite('lumiHumanAll.db') -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact