Glad you got things working again. This illustrates some of the perils of combining packages targeted at different releases. It needs to be done with great care and preferably is not done at all. 2010/4/7 Mayte Suarez-Farinas <farinam@mail.rockefeller.edu> > Dear Vincent. > Thanks alot. I had also to reinstall hgu133plus pacakeges that way but > that did the trick!!!! > > best > > Mayte Suarez-Farinas > Research Associate, The Rockefeller University > Biostatistician, The Rockefeller University Hospital > 1230 York Ave, Box 178, > New York, NY, 10021 > +1(212) 327-8213 > > > > > On Apr 7, 2010, at 12:08 PM, Vincent Carey wrote: > > OK, the decompress1 error has gone away. This means you have incompatible > infrastructure. Your version of AnnotationDbi seems "too new" relative to R > 2.10.1. I just did biocLite for that version and it returned AnnotationDbi > 1.8.2 > > Could it be that you grabbed a devel version of AnnotationDbi package for > some reason? I suggest reinstalling that via biocLite and trying again. > > On Wed, Apr 7, 2010 at 10:58 AM, Mayte Suarez-Farinas < > farinam@mail.rockefeller.edu> wrote: > >> Dear Vincent, >> I did as you suggested, still error ;-) >> here is my session >> >> >> ---------------------------------------- >> library(annaffy) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: GO.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Error in checkDBSCHEMA(dbconn, "GO_DB") : >> invalid DB schema version (found 2.0, expected 2.1) >> Error : .onLoad failed in 'loadNamespace' for 'GO.db' >> Error: package 'GO.db' could not be loaded >> > library(GO) >> Error in library(GO) : there is no package called 'GO' >> > library(GO.db) >> Error in checkDBSCHEMA(dbconn, "GO_DB") : >> invalid DB schema version (found 2.0, expected 2.1) >> Error : .onLoad failed in 'loadNamespace' for 'GO.db' >> Error: package/namespace load failed for 'GO.db' >> ---------------------------------------- >> >> >> Mayte Suarez-Farinas >> Research Associate, The Rockefeller University >> Biostatistician, The Rockefeller University Hospital >> 1230 York Ave, Box 178, >> New York, NY, 10021 >> +1(212) 327-8213 >> >> >> >> >> On Apr 7, 2010, at 10:52 AM, Vincent Carey wrote: >> >> The decompress message suggests that you did not shut down your R session >> subsequent to reinstallation of package. Please shut it down and restart >> and reattach package and send any subsequent errors. The DBSCHEMA issue is >> known, related to transition to next release. There are workarounds if >> necessary but the approach you've taken should work once you get around the >> 'internal error', which I believe just requires a restart of R. >> >> On Wed, Apr 7, 2010 at 10:39 AM, Mayte Suarez-Farinas < >> farinam@mail.rockefeller.edu> wrote: >> >>> Hi >>> >>> I have been getting an error in packages db family. >>> First I was getting "Error in checkDBSCHEMA(dbconn, "GO_DB") : >>> invalid DB schema version (found 2.0, expected 2.1)" >>> I decided to reinstall R with version 2.10.1 and reinstall all packages >>> again. >>> still I have problems with GO. >>> I reinstalled through the Package Manager and by using biocLite directly. >>> It installed fine but when I load it I got the following error: >>> >>> library(GO.db) >>> Error in get(hookname, envir = env, inherits = FALSE) : >>> internal error -3 in R_decompress1 >>> Error: package/namespace load failed for 'GO.db' >>> >>> I hope someone can guide me... >>> Best >>> Mayte >>> >>> sessionInfo() >>> R version 2.10.1 (2009-12-14) >>> x86_64-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] RSQLite_0.7-3 DBI_0.2-5 AnnotationDbi_1.9.8 >>> Biobase_2.6.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.24.2 affyio_1.14.0 annotate_1.24.1 >>> Biostrings_2.14.12 >>> [5] gcrma_2.18.1 genefilter_1.28.2 IRanges_1.4.16 >>> preprocessCore_1.8.0 >>> [9] simpleaffy_2.22.0 splines_2.10.1 survival_2.35-7 >>> tools_2.10.1 >>> [13] xtable_1.5-6 >>> >>> >>> >>> >>> Mayte Suarez-Farinas >>> Research Associate, The Rockefeller University >>> Biostatistician, The Rockefeller University Hospital >>> 1230 York Ave, Box 178, >>> New York, NY, 10021 >>> +1(212) 327-8213 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> > > [[alternative HTML version deleted]]