On 10.05.2010 22:44, James W. MacDonald wrote: > Hi Uwe, > > Uwe Ligges wrote: >> Hi, >> >> loading package "org.Hs.eg.db" fails for me these days, see below for >> details. I guess this is related to the recent "AnnotationDbi" update >> on BioC and this is the package's maintainer address I found ... > > What version of org.Hs.eg.db do you have? This isn't a problem for me. Thanks for the answer. My apologies, thought I reported it in my sessionInfo(). I have the most recent one: 2.4.1. Since it apparently does not happen on other installations, I will debug later this day ... Best wishes, Uwe > > library(org.Hs.eg.db) > Loading required package: AnnotationDbi > 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: DBI > > sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51890) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-0 DBI_0.2-5 > [4] AnnotationDbi_1.10.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Best, > > Jim > > >> >> Best wishes, >> Uwe >> >> >> >> >> > library("org.Hs.eg.db") >> Error in stop(msg, " ", errors, domain = NA) : >> no function to return from, jumping to top level >> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: >> call: is(object, Cl) >> error: error in evaluating the argument 'drv' in selecting a method >> for function 'dbConnect' >> Error: package/namespace load failed for 'org.Hs.eg.db' >> >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >> LC_MONETARY=German_Germany.1252 >> [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] RSQLite_0.9-0 DBI_0.2-5 AnnotationDbi_1.10.1 Biobase_2.8.0 >> [5] lattice_0.18-5 fortunes_1.3-7 >> >> loaded via a namespace (and not attached): >> [1] grid_2.11.0 >> >> _______________________________________________ >> 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 >

It looks like both AnnotationDbi and RSQLite cannot be installed in a library on a samba network share. Currently I have no idea why that happens... Installing both into a local library seems to work. Evgenia: just install the two mentioned packages in a local library and try again. Best wishes, Uwe On 10.05.2010 22:44, James W. MacDonald wrote: > Hi Uwe, > > Uwe Ligges wrote: >> Hi, >> >> loading package "org.Hs.eg.db" fails for me these days, see below for >> details. I guess this is related to the recent "AnnotationDbi" update >> on BioC and this is the package's maintainer address I found ... > > What version of org.Hs.eg.db do you have? This isn't a problem for me. > > > library(org.Hs.eg.db) > Loading required package: AnnotationDbi > 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: DBI > > sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51890) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-0 DBI_0.2-5 > [4] AnnotationDbi_1.10.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Best, > > Jim > > >> >> Best wishes, >> Uwe >> >> >> >> >> > library("org.Hs.eg.db") >> Error in stop(msg, " ", errors, domain = NA) : >> no function to return from, jumping to top level >> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: >> call: is(object, Cl) >> error: error in evaluating the argument 'drv' in selecting a method >> for function 'dbConnect' >> Error: package/namespace load failed for 'org.Hs.eg.db' >> >> >> > sessionInfo() >> R version 2.11.0 (2010-04-22) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >> LC_MONETARY=German_Germany.1252 >> [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] RSQLite_0.9-0 DBI_0.2-5 AnnotationDbi_1.10.1 Biobase_2.8.0 >> [5] lattice_0.18-5 fortunes_1.3-7 >> >> loaded via a namespace (and not attached): >> [1] grid_2.11.0 >> >> _______________________________________________ >> 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 >