Hello everyone, I have a problem when loading the library: IlluminaHumanMethylation27k.db I installed the package from zip (from the Bioconductor website), and also installed all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums checked" But when I am trying to load this library I get an error: > library(IlluminaHumanMethylation27k.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: org.Hs.eg.db Loading required package: DBI Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation27k.db', details: call: sqliteExecStatement(con, statement, bind.data) error: RS-DBI driver: (error in statement: near "s": syntax error) Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db' I have tried the following things: - I reinstalled the packages from Bioconductor (AnnotationDbi, Biobase, org.Hs.eg.db and DBI) - restarted R > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 [4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.10.2 Biobase_2.8.0 > traceback() 2: stop(gettextf("package/namespace load failed for '%s'", package), call. = FALSE, domain = NA) 1: library(IlluminaHumanMethylation27k.db) Thank you in advance, Kind regards, Kristel van Eijk PhD student (University Medical Center Utrecht, The Netherlands) [[alternative HTML version deleted]]

Hi Kristel, On 8/30/2010 5:37 AM, Kristel van Eijk wrote: > Hello everyone, > > I have a problem when loading the library: IlluminaHumanMethylation27k.db > I installed the package from zip (from the Bioconductor website), and also > installed all the packages it asked for. It went all succesfull: > > "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums > checked" > > But when I am trying to load this library I get an error: > >> library(IlluminaHumanMethylation27k.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: org.Hs.eg.db > Loading required package: DBI > Error : .onLoad failed in loadNamespace() for > 'IlluminaHumanMethylation27k.db', details: > call: sqliteExecStatement(con, statement, bind.data) > error: RS-DBI driver: (error in statement: near "s": syntax error) > Error: package/namespace load failed for 'IlluminaHumanMethylation27k.db' > > I have tried the following things: > - I reinstalled the packages from Bioconductor (AnnotationDbi, Biobase, > org.Hs.eg.db and DBI) > - restarted R Did you try re-installing IlluminaHumanMethylation27k.db? I get this package to load without problems. Also, you indicate that you are going to the website to get the files for installation. This is not the best way to do things. Instead, use biocLite(). source("http://www.bioconductor.org/biocLite.R") biocLite("IlluminaHumanMethylation27k.db") Best, Jim > >> sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 > LC_MONETARY=Dutch_Netherlands.1252 > [4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 > AnnotationDbi_1.10.2 Biobase_2.8.0 > >> traceback() > 2: stop(gettextf("package/namespace load failed for '%s'", package), > call. = FALSE, domain = NA) > 1: library(IlluminaHumanMethylation27k.db) > > > Thank you in advance, > > Kind regards, > > Kristel van Eijk > PhD student (University Medical Center Utrecht, The Netherlands) > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues