(cc'ing list, for posterity) On 06/02/2012 01:22 PM, Martin Morgan wrote: > On 06/02/2012 01:08 PM, sheng zhao wrote: >> Hi Martin, >> >> My answer is yes. Please see following: >> >> >> mac$ R --vanilla >> >> R version 2.15.0 (2012-03-30) >> Copyright (C) 2012 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > library(GO.db) >> Loading required package: AnnotationDbi >> Loading required package: BiocGenerics >> >> Attaching package: 'BiocGenerics' >> >> The following object(s) are masked from 'package:stats': >> >> xtabs >> >> The following object(s) are masked from 'package:base': >> >> Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, >> colnames, duplicated, eval, get, intersect, lapply, mapply, mget, >> order, paste, pmax, pmax.int <http: pmax.int="">, pmin, pmin.int >> <http: pmin.int="">, rbind, rep.int <http: rep.int="">, >> rownames, sapply, setdiff, table, tapply, union, unique >> >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> Loading required package: DBI >> Error : .onLoad failed in loadNamespace() for 'GO.db', details: >> call: ls(envir, all.names = TRUE) >> error: 7 arguments passed to .Internal(identical) which requires 6 >> Error: package/namespace load failed for 'GO.db' >> > > I am looking at Prof. Ripley's post here > > http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal- identical-which-requires-6-td4548460.html > > > and the time stamp on your version of R (March 30). I do not really have > a good suggestion; perhaps (a) traceback() after the error; (b) > installing GO.db from source (biocLite("GO.db", type="source")). And since > > trace(loadNamespace, tracer=quote(print(package))) > library(GO.db) > > ends with > > Loading required package: DBI > Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry > [1] "DBI" > Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry > [1] "RSQLite" > > for me these two packages also are candidates for suspicion. > > Martin > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

On Mon, Jun 4, 2012 at 11:18 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > (cc'ing list, for posterity) > > On 06/02/2012 01:22 PM, Martin Morgan wrote: >> >> On 06/02/2012 01:08 PM, sheng zhao wrote: >>> >>> Hi Martin, >>> >>> My answer is yes. Please see following: >>> >>> >>> mac$ R --vanilla >>> >>> R version 2.15.0 (2012-03-30) >>> Copyright (C) 2012 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> > library(GO.db) >>> Loading required package: AnnotationDbi >>> >>> Loading required package: BiocGenerics >>> >>> Attaching package: 'BiocGenerics' >>> >>> The following object(s) are masked from 'package:stats': >>> >>> xtabs >>> >>> The following object(s) are masked from 'package:base': >>> >>> Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, >>> colnames, duplicated, eval, get, intersect, lapply, mapply, mget, >>> order, paste, pmax, pmax.int <http: pmax.int="">, pmin, pmin.int >>> <http: pmin.int="">, rbind, rep.int <http: rep.int="">, >>> rownames, sapply, setdiff, table, tapply, union, unique >>> >>> Loading required package: Biobase >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material; view with >>> 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>> >>> Loading required package: DBI >>> Error : .onLoad failed in loadNamespace() for 'GO.db', details: >>> call: ls(envir, all.names = TRUE) >>> error: 7 arguments passed to .Internal(identical) which requires 6 >>> Error: package/namespace load failed for 'GO.db' >>> >> I experienced the same problem, but fixed it by following Prof. Ripley's advice and updating to R-patched (which you can get at http://r.research.att.com/). Thanks, Dan >> I am looking at Prof. Ripley's post here >> >> >> http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal- identical-which-requires-6-td4548460.html >> >> >> and the time stamp on your version of R (March 30). I do not really have >> a good suggestion; perhaps (a) traceback() after the error; (b) >> installing GO.db from source (biocLite("GO.db", type="source")). And since >> >> trace(loadNamespace, tracer=quote(print(package))) >> library(GO.db) >> >> ends with >> >> Loading required package: DBI >> Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry >> [1] "DBI" >> Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry >> [1] "RSQLite" >> >> for me these two packages also are candidates for suspicion. >> >> Martin >> >> >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor