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Hi Marco, Thanks for reporting this! Since head/tail are already generics defined in the "utils" package, they should not be redefined in Rgraphviz. Only methods for "AgEdge" objects should go there. I've just fixed this in Rgraphviz 1.14.1 (release) and Rgraphviz 1.15.5 (devel). These new versions should become available via biocLite() in about 26 hours for the former and 14 hours for the latter. Cheers, H. marco zucchelli wrote: > Dear all, > > seems weird but looks like Rgraphviz redefines the function head() ?? > I use fedora 5. > > Regards > > Marco > > ######################################### >> head(gene.list) > chromosome_name start_position end_position entrezgene haplotype length > 1 1 58954 59871 79501 1 1060001 > 2 1 357522 358460 26683 1 1060001 > 3 1 357522 358460 81399 1 1060001 > 4 1 357522 358460 729759 1 1060001 > 5 1 610959 611897 26683 1 1060001 > 6 1 610959 611897 81399 1 1060001 >> library(Rgraphviz) > Loading required package: graph > Loading required package: geneplotter > Loading required package: annotate > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'annotate' > > > The following object(s) are masked from package:biomaRt : > > getGO > > Loading required package: lattice > KernSmooth 2.22 installed > Copyright M. P. Wand 1997 > > Attaching package: 'Rgraphviz' > > > The following object(s) are masked from package:annotate : > > toFile > >> head(gene.list) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "head", for > signature "data.frame" >> head > standardGeneric for "head" defined from package "Rgraphviz" > > function (x, ...) > standardGeneric("head") > <environment: 0x3189f70=""> > Methods may be defined for arguments: x > > > sessionInfo() >> sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "datasets" "utils" > [7] "methods" "base" > > other attached packages: > matlab Rgraphviz geneplotter lattice > annotate > "0.8-1" "1.14.0" "1.14.0" "0.15-4" " > 1.14.1" > Biobase graph humanLLMappings biomaRt > RCurl > "1.14.0" "1.14.2" "1.16.0" "1.10.0" " > 0.8-0" > XML > "1.9-0" > > [[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