Hello, I have installed GGtools and GGBase and when I try to load them, I keep getting the following error messages. I really appreciate if someone can help me in sorting this problem. Thank you, Neel [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0] [Workspace restored from /Users/naluru/.RData] [History restored from /Users/naluru/.Rapp.history] 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: snpMatrix Loading required package: survival Loading required package: splines Loading required package: RSQLite Loading required package: DBI Error in as.environment(pos) : no item called "newtable" on the search list In addition: Warning message: In objects(newtable, all.names = TRUE) : ?newtable? converted to character string Error: package/namespace load failed for 'GGBase' Loading required package: GGBase Error in as.environment(pos) : no item called "newtable" on the search list In addition: Warning message: In objects(newtable, all.names = TRUE) : ?newtable? converted to character string Error: package 'GGBase' could not be loaded > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.9-4 DBI_0.2-5 snpMatrix_1.14.1 survival_2.36-2 Biobase_2.10.0 loaded via a namespace (and not attached): [1] annotate_1.28.0 AnnotationDbi_1.12.0 graph_1.28.0 GSEABase_1.12.2 tools_2.12.1 [6] XML_3.2-0 xtable_1.5-6 > Neel Aluru Visiting Investigator Biology Department Redfield Building 3-04 Woods Hole Oceanographic Institution 45, Water Street Woods Hole, MA naluru at whoi.edu 508-289-3607

This problem was addressed on Feb 7. Let us know if the solution does not work for you. The problem concerns a dependency of Ruuid infrastructure on glib2, which is not uniformly available on MacOSX machines. Quoting below from the Feb 7 exchange Dear Vincent, Thanks a lot. I have got GGtools installed in my Mac book pro (with updated Mac OS and Xcode). What I have done: (1). install fink in order to let all unix program run in Mac, following the manual in fink website (http://www.finkproject.org/). (2). then, run "sudo fink install glib glib2-dev". (3). next, log in R, and source("http://bioconductor.org/biocLite.R") biocLite("Ruuid", type="source") # you must install Ruuid from source. biocLite("GGtools") (4). invoke GGtools library(GGtools) I need to mention that all my progresses were got under helps of Mr. Vincent and Martin, especially Vincent has given me much. Thanks a lot. Best, On Sat, Feb 26, 2011 at 6:42 AM, Neel Aluru <naluru at="" whoi.edu=""> wrote: > Hello, > > I have installed GGtools and GGBase and when I try to load them, I keep getting the following error messages. I really appreciate if someone can help me in sorting this problem. > > Thank you, > Neel > > > [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0] > > [Workspace restored from /Users/naluru/.RData] > [History restored from /Users/naluru/.Rapp.history] > > 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: snpMatrix > Loading required package: survival > Loading required package: splines > Loading required package: RSQLite > Loading required package: DBI > Error in as.environment(pos) : > ?no item called "newtable" on the search list > In addition: Warning message: > In objects(newtable, all.names = TRUE) : > ??newtable? converted to character string > Error: package/namespace load failed for 'GGBase' > Loading required package: GGBase > Error in as.environment(pos) : > ?no item called "newtable" on the search list > In addition: Warning message: > In objects(newtable, all.names = TRUE) : > ??newtable? converted to character string > Error: package 'GGBase' could not be loaded > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] RSQLite_0.9-4 ? ?DBI_0.2-5 ? ? ? ?snpMatrix_1.14.1 survival_2.36-2 ?Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] annotate_1.28.0 ? ? ?AnnotationDbi_1.12.0 graph_1.28.0 ? ? ? ? GSEABase_1.12.2 ? ? ?tools_2.12.1 > [6] XML_3.2-0 ? ? ? ? ? ?xtable_1.5-6 >> > > > Neel Aluru > Visiting Investigator > Biology Department > Redfield Building 3-04 > Woods Hole Oceanographic Institution > 45, Water Street > Woods Hole, MA > > naluru at whoi.edu > 508-289-3607 > > _______________________________________________ > 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 >