Dear List, I am having difficulty installing oneChannelGUI ion a PC in Vista. Upon attempting to load oneChannelGUI from the pull-down menu I get the following response culminating in an error message: ####################################### Loading required package: affylmGUI Loading required package: limma Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: affy Loading required package: affyio ActiveTcl was found in the Windows Registry (for CURRENT_USER), installed in C:\Tcl This directory will be added to the Tcl search path to enable affylmGUI to find the Tktable and BWidget extensions. To begin, type affylmGUI() or use the pull-down menu. Searching for user-defined affylmGUI commands in C:/Users/Michael/ Documents/R/win-library/2.10/affylmGUI/etc ... Loading required package: tkWidgets Loading required package: widgetTools Loading required package: DynDoc Loading required package: tools Loading required package: GOstats Loading required package: Category Loading required package: AnnotationDbi Loading required package: graph Loading required package: DBI Error in checkDBSCHEMA(dbconn, "GO_DB") : invalid DB schema version (found 2.1, expected 2.0) Error : .onLoad failed in 'loadNamespace' for 'GO.db' Error: package 'GOstats' could not be loaded ####################################### Here are the details of my session: > sessionInfo() R version 2.10.1 (2009-12-14) 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] tools tcltk stats graphics grDevices utils datasets [8] methods base other attached packages: [1] RSQLite_0.9-0 DBI_0.2-5 graph_1.26.0 [4] Category_2.12.1 AnnotationDbi_1.8.2 tkWidgets_1.24.0 [7] DynDoc_1.24.0 widgetTools_1.24.0 affylmGUI_1.20.0 [10] affyio_1.14.0 affy_1.24.2 limma_3.2.3 [13] Biobase_2.6.1 loaded via a namespace (and not attached): [1] annotate_1.24.1 genefilter_1.28.2 GSEABase_1.8.0 [4] preprocessCore_1.8.0 RBGL_1.24.0 splines_2.10.1 [7] survival_2.35-7 XML_3.1-0 xtable_1.5-6 > ####################################### I would appreciate any advice you might offer. Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, Philip Klass

Hi Richard, Richard Friedman wrote: > Dear List, > > > > I am having difficulty installing oneChannelGUI ion a PC in Vista. > > Upon attempting to load oneChannelGUI from the pull-down menu I get the > following response > > culminating in an error message: > > ####################################### > > > > Loading required package: affylmGUI > > Loading required package: limma > Loading required package: tcltk > Loading Tcl/Tk interface ... done > Loading required package: affy > Loading required package: affyio > > ActiveTcl was found in the Windows Registry (for CURRENT_USER), > installed in > C:\Tcl > This directory will be added to the Tcl search path to enable affylmGUI > to find the Tktable and BWidget extensions. > > To begin, type affylmGUI() or use the pull-down menu. > > Searching for user-defined affylmGUI commands in > C:/Users/Michael/Documents/R/win-library/2.10/affylmGUI/etc ... > Loading required package: tkWidgets > Loading required package: widgetTools > Loading required package: DynDoc > Loading required package: tools > Loading required package: GOstats > Loading required package: Category > Loading required package: AnnotationDbi > Loading required package: graph > Loading required package: DBI > Error in checkDBSCHEMA(dbconn, "GO_DB") : > invalid DB schema version (found 2.1, expected 2.0) > Error : .onLoad failed in 'loadNamespace' for 'GO.db' > Error: package 'GOstats' could not be loaded This isn't a problem loading onechannelGUI, it is a problem with your GO.db version. It looks like you installed (by hand?) a version of GO.db from BioC 2.6 into your BioC 2.5 installation. Personally, I would upgrade to R-2.11.1 and BioC 2.6. However, if you want to stay with what you have, try biocLite("GO.db") library(onechannelGUI) Best, Jim > > ####################################### > > Here are the details of my session: > > > > sessionInfo() > R version 2.10.1 (2009-12-14) > 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] tools tcltk stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] RSQLite_0.9-0 DBI_0.2-5 graph_1.26.0 > [4] Category_2.12.1 AnnotationDbi_1.8.2 tkWidgets_1.24.0 > [7] DynDoc_1.24.0 widgetTools_1.24.0 affylmGUI_1.20.0 > [10] affyio_1.14.0 affy_1.24.2 limma_3.2.3 > [13] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] annotate_1.24.1 genefilter_1.28.2 GSEABase_1.8.0 > [4] preprocessCore_1.8.0 RBGL_1.24.0 splines_2.10.1 > [7] survival_2.35-7 XML_3.1-0 xtable_1.5-6 > > > > ####################################### > > I would appreciate any advice you might offer. > > Thanks and best wishes, > > Rich > > ------------------------------------------------------------ > > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > Philip Klass > > _______________________________________________ > 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