[BioC] Difficulty installing oneChannelGUI in Vista

[James W. MacDonald]

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
> 
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-- 
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
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