[BioC] oneChannelGUI

Thu Nov 18 18:47:56 CET 2010

Marcos,

	I checked and saw it at the site,
Make sure that you have "Bioconductor binary".
If it is not there, try a differnet mirror.

	I hope this helps,
Rich
On Nov 18, 2010, at 12:45 PM, Marcos Pinho wrote:

> Richard,
>
> I did that and installed Active TCL, but cannot find package  
> "Genominator" at the install pulldown or at the bioconductor site. I  
> hope some of the developers of oneChannelGUI could shed some light  
> into this problem!
>
> Thanks for the help
>
> Cheers,
>
> Marcos
>
> On Thu, Nov 18, 2010 at 3:39 PM, Richard Friedman <friedman at cancercenter.columbia.edu 
> > wrote:
> Marcos,
>
>        I am hazy on details but I believe that Googling the ActiveTCl
> site and going there can get you Tktable and BWidget.
>
>        You might try installing Genominator from the Install pulldown.
>
> I hope that this is of some help,
> Rich
>
>
> On Nov 18, 2010, at 12:26 PM, Marcos Pinho wrote:
>
> Richard and list,
>
> I tryed to install but keep getting error messages such as:
>
> 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: limma
> Loading required package: affylmGUI
> Loading required package: tcltk
> Loading Tcl/Tk interface ... done
> Loading required package: affy
> Loading required package: affyio
>
> Warning: ActiveTcl could not be found in the Windows Registry.
>
> Either it has not been installed or it has not been installed with  
> sufficient privileges.
>
>
> affylmGUI requires the Tcl/Tk extensions Tktable and BWidget which  
> are not distributed with R,
>
> but they are distributed with ActiveTcl.
>
> To begin, type affylmGUI() or use the pull-down menu.
>
> Searching for user-defined affylmGUI commands in C:/PROGRA~1/R/ 
> R-212~1.0/library/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
> Loading required package: preprocessCore
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:Biobase':
>
>    updateObject
>
> The following object(s) are masked from 'package:base':
>
>    cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, table
>
> Loading required package: edgeR
> Loading required package: Genominator
> Error: package 'Genominator' could not be loaded
> In addition: Warning message:
> In library(pkg, character.only = TRUE, logical.return = TRUE,  
> lib.loc = lib.loc) :
>  there is no package called 'Genominator'
> >
>
> Once I try to install these missing package I get another error  
> message:
>
>
> >    source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
> >  biocLite("Genominator")
> Using R version 2.12.0, biocinstall version 2.7.4.
> Installing Bioconductor version 2.7 packages:
> [1] "Genominator"
> Please wait...
>
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘Genominator’ is not available
>
>
> On Thu, Nov 18, 2010 at 12:47 PM, Richard Friedman <friedman at cancercenter.columbia.edu 
> > wrote:
> Dear Marcos,
>
>       You have install the genefilter and Category packages.
> I do not recall the Rgraphviz parts.
>
> I hope that this helps somewhat,
> 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/
>
> "Did he win the Nobel prize or the Ig Nobel
> prize for levitating the frog?".
> Rose Friedman, age 14
>
>
>
>
>
> On Nov 18, 2010, at 9:28 AM, Marcos Pinho wrote:
>
> Dear List,
>
> I have encontered some problems after following the instaltion  
> instructions
> for the oneChannelGui software
>
> library(oneChannelGUI)
> 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: limma
> Loading required package: affylmGUI
> 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/mbpinho/Documents/R/win-library/2.12/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
> Error in loadNamespace(imp[[1L]], c(lib.loc, .libPaths())) :
>  there is no package called 'genefilter'
> Error: package 'Category' could not be loaded
>
>
>
> Could anybody shed some light to what possible mistakes that I made  
> during
> instalation? I followed the steps on the software developer page.
>
> Also could someone clarify on how to install the Rgraphviz for the
> oneChannelGUI. The instructions were not really clear to me.
>
> Regards,
>
> -- 
> Marcos B. Pinho
>
> Instituto Nacional de Câncer - INCA
> Rio de Janeiro - Brasil
>
>       [[alternative HTML version deleted]]
>
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>
>
>
> -- 
> Marcos B. Pinho
> Programa de Engenharia Química - PEQ
> Laboratório de Engenharia de Cultivos Celulares- LECC
> Universidade Federal do Rio de Janeiro - UFRJ
> Instituto Nacional de Câncer - INCA
> Rio de Janeiro - Brasil
>
>
>
>
> -- 
> Marcos B. Pinho
> Programa de Engenharia Química - PEQ
> Laboratório de Engenharia de Cultivos Celulares- LECC
> Universidade Federal do Rio de Janeiro - UFRJ
> Instituto Nacional de Câncer - INCA
> Rio de Janeiro - Brasil