[BioC] oneChannelGUI

[Richard Friedman]

I have a Mac. That explains it,
Rich
On Nov 18, 2010, at 12:58 PM, Dan Tenenbaum wrote:

>
>
> On Thu, Nov 18, 2010 at 9:45 AM, Marcos Pinho <pinho.microarray at gmail.com 
> > 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!
>
>
>
> Hello Marcos,
>
> It does appear that the Windows binary versions of Genominator are  
> not on the Bioconductor website nor any of our mirrors. We will work  
> to resolve this immediately.
>
> In the meantime, I have verified that a source installation of  
> Genominator will work on Windows.
> Try the following:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("Genominator", type="source")
>
> Dan
>
>
>
>
>
> 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/<http://cancercenter.columbia.edu/%7Efriedman/ 
> >
> >>
> >> "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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> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
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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
>
>        [[alternative HTML version deleted]]
>
>
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