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@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@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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>


-- 
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]]

