oneChannelGUI
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Marcos Pinho ▴ 200
@marcos-pinho-3584
Last seen 10.3 years ago
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]]
Rgraphviz affylmGUI oneChannelGUI Rgraphviz affylmGUI oneChannelGUI • 2.1k views
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@richard-friedman-513
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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 C?ncer - INCA > Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
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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.colu="" mbia.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]]
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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 C?ncer - INCA > Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > > > > -- > Marcos B. Pinho > Programa de Engenharia Qu?mica - PEQ > Laborat?rio de Engenharia de Cultivos Celulares- LECC > Universidade Federal do Rio de Janeiro - UFRJ > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil
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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@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@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.col="" umbia.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 >> > > -- 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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On Thu, Nov 18, 2010 at 9:45 AM, Marcos Pinho <pinho.microarray@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@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@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 > >> > > > > > > > -- > 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]] > > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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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.c="" olumbia.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 C?ncer - INCA > >> Rio de Janeiro - Brasil > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> 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 > >> > >> > >> > >> > >> -- > >> Marcos B. Pinho > >> Programa de Engenharia Qu?mica - PEQ > >> Laborat?rio de Engenharia de Cultivos Celulares- LECC > >> Universidade Federal do Rio de Janeiro - UFRJ > >> Instituto Nacional de C?ncer - INCA > >> Rio de Janeiro - Brasil > >> > > > > > > > -- > Marcos B. Pinho > Programa de Engenharia Qu?mica - PEQ > Laborat?rio de Engenharia de Cultivos Celulares- LECC > Universidade Federal do Rio de Janeiro - UFRJ > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 >
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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 C?ncer - INCA > Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > > > > -- > Marcos B. Pinho > Programa de Engenharia Qu?mica - PEQ > Laborat?rio de Engenharia de Cultivos Celulares- LECC > Universidade Federal do Rio de Janeiro - UFRJ > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil > > > > > -- > Marcos B. Pinho > Programa de Engenharia Qu?mica - PEQ > Laborat?rio de Engenharia de Cultivos Celulares- LECC > Universidade Federal do Rio de Janeiro - UFRJ > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil
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@raffaele-calogero-294
Last seen 9.1 years ago
Italy/Turin/University of Torino
Hi, I am the maintainer of oneChannelGUI, I did not realized that the Genominator package is not available for windows platform on Bioconductor. In the mean time the problem will be fixed at the official site, you can use the compiled version I produced on my window computer: 64bit version http://www.bioinformatica.unito.it/downloads/w64/Genominator_1.4.0.zip 32bits version http://www.bioinformatica.unito.it/downloads/w32/Genominator_1.4.0.zip Cheers Raffaele Date: Thu, 18 Nov 2010 13:01:31 -0500 From: Richard Friedman<friedman@cancercenter.columbia.edu> To: Dan Tenenbaum<dtenenba at="" fhcrc.org=""> Cc: Marcos Pinho<pinho.microarray at="" gmail.com="">, bioconductor at stat.math.ethz.ch Subject: Re: [BioC] oneChannelGUI Message-ID: <4BC84278-6472-4895-94AB-CBBA58F458E7 at cancercenter.columbia.edu> Content-Type: text/plain; charset=WINDOWS-1252; format=flowed; delsp=yes 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 > > > > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0116706487 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it
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