Package qvalue - can it be installed without TCL-TK support?
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@giuseppe-gallone-6092
Last seen 7.9 years ago
Hi I need the qvalue package however I don't need the TCL-TK interface. My R installation was compiled without native TCL-TK support and it is inconvenient for me atm to reinstall/replace etc to add support. As a consequence, as it stands it seems I cannot get qvalue to work on my system. Does anybody know of a way to install and run qvalue excluding the TCL-TK bindings? Best regards Giuseppe
qvalue qvalue • 2.0k views
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@storey-john-d-6576
Last seen 2.6 years ago
United States

qvalue version 1.43.0 and all subsequent versions will not longer use tcltk.

For those interested, a point-and-click Shiny version of qvalue is available here:  http://qvalue.princeton.edu/

 

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John Blischak ▴ 190
@john-blischak-6562
Last seen 4.8 years ago
A short-term solution would be to download the source code and just directly use the qvalue function. wget http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.38. 0.tar.gz tar xzf qvalue_1.38.0.tar.gz Then source the code in R: source("qvalue/R/qvalue.R") If you wanted to install, you could edit the source code. I'd imagine deleting the function qvalue.gui and removing the references to tcltk in the package DESCRIPTION and NAMESPACE would allow you to install it from source. John On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone < giuseppe.gallone@dpag.ox.ac.uk> wrote: > Hi > > I need the qvalue package however I don't need the TCL-TK interface. > > My R installation was compiled without native TCL-TK support and it is > inconvenient for me atm to reinstall/replace etc to add support. > > As a consequence, as it stands it seems I cannot get qvalue to work on my > system. > > Does anybody know of a way to install and run qvalue excluding the TCL-TK > bindings? > > Best regards > Giuseppe > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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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John thanks, I will try what you suggested. Best wishes Giuseppe On 05/23/14 15:31, John Blischak wrote: > A short-term solution would be to download the source code and just > directly use the qvalue function. > > wget > http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.3 8.0.tar.gz > tar xzf qvalue_1.38.0.tar.gz > > Then source the code in R: > source("qvalue/R/qvalue.R") > > If you wanted to install, you could edit the source code. I'd imagine > deleting the function qvalue.gui and removing the references to tcltk in > the package DESCRIPTION and NAMESPACE would allow you to install it from > source. > > John > > > On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone > <giuseppe.gallone at="" dpag.ox.ac.uk="" <mailto:giuseppe.gallone="" at="" dpag.ox.ac.uk="">> > wrote: > > Hi > > I need the qvalue package however I don't need the TCL-TK interface. > > My R installation was compiled without native TCL-TK support and it > is inconvenient for me atm to reinstall/replace etc to add support. > > As a consequence, as it stands it seems I cannot get qvalue to work > on my system. > > Does anybody know of a way to install and run qvalue excluding the > TCL-TK bindings? > > Best regards > Giuseppe > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >
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Another solution is to find an old version of qvalue, e.g., here: http://cran.r-project.org/src/contrib/Archive/qvalue/ The version 1.1.1 is, to the best of my knowledge, the last that did not use the graphical interface and the Tcl/Tk that comes with it. Peter On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: > John > > thanks, I will try what you suggested. > > Best wishes > Giuseppe > > > On 05/23/14 15:31, John Blischak wrote: >> >> A short-term solution would be to download the source code and just >> directly use the qvalue function. >> >> wget >> >> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1. 38.0.tar.gz >> tar xzf qvalue_1.38.0.tar.gz >> >> Then source the code in R: >> source("qvalue/R/qvalue.R") >> >> If you wanted to install, you could edit the source code. I'd imagine >> deleting the function qvalue.gui and removing the references to tcltk in >> the package DESCRIPTION and NAMESPACE would allow you to install it from >> source. >> >> John >> >> >> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >> <giuseppe.gallone at="" dpag.ox.ac.uk="" <mailto:giuseppe.gallone="" at="" dpag.ox.ac.uk="">> >> >> wrote: >> >> Hi >> >> I need the qvalue package however I don't need the TCL-TK interface. >> >> My R installation was compiled without native TCL-TK support and it >> is inconvenient for me atm to reinstall/replace etc to add support. >> >> As a consequence, as it stands it seems I cannot get qvalue to work >> on my system. >> >> Does anybody know of a way to install and run qvalue excluding the >> TCL-TK bindings? >> >> Best regards >> Giuseppe >> >> _________________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/__listinfo/bioconductor >> >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Guiseppe, If I may shamelessly promote a package from my former group, fdrtool (CRAN) http://strimmerlab.org/software/fdrtool/ essentially uses the qvalue algorithm if you give it p-values, so the results should be the same. Best wishes, Bernd On Fri, 23 May 2014 09:05:15 -0700 Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: > Another solution is to find an old version of qvalue, e.g., here: > > http://cran.r-project.org/src/contrib/Archive/qvalue/ > > The version 1.1.1 is, to the best of my knowledge, the last that did > not use the graphical interface and the Tcl/Tk that comes with it. > > Peter > > > On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone > <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: > > John > > > > thanks, I will try what you suggested. > > > > Best wishes > > Giuseppe > > > > > > On 05/23/14 15:31, John Blischak wrote: > >> > >> A short-term solution would be to download the source code and just > >> directly use the qvalue function. > >> > >> wget > >> > >> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_ 1.38.0.tar.gz > >> tar xzf qvalue_1.38.0.tar.gz > >> > >> Then source the code in R: > >> source("qvalue/R/qvalue.R") > >> > >> If you wanted to install, you could edit the source code. I'd imagine > >> deleting the function qvalue.gui and removing the references to tcltk in > >> the package DESCRIPTION and NAMESPACE would allow you to install it from > >> source. > >> > >> John > >> > >> > >> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone > >> <giuseppe.gallone at="" dpag.ox.ac.uk="" <mailto:giuseppe.gallone="" at="" dpag.ox.ac.uk="">> > >> > >> wrote: > >> > >> Hi > >> > >> I need the qvalue package however I don't need the TCL-TK interface. > >> > >> My R installation was compiled without native TCL-TK support and it > >> is inconvenient for me atm to reinstall/replace etc to add support. > >> > >> As a consequence, as it stands it seems I cannot get qvalue to work > >> on my system. > >> > >> Does anybody know of a way to install and run qvalue excluding the > >> TCL-TK bindings? > >> > >> Best regards > >> Giuseppe > >> > >> _________________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > >> https://stat.ethz.ch/mailman/__listinfo/bioconductor > >> > >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >> Search the archives: > >> http://news.gmane.org/gmane.__science.biology.informatics.__conductor > >> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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As John suggested, the solution is: downloaded the package from: http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalue_1 .38.0.tar.gz untar and modify the file qvalue/NAMESPACE: delete the following lines: importFrom(tcltk, tclvalue, "tclvalue<-", tclVar, tkbutton, tkcheckbutton, tkconfigure, tkdestroy, tkentry, tkframe, tkgetOpenFile, tkgetSaveFile, tkgrid, tkinsert, tklabel, tkpack, tkradiobutton, tkscrollbar, tkset, tktext, tktoplevel, tkwm.focusmodel, tkwm.title, tkyview) and delete the word "qvalue.gui," from the line: export(plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, summary.qvalue) then re compressed the qvalue directory into qvalue_1.38.0.tar.gz and install it using install.packages(). done. Best, pengcheng On 2014/5/24 0:32, Bernd Klaus wrote: > Hi Guiseppe, > > If I may shamelessly promote a package from my former group, > > fdrtool (CRAN) > > http://strimmerlab.org/software/fdrtool/ > > essentially uses the qvalue algorithm if you give it p-values, > so the results should be the same. > > Best wishes, > > Bernd > > > On Fri, 23 May 2014 09:05:15 -0700 > Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: > >> Another solution is to find an old version of qvalue, e.g., here: >> >> http://cran.r-project.org/src/contrib/Archive/qvalue/ >> >> The version 1.1.1 is, to the best of my knowledge, the last that did >> not use the graphical interface and the Tcl/Tk that comes with it. >> >> Peter >> >> >> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone >> <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: >>> John >>> >>> thanks, I will try what you suggested. >>> >>> Best wishes >>> Giuseppe >>> >>> >>> On 05/23/14 15:31, John Blischak wrote: >>>> A short-term solution would be to download the source code and just >>>> directly use the qvalue function. >>>> >>>> wget >>>> >>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_ 1.38.0.tar.gz >>>> tar xzf qvalue_1.38.0.tar.gz >>>> >>>> Then source the code in R: >>>> source("qvalue/R/qvalue.R") >>>> >>>> If you wanted to install, you could edit the source code. I'd imagine >>>> deleting the function qvalue.gui and removing the references to tcltk in >>>> the package DESCRIPTION and NAMESPACE would allow you to install it from >>>> source. >>>> >>>> John >>>> >>>> >>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >>>> <giuseppe.gallone at="" dpag.ox.ac.uk="" <mailto:giuseppe.gallone="" at="" dpag.ox.ac.uk="">> >>>> >>>> wrote: >>>> >>>> Hi >>>> >>>> I need the qvalue package however I don't need the TCL-TK interface. >>>> >>>> My R installation was compiled without native TCL-TK support and it >>>> is inconvenient for me atm to reinstall/replace etc to add support. >>>> >>>> As a consequence, as it stands it seems I cannot get qvalue to work >>>> on my system. >>>> >>>> Does anybody know of a way to install and run qvalue excluding the >>>> TCL-TK bindings? >>>> >>>> Best regards >>>> Giuseppe >>>> >>>> _________________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>> >>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Excellent, thanks a lot for your help Best Giuseppe On 05/26/14 04:19, Pengcheng Yang wrote: > As John suggested, the solution is: > > downloaded the package from: > http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalue _1.38.0.tar.gz > > > untar and modify the file qvalue/NAMESPACE: > > delete the following lines: > > importFrom(tcltk, tclvalue, "tclvalue<-", tclVar, tkbutton, > tkcheckbutton, tkconfigure, tkdestroy, tkentry, tkframe, > tkgetOpenFile, tkgetSaveFile, tkgrid, tkinsert, tklabel, > tkpack, tkradiobutton, tkscrollbar, tkset, tktext, > tktoplevel, tkwm.focusmodel, tkwm.title, tkyview) > > and delete the word "qvalue.gui," from the line: > export(plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, > summary.qvalue) > > then re compressed the qvalue directory into qvalue_1.38.0.tar.gz and > install it using install.packages(). > > done. > > Best, > pengcheng > > On 2014/5/24 0:32, Bernd Klaus wrote: >> Hi Guiseppe, >> >> If I may shamelessly promote a package from my former group, >> >> fdrtool (CRAN) >> >> http://strimmerlab.org/software/fdrtool/ >> >> essentially uses the qvalue algorithm if you give it p-values, >> so the results should be the same. >> >> Best wishes, >> >> Bernd >> >> >> On Fri, 23 May 2014 09:05:15 -0700 >> Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: >> >>> Another solution is to find an old version of qvalue, e.g., here: >>> >>> http://cran.r-project.org/src/contrib/Archive/qvalue/ >>> >>> The version 1.1.1 is, to the best of my knowledge, the last that did >>> not use the graphical interface and the Tcl/Tk that comes with it. >>> >>> Peter >>> >>> >>> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone >>> <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: >>>> John >>>> >>>> thanks, I will try what you suggested. >>>> >>>> Best wishes >>>> Giuseppe >>>> >>>> >>>> On 05/23/14 15:31, John Blischak wrote: >>>>> A short-term solution would be to download the source code and just >>>>> directly use the qvalue function. >>>>> >>>>> wget >>>>> >>>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue _1.38.0.tar.gz >>>>> >>>>> tar xzf qvalue_1.38.0.tar.gz >>>>> >>>>> Then source the code in R: >>>>> source("qvalue/R/qvalue.R") >>>>> >>>>> If you wanted to install, you could edit the source code. I'd imagine >>>>> deleting the function qvalue.gui and removing the references to >>>>> tcltk in >>>>> the package DESCRIPTION and NAMESPACE would allow you to install it >>>>> from >>>>> source. >>>>> >>>>> John >>>>> >>>>> >>>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >>>>> <giuseppe.gallone at="" dpag.ox.ac.uk="">>>>> <mailto:giuseppe.gallone at="" dpag.ox.ac.uk="">> >>>>> >>>>> wrote: >>>>> >>>>> Hi >>>>> >>>>> I need the qvalue package however I don't need the TCL-TK >>>>> interface. >>>>> >>>>> My R installation was compiled without native TCL-TK support >>>>> and it >>>>> is inconvenient for me atm to reinstall/replace etc to add >>>>> support. >>>>> >>>>> As a consequence, as it stands it seems I cannot get qvalue to >>>>> work >>>>> on my system. >>>>> >>>>> Does anybody know of a way to install and run qvalue excluding >>>>> the >>>>> TCL-TK bindings? >>>>> >>>>> Best regards >>>>> Giuseppe >>>>> >>>>> _________________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>>> >>>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>> Search the archives: >>>>> >>>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>>> >>>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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I took the liberty of updating qvalue to make it use tcltk if available, but not to require tcltk. This is in the 'devel' branch, version 1.39.1, probably available after noon Tuesday, Seattle time. Martin On 05/26/2014 06:20 AM, Giuseppe Gallone wrote: > Excellent, thanks a lot for your help > > Best > Giuseppe > > On 05/26/14 04:19, Pengcheng Yang wrote: >> As John suggested, the solution is: >> >> downloaded the package from: >> http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalu e_1.38.0.tar.gz >> >> >> >> untar and modify the file qvalue/NAMESPACE: >> >> delete the following lines: >> >> importFrom(tcltk, tclvalue, "tclvalue<-", tclVar, tkbutton, >> tkcheckbutton, tkconfigure, tkdestroy, tkentry, tkframe, >> tkgetOpenFile, tkgetSaveFile, tkgrid, tkinsert, tklabel, >> tkpack, tkradiobutton, tkscrollbar, tkset, tktext, >> tktoplevel, tkwm.focusmodel, tkwm.title, tkyview) >> >> and delete the word "qvalue.gui," from the line: >> export(plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, >> summary.qvalue) >> >> then re compressed the qvalue directory into qvalue_1.38.0.tar.gz and >> install it using install.packages(). >> >> done. >> >> Best, >> pengcheng >> >> On 2014/5/24 0:32, Bernd Klaus wrote: >>> Hi Guiseppe, >>> >>> If I may shamelessly promote a package from my former group, >>> >>> fdrtool (CRAN) >>> >>> http://strimmerlab.org/software/fdrtool/ >>> >>> essentially uses the qvalue algorithm if you give it p-values, >>> so the results should be the same. >>> >>> Best wishes, >>> >>> Bernd >>> >>> >>> On Fri, 23 May 2014 09:05:15 -0700 >>> Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: >>> >>>> Another solution is to find an old version of qvalue, e.g., here: >>>> >>>> http://cran.r-project.org/src/contrib/Archive/qvalue/ >>>> >>>> The version 1.1.1 is, to the best of my knowledge, the last that did >>>> not use the graphical interface and the Tcl/Tk that comes with it. >>>> >>>> Peter >>>> >>>> >>>> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone >>>> <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: >>>>> John >>>>> >>>>> thanks, I will try what you suggested. >>>>> >>>>> Best wishes >>>>> Giuseppe >>>>> >>>>> >>>>> On 05/23/14 15:31, John Blischak wrote: >>>>>> A short-term solution would be to download the source code and just >>>>>> directly use the qvalue function. >>>>>> >>>>>> wget >>>>>> >>>>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalu e_1.38.0.tar.gz >>>>>> >>>>>> >>>>>> tar xzf qvalue_1.38.0.tar.gz >>>>>> >>>>>> Then source the code in R: >>>>>> source("qvalue/R/qvalue.R") >>>>>> >>>>>> If you wanted to install, you could edit the source code. I'd imagine >>>>>> deleting the function qvalue.gui and removing the references to >>>>>> tcltk in >>>>>> the package DESCRIPTION and NAMESPACE would allow you to install it >>>>>> from >>>>>> source. >>>>>> >>>>>> John >>>>>> >>>>>> >>>>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >>>>>> <giuseppe.gallone at="" dpag.ox.ac.uk="">>>>>> <mailto:giuseppe.gallone at="" dpag.ox.ac.uk="">> >>>>>> >>>>>> wrote: >>>>>> >>>>>> Hi >>>>>> >>>>>> I need the qvalue package however I don't need the TCL-TK >>>>>> interface. >>>>>> >>>>>> My R installation was compiled without native TCL-TK support >>>>>> and it >>>>>> is inconvenient for me atm to reinstall/replace etc to add >>>>>> support. >>>>>> >>>>>> As a consequence, as it stands it seems I cannot get qvalue to >>>>>> work >>>>>> on my system. >>>>>> >>>>>> Does anybody know of a way to install and run qvalue excluding >>>>>> the >>>>>> TCL-TK bindings? >>>>>> >>>>>> Best regards >>>>>> Giuseppe >>>>>> >>>>>> _________________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>>>> >>>>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>> Search the archives: >>>>>> >>>>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>>>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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We’re also about to release a version 2.x of qvalue that includes new functionality and resolves this issue. The temporary fix is okay with me. John From: Martin Morgan mtmorgan@fhcrc.org<mailto:mtmorgan@fhcrc.org> Reply: Martin Morgan mtmorgan@fhcrc.org<mailto:mtmorgan@fhcrc.org> Date: May 26, 2014 at 1:24:24 PM To: Giuseppe Gallone giuseppe.gallone@dpag.ox.ac.uk<mailto:giuseppe.gallone@dpag.ox.ac.uk> Cc: bioconductor@r-project.org bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] Package qvalue - can it be installed without TCL- TK support? I took the liberty of updating qvalue to make it use tcltk if available, but not to require tcltk. This is in the 'devel' branch, version 1.39.1, probably available after noon Tuesday, Seattle time. Martin On 05/26/2014 06:20 AM, Giuseppe Gallone wrote: > Excellent, thanks a lot for your help > > Best > Giuseppe > > On 05/26/14 04:19, Pengcheng Yang wrote: >> As John suggested, the solution is: >> >> downloaded the package from: >> http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalu e_1.38.0.tar.gz >> >> >> >> untar and modify the file qvalue/NAMESPACE: >> >> delete the following lines: >> >> importFrom(tcltk, tclvalue, "tclvalue<-", tclVar, tkbutton, >> tkcheckbutton, tkconfigure, tkdestroy, tkentry, tkframe, >> tkgetOpenFile, tkgetSaveFile, tkgrid, tkinsert, tklabel, >> tkpack, tkradiobutton, tkscrollbar, tkset, tktext, >> tktoplevel, tkwm.focusmodel, tkwm.title, tkyview) >> >> and delete the word "qvalue.gui," from the line: >> export(plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, >> summary.qvalue) >> >> then re compressed the qvalue directory into qvalue_1.38.0.tar.gz and >> install it using install.packages(). >> >> done. >> >> Best, >> pengcheng >> >> On 2014/5/24 0:32, Bernd Klaus wrote: >>> Hi Guiseppe, >>> >>> If I may shamelessly promote a package from my former group, >>> >>> fdrtool (CRAN) >>> >>> http://strimmerlab.org/software/fdrtool/ >>> >>> essentially uses the qvalue algorithm if you give it p-values, >>> so the results should be the same. >>> >>> Best wishes, >>> >>> Bernd >>> >>> >>> On Fri, 23 May 2014 09:05:15 -0700 >>> Peter Langfelder <peter.langfelder@gmail.com> wrote: >>> >>>> Another solution is to find an old version of qvalue, e.g., here: >>>> >>>> http://cran.r-project.org/src/contrib/Archive/qvalue/ >>>> >>>> The version 1.1.1 is, to the best of my knowledge, the last that did >>>> not use the graphical interface and the Tcl/Tk that comes with it. >>>> >>>> Peter >>>> >>>> >>>> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone >>>> <giuseppe.gallone@dpag.ox.ac.uk> wrote: >>>>> John >>>>> >>>>> thanks, I will try what you suggested. >>>>> >>>>> Best wishes >>>>> Giuseppe >>>>> >>>>> >>>>> On 05/23/14 15:31, John Blischak wrote: >>>>>> A short-term solution would be to download the source code and just >>>>>> directly use the qvalue function. >>>>>> >>>>>> wget >>>>>> >>>>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalu e_1.38.0.tar.gz >>>>>> >>>>>> >>>>>> tar xzf qvalue_1.38.0.tar.gz >>>>>> >>>>>> Then source the code in R: >>>>>> source("qvalue/R/qvalue.R") >>>>>> >>>>>> If you wanted to install, you could edit the source code. I'd imagine >>>>>> deleting the function qvalue.gui and removing the references to >>>>>> tcltk in >>>>>> the package DESCRIPTION and NAMESPACE would allow you to install it >>>>>> from >>>>>> source. >>>>>> >>>>>> John >>>>>> >>>>>> >>>>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >>>>>> <giuseppe.gallone@dpag.ox.ac.uk>>>>>> <mailto:giuseppe.gallone@dpag.ox.ac.uk>> >>>>>> >>>>>> wrote: >>>>>> >>>>>> Hi >>>>>> >>>>>> I need the qvalue package however I don't need the TCL-TK >>>>>> interface. >>>>>> >>>>>> My R installation was compiled without native TCL-TK support >>>>>> and it >>>>>> is inconvenient for me atm to reinstall/replace etc to add >>>>>> support. >>>>>> >>>>>> As a consequence, as it stands it seems I cannot get qvalue to >>>>>> work >>>>>> on my system. >>>>>> >>>>>> Does anybody know of a way to install and run qvalue excluding >>>>>> the >>>>>> TCL-TK bindings? >>>>>> >>>>>> Best regards >>>>>> Giuseppe >>>>>> >>>>>> _________________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >>>>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>>>> >>>>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>>>> Search the archives: >>>>>> >>>>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>>>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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Dear Bernd thanks, I will definitely test it. Best wishes, Giuseppe On 05/23/14 17:32, Bernd Klaus wrote: > Hi Guiseppe, > > If I may shamelessly promote a package from my former group, > > fdrtool (CRAN) > > http://strimmerlab.org/software/fdrtool/ > > essentially uses the qvalue algorithm if you give it p-values, > so the results should be the same. > > Best wishes, > > Bernd > > > On Fri, 23 May 2014 09:05:15 -0700 > Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: > >> Another solution is to find an old version of qvalue, e.g., here: >> >> http://cran.r-project.org/src/contrib/Archive/qvalue/ >> >> The version 1.1.1 is, to the best of my knowledge, the last that did >> not use the graphical interface and the Tcl/Tk that comes with it. >> >> Peter >> >> >> On Fri, May 23, 2014 at 8:51 AM, Giuseppe Gallone >> <giuseppe.gallone at="" dpag.ox.ac.uk=""> wrote: >>> John >>> >>> thanks, I will try what you suggested. >>> >>> Best wishes >>> Giuseppe >>> >>> >>> On 05/23/14 15:31, John Blischak wrote: >>>> >>>> A short-term solution would be to download the source code and just >>>> directly use the qvalue function. >>>> >>>> wget >>>> >>>> http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_ 1.38.0.tar.gz >>>> tar xzf qvalue_1.38.0.tar.gz >>>> >>>> Then source the code in R: >>>> source("qvalue/R/qvalue.R") >>>> >>>> If you wanted to install, you could edit the source code. I'd imagine >>>> deleting the function qvalue.gui and removing the references to tcltk in >>>> the package DESCRIPTION and NAMESPACE would allow you to install it from >>>> source. >>>> >>>> John >>>> >>>> >>>> On Fri, May 23, 2014 at 7:44 AM, Giuseppe Gallone >>>> <giuseppe.gallone at="" dpag.ox.ac.uk="" <mailto:giuseppe.gallone="" at="" dpag.ox.ac.uk="">> >>>> >>>> wrote: >>>> >>>> Hi >>>> >>>> I need the qvalue package however I don't need the TCL-TK interface. >>>> >>>> My R installation was compiled without native TCL-TK support and it >>>> is inconvenient for me atm to reinstall/replace etc to add support. >>>> >>>> As a consequence, as it stands it seems I cannot get qvalue to work >>>> on my system. >>>> >>>> Does anybody know of a way to install and run qvalue excluding the >>>> TCL-TK bindings? >>>> >>>> Best regards >>>> Giuseppe >>>> >>>> _________________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>> https://stat.ethz.ch/mailman/__listinfo/bioconductor >>>> >>>> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.__science.biology.informatics.__conductor >>>> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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