Getting LimmaGUI to run
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@chris-umbricht-1329
Last seen 10.2 years ago
I'm trying to invoke limmaGUI(), and get the following message from the limmaGUI App(?)/window (R2.1, BioC 1.6, OS X.3.9) "Cannot find Tcl/Tk package "BWidget". limmaGUI cannot continue. limmaGUI requires the Tcl/Tk extensions, BWidget and Tktable." as well as a bunch of unix directory stuff discussing if R can find the right path for the Tcl/Tk extensions in a special error popupwindow. Am I correct in assuming my Tcl/Tk environment is ok except for the missing BWidget ? Tktable, since the R package manager lists them as loaded (*)? And if so, where do I find the BWidget ? Tktable extensions? (*) including: tcltk, tkWidgets, widgetTools, but NOT widgetInvoke, which gives me the following error: "Loading required package: RGtk Error in eval(expr, envir, enclos) : Requires RGtk Error: unable to load R code in package 'widgetInvoke' Error: package/namespace load failed for 'widgetInvoke'" Moreover, when I try to download tkrplot from CRAN, I get: "trying URL 'http://cran.us.r-project.org/bin/macosx/2.1/tkrplot_0.0-12.tgz' Error in download.file(url, destfile, method, mode = "wb") : cannot open URL 'http://cran.us.r-project.org/bin/macosx/2.1/tkrplot_0.0-12.tgz' trying URL 'http://cran.us.r-project.org/bin/macosx/2.1/PACKAGES' Content type 'text/plain' length 27380 bytes opened URL ================================================== downloaded 26Kb" thanks for your time. chris
tkWidgets widgetTools limmaGUI widgetInvoke tkWidgets widgetTools limmaGUI widgetInvoke • 2.2k views
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stefano iacus ▴ 430
@stefano-iacus-995
Last seen 10.2 years ago
There is no binary for tkrplot for OS X yet, but you can install it from source with manual tricks here is a msg from Jan De Leeuw on the subject --start of msg-- Yes, there is a way to make it work. You have to download it, then build it with R CMD INSTALL, and then move to the src directory and repeat the final link statement (cut and paste) with the "--bundle -o tkrplot.so" replaced by "--dynamic -o libtkrplot.dylib". Then move libtrkplot.dylib by hand to the lib dirctory of the tkrplot installation and change the code at the end of tkrplot.R such that it uses the dylib extension. R CMS SHLIB just builds a bundle, not a library. --end of msg-- to install from source you need to go into the shell and not the R.app stefano On 08/lug/05, at 22:47, chris umbricht wrote: > I'm trying to invoke limmaGUI(), > and get the following message from the limmaGUI App(?)/window > (R2.1, BioC 1.6, OS X.3.9) > > "Cannot find Tcl/Tk package "BWidget". limmaGUI cannot continue. > > limmaGUI requires the Tcl/Tk extensions, BWidget and Tktable." > > as well as a bunch of unix directory stuff discussing if R can find > the > right path for the Tcl/Tk extensions in a special error popupwindow. > > Am I correct in assuming my Tcl/Tk environment is ok except for the > missing BWidget ? Tktable, since the R package manager lists them as > loaded (*)? > > And if so, where do I find the BWidget ? Tktable extensions? > > (*) including: tcltk, tkWidgets, widgetTools, but NOT widgetInvoke, > which gives me the following error: > "Loading required package: RGtk > Error in eval(expr, envir, enclos) : Requires RGtk > Error: unable to load R code in package 'widgetInvoke' > Error: package/namespace load failed for 'widgetInvoke'" > > > > Moreover, when I try to download tkrplot from CRAN, I get: > > "trying URL > 'http://cran.us.r-project.org/bin/macosx/2.1/tkrplot_0.0-12.tgz' > Error in download.file(url, destfile, method, mode = "wb") : > cannot open URL > 'http://cran.us.r-project.org/bin/macosx/2.1/tkrplot_0.0-12.tgz' > trying URL 'http://cran.us.r-project.org/bin/macosx/2.1/PACKAGES' > Content type 'text/plain' length 27380 bytes > opened URL > ================================================== > downloaded 26Kb" > > > > thanks for your time. > > chris > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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@chris-umbricht-1329
Last seen 10.2 years ago
Right, so how do I change the .RData back to not containing tcltk calls? I tried the (to me) obvious steps of unchecking anything tcltk-related in the manager, and trying to clear the workspace etc. without apparent effect... c. On Jul 11, 2005, at 12:39 PM, stefano iacus wrote: > Hi Chris, > no it has always been the case. And the problem is that probably your > .RData contains calls to tcltk. > Any call to tcltk, X11 etc requires a X11 server to be running. > btw, I need more detailed bug report that this. > stefano
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@chris-umbricht-1329
Last seen 10.2 years ago
Rob, thanks for your feedback, and I do understand your directions, i.e. I think I will be able to navigate this X11 dependency with your suggestions. I was trying to give Stefano some feedback, since he is heavily involved in developing the OS X version of R.App, and I'm trying to distinguish between my misunderstanding some elements of the GUI vs having a corrupted installation. It seems to me that having to delete the .RData file from the terminal should not be necessary as routine measure... I'm hoping he will chime in, since he asked me for more details earlier, but I'm not sure what he needs. On Jul 11, 2005, at 4:18 PM, Rob J Goedman wrote: > Chris, > > Remove .RData (as in previous emails). > Start R and close R. When it asks if you want to save > the session, choose Save to create a new .RData file. > > I nearly always select Don't Save, which will not create a new > .Rdata file. > > If you don't load tcltk, jpeg and/or png, e.g. used in marray, (maybe > there are a few other packages that will require X11), you don't need > X11 and it will not end up as a dependency in .RData. > > Or you can automatically start X11 when you login (Drag it to Login > items of your Account is System Preferences). > > Rob > > > On Jul 11, 2005, at 12:44 PM, chris umbricht wrote: > >> Right, so how do I change the .RData back to not containing tcltk >> calls? >> >> I tried the (to me) obvious steps of unchecking anything tcltk- related >> in the manager, and trying to clear the workspace etc. without >> apparent >> effect... >> >> c. >> >> >> On Jul 11, 2005, at 12:39 PM, stefano iacus wrote: >> >> >>> Hi Chris, >>> no it has always been the case. And the problem is that probably your >>> .RData contains calls to tcltk. >>> Any call to tcltk, X11 etc requires a X11 server to be running. >>> btw, I need more detailed bug report that this. >>> stefano >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >
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On 11/lug/05, at 22:26, chris umbricht wrote: > Rob, > > thanks for your feedback, and I do understand your directions, i.e. I > think I will be able to navigate this X11 dependency with your > suggestions. > > I was trying to give Stefano some feedback, since he is heavily > involved in developing the OS X version of R.App, and I'm trying to > distinguish between my misunderstanding some elements of the GUI vs > having a corrupted installation. It seems to me that having to delete > the .RData file from the terminal should not be necessary as routine > measure... > > I'm hoping he will chime in, since he asked me for more details > earlier, but I'm not sure what he needs. it R quits "unexpectedly" the finder will tell you, just press the button concerning the crash report (I think is something like "send report") stefano > > > On Jul 11, 2005, at 4:18 PM, Rob J Goedman wrote: > > >> Chris, >> >> Remove .RData (as in previous emails). >> Start R and close R. When it asks if you want to save >> the session, choose Save to create a new .RData file. >> >> I nearly always select Don't Save, which will not create a new >> .Rdata file. >> >> If you don't load tcltk, jpeg and/or png, e.g. used in marray, (maybe >> there are a few other packages that will require X11), you don't need >> X11 and it will not end up as a dependency in .RData. >> >> Or you can automatically start X11 when you login (Drag it to Login >> items of your Account is System Preferences). >> >> Rob >> >> >> On Jul 11, 2005, at 12:44 PM, chris umbricht wrote: >> >> >>> Right, so how do I change the .RData back to not containing tcltk >>> calls? >>> >>> I tried the (to me) obvious steps of unchecking anything tcltk- >>> related >>> in the manager, and trying to clear the workspace etc. without >>> apparent >>> effect... >>> >>> c. >>> >>> >>> On Jul 11, 2005, at 12:39 PM, stefano iacus wrote: >>> >>> >>> >>>> Hi Chris, >>>> no it has always been the case. And the problem is that probably >>>> your >>>> .RData contains calls to tcltk. >>>> Any call to tcltk, X11 etc requires a X11 server to be running. >>>> btw, I need more detailed bug report that this. >>>> stefano >>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Stefano, re: "if R quits "unexpectedly" the finder will tell you, just press the button concerning the crash report" R quits immediately after starting up, and the finder does not generate a crash report. As I understood from both your and Rob's comments, it appears simply that my .RData file contains X11 dependent processes, eg tkltk. So I can avoid the problem by prestarting the X11 window, which is fine. My question to you is, how do I undo that dependecy in the R.app (1.12, build 1622) short of trashing the RData file from within the terminal window? Am I wrong in assuming the workspace menu items are designed to get back to the original, non-X11 dependent environment? If so, is there another way? thanks chris On Jul 15, 2005, at 5:44 AM, stefano iacus wrote: > > On 11/lug/05, at 22:26, chris umbricht wrote: > >> Rob, >> >> thanks for your feedback, and I do understand your directions, i.e. I >> think I will be able to navigate this X11 dependency with your >> suggestions. >> >> I was trying to give Stefano some feedback, since he is heavily >> involved in developing the OS X version of R.App, and I'm trying to >> distinguish between my misunderstanding some elements of the GUI vs >> having a corrupted installation. It seems to me that having to delete >> the .RData file from the terminal should not be necessary as routine >> measure... >> >> I'm hoping he will chime in, since he asked me for more details >> earlier, but I'm not sure what he needs. > > it R quits "unexpectedly" the finder will tell you, just press the > button concerning the crash report (I think is something like "send > report") > stefano > > >> >> >> On Jul 11, 2005, at 4:18 PM, Rob J Goedman wrote: >> >> >>> Chris, >>> >>> Remove .RData (as in previous emails). >>> Start R and close R. When it asks if you want to save >>> the session, choose Save to create a new .RData file. >>> >>> I nearly always select Don't Save, which will not create a new >>> .Rdata file. >>> >>> If you don't load tcltk, jpeg and/or png, e.g. used in marray, (maybe >>> there are a few other packages that will require X11), you don't need >>> X11 and it will not end up as a dependency in .RData. >>> >>> Or you can automatically start X11 when you login (Drag it to Login >>> items of your Account is System Preferences). >>> >>> Rob >>> >>> >>> On Jul 11, 2005, at 12:44 PM, chris umbricht wrote: >>> >>> >>>> Right, so how do I change the .RData back to not containing tcltk >>>> calls? >>>> >>>> I tried the (to me) obvious steps of unchecking anything >>>> tcltk-related >>>> in the manager, and trying to clear the workspace etc. without >>>> apparent >>>> effect... >>>> >>>> c. >>>> >>>> >>>> On Jul 11, 2005, at 12:39 PM, stefano iacus wrote: >>>> >>>> >>>> >>>>> Hi Chris, >>>>> no it has always been the case. And the problem is that probably >>>>> your >>>>> .RData contains calls to tcltk. >>>>> Any call to tcltk, X11 etc requires a X11 server to be running. >>>>> btw, I need more detailed bug report that this. >>>>> stefano
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On 15/lug/05, at 17:47, chris umbricht wrote: > Stefano, > > re: "if R quits "unexpectedly" the finder will tell you, just press > the button concerning the crash report" > > R quits immediately after starting up, and the finder does not > generate a crash report. > umh, probably the report is generated but not shown by the Finder. > > As I understood from both your and Rob's comments, it appears > simply that my .RData file contains X11 dependent processes, eg tkltk. > So I can avoid the problem by prestarting the X11 window, which is > fine. > > My question to you is, how do I undo that dependecy in the R.app > (1.12, build 1622) short of trashing the RData file from within the > terminal window? > > try the following with X11 running launch R.app (should not quit) and in R Console > (.packages()) does tcltk appear in this list? If so type > detach(package:tcltk) and check that it is no longer there with > (.packages()) now > save.image() quit R, shut down the X11 window server and try to restart R.app. Let me know stefano > Am I wrong in assuming the workspace menu items are designed to get > back to the original, non-X11 dependent environment? If so, is > there another way? > > thanks > > chris > > > On Jul 15, 2005, at 5:44 AM, stefano iacus wrote: > > > >> >> On 11/lug/05, at 22:26, chris umbricht wrote: >> >> >> >>> Rob, >>> >>> thanks for your feedback, and I do understand your directions, >>> i.e. I >>> think I will be able to navigate this X11 dependency with your >>> suggestions. >>> >>> I was trying to give Stefano some feedback, since he is heavily >>> involved in developing the OS X version of R.App, and I'm trying to >>> distinguish between my misunderstanding some elements of the GUI vs >>> having a corrupted installation. It seems to me that having to >>> delete >>> the .RData file from the terminal should not be necessary as routine >>> measure... >>> >>> I'm hoping he will chime in, since he asked me for more details >>> earlier, but I'm not sure what he needs. >>> >>> >> >> it R quits "unexpectedly" the finder will tell you, just press the >> button concerning the crash report (I think is something like >> "send report") >> stefano >> >> >> >> >>> >>> >>> On Jul 11, 2005, at 4:18 PM, Rob J Goedman wrote: >>> >>> >>> >>> >>>> Chris, >>>> >>>> Remove .RData (as in previous emails). >>>> Start R and close R. When it asks if you want to save >>>> the session, choose Save to create a new .RData file. >>>> >>>> I nearly always select Don't Save, which will not create a new >>>> .Rdata file. >>>> >>>> If you don't load tcltk, jpeg and/or png, e.g. used in marray, >>>> (maybe >>>> there are a few other packages that will require X11), you don't >>>> need >>>> X11 and it will not end up as a dependency in .RData. >>>> >>>> Or you can automatically start X11 when you login (Drag it to Login >>>> items of your Account is System Preferences). >>>> >>>> Rob >>>> >>>> >>>> On Jul 11, 2005, at 12:44 PM, chris umbricht wrote: >>>> >>>> >>>> >>>> >>>>> Right, so how do I change the .RData back to not containing tcltk >>>>> calls? >>>>> >>>>> I tried the (to me) obvious steps of unchecking anything tcltk- >>>>> related >>>>> in the manager, and trying to clear the workspace etc. without >>>>> apparent >>>>> effect... >>>>> >>>>> c. >>>>> >>>>> >>>>> On Jul 11, 2005, at 12:39 PM, stefano iacus wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> Hi Chris, >>>>>> no it has always been the case. And the problem is that >>>>>> probably your >>>>>> .RData contains calls to tcltk. >>>>>> Any call to tcltk, X11 etc requires a X11 server to be running. >>>>>> btw, I need more detailed bug report that this. >>>>>> stefano >>>>>> > >
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>> Stefano, >> >> re: "if R quits "unexpectedly" the finder will tell you, just press >> the button concerning the crash report" >> >> R quits immediately after starting up, and the finder does not >> generate a crash report. >> > umh, probably the report is generated but not shown by the Finder. Well, I do get finder reports if other Apps crash... if you are right, can I retrieve it somewhere? >> >> As I understood from both your and Rob's comments, it appears simply >> that my .RData file contains X11 dependent processes, eg tkltk. >> So I can avoid the problem by prestarting the X11 window, which is >> fine. >> >> My question to you is, how do I undo that dependecy in the R.app >> (1.12, build 1622) short of trashing the RData file from within the >> terminal window? >> >> > > try the following with X11 running > launch R.app (should not quit) > and in R Console > > > (.packages()) > (.packages()) [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" However, this is how the R.app console comes up on its own: > R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. Loading Tcl/Tk interface ... done [Previously saved workspace restored] > It seems the culprit is the loading tcltk ... line. How Do I change/remove it from the default start up? > > does tcltk appear in this list? If so type > > > detach(package:tcltk) > > and check that it is no longer there with > > (.packages()) > > now > > save.image() > > quit R, shut down the X11 window server and try to restart R.app. Let > me know > stefano > > > >> Am I wrong in assuming the workspace menu items are designed to get >> back to the original, non-X11 dependent environment? If so, is there >> another way?
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@chris-umbricht-1329
Last seen 10.2 years ago
Thanks, Stefano, that worked. Just for my benefit, how does "rm(list=ls(all.names=T))" differ from what you achieve using the menu commands, e.g. "clear workspace, save workspace, save default workspace"? Do they have no effect on the .RData file? c. On Jul 19, 2005, at 6:35 AM, stefano iacus wrote: > Hi Chris, > > it seems that in your workspace there are lots of tcltk dependencies. > > Loading Tcl/Tk interface ... done > > ls(all.names=T) > [1] ".JustAskedWhetherToSave" ".Random.seed" ".Traceback" > [4] ".affylmGUIglobals" ".limmaGUIglobals" ".required" > [7] "dati" "r" "x" > > > and in particular the offending one, i.e. the one causing tcltk to be > loaded are > .affylmGUIglobals > .limmaGUIglobals > and the forth argument in .required > > my suggestion is to do something like > rm(list=ls(all.names=T)) > save.image() > this will clean up your .RData file > stefano
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emh, clear workspace just do rm(list=ls()) which is not enough in your case as all your "troubles" comes from .* named objects. save (default) workspace : save.image() with file argument ".RData" save workspace file: save.image(file=file.choose()) stefano On 19/lug/05, at 17:06, chris umbricht wrote: > Thanks, Stefano, that worked. > > Just for my benefit, how does > > "rm(list=ls(all.names=T))" > > differ from what you achieve using the menu commands, e.g. "clear > workspace, save workspace, save default workspace"? > > Do they have no effect on the .RData file? > > c. > > On Jul 19, 2005, at 6:35 AM, stefano iacus wrote: > > >> Hi Chris, >> >> it seems that in your workspace there are lots of tcltk dependencies. >> >> Loading Tcl/Tk interface ... done >> > ls(all.names=T) >> [1] ".JustAskedWhetherToSave" ".Random.seed" ".Traceback" >> [4] ".affylmGUIglobals" ".limmaGUIglobals" ".required" >> [7] "dati" "r" "x" >> > >> and in particular the offending one, i.e. the one causing tcltk to >> be loaded are >> .affylmGUIglobals >> .limmaGUIglobals >> and the forth argument in .required >> >> my suggestion is to do something like >> rm(list=ls(all.names=T)) >> save.image() >> this will clean up your .RData file >> stefano >
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