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Question: [Bioc-devel] Tcl/TK pckage "Bwidget"
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gravatar for Keith Satterley
10.6 years ago by
Australia
Keith Satterley450 wrote:
Hi Angel, As Sean says, it helps you more if you provide sessionInfo() output. I have been writing some notes recently for people who have had this sort of problem with limmaGUI or affylmGUI. An extract from these notes is shown below: ************************************************ Tcl/Tk issues with R and limmaGUI and affylmGUI. ================================================ First a note on Terminology: ---------------------------- I use "Tcl/Tk" to refer to the Tool Command Language/Tool Kit package of software that is installed on the current operating system. I use "tcltk" to refer to the R package that can be installed into the R installation which allows R to interface to the Tcl/TK language. Advice about the Linux OS should probably apply to several other versions of unix, however Mac OSX is referred to separately. Tcl/Tk needs to be installed on your OS if you wish to use limmaGUI and affylmGUI. In fact Tcl/Tk has many packages written for it and to be precise, the particular Tcl/Tk packages that are called by R packages must be installed into Tcl/Tk on your computer. Tcl/Tk packages maybe installed in /usr/lib or /usr/local/lib. For eg. On my Linux computer, Tktable2.9 is in /usr/lib/ and the BWidget package is located in /usr/local/lib/. Tcl/Tk packages on my Linux box use the X11 windowing system. For MS Windows systems, ActiveState Tcl can be installed in C:\Tcl\bin and C:\Tcl\bin should be in the path. ActiveState Tcl/Tk uses the MS Windowing system and does not need an X11 server. ActiveState Tcl/Tk is available from: http://www.activestate.com/Products/ActiveTcl/ For Mac OSX, The Tcl/Tk libraries that use the Mac Native Windowing system are installed on a standard installation of Mac OSX, usually in MacHDname/System/Library/Tcl. However limmaGUI and affylmGUI do not use these and require the Tcl/Tk libraries that are linked into the X11 windowing system. Tcl/Tk for X11 is distributed with R and is installed during the installation of R for Mac OSX, usually into /usr/local/lib. Tcl/Tk for X11 can be installed separately if it wasn't installed with R. R and Tcl/Tk and X11. ===================== If an R package is going to use Tcl/Tk then the interface package tcltk must be installed into R. (It is installed with a standard install of R). If an R package uses Tcl/Tk then Tcl/Tk must be installed on the OS before the R package can be installed into R. Also the X Server should be running on Mac OSX and Linux when these packages are installed, which is normal for Linux, but not for Mac OSX. On Linux and Mac OSX you will need to have an X11 server running and you will needed to have defined your DISPLAY environment variable. This can be done in a bash shell using a command like this: export DISPLAY=localhost:0 or if your are displaying on another computer, it maybe, for example: export DISPLAY=pc512.mydomain.edu.au:0 One of these commands should be in your .bashrc file (or equivalent for other shells). Check the value of your DISPLAY variable on your unix/Mac OSX computer using echo $DISPLAY assuming you are using a bash shell. Tktable and BWidget: ==================== These two Tcl/Tk packages are needed by affylmGUI and limmaGUI for their functionality. BWidget ------- BWidget is a package written entirely in the tcl scripting language (ie. it is all text files) and hence is not compiled. Consequently it is the same on any platform and should be in the Tcl/Tk auto_path. On my MS Windows computer the bwidget1.7 folder is located in C:\Tcl\lib. On my Mac OSX computer the folder BWidget-1.7.0 is located in /usr/local/lib. On my Linux computer, the directory BWidget-1.7.0 is in /usr/local/lib. To find where these files (if at all), are installed on unix based computers( including Mac OSX), use the command: %find / -name "BWi*" -print 2>/dev/null (Use man on the find command for more detail). This will list all files on your computer (that you have permission to read) for files beginning with "BWi". Tktable ------- Tktable has some code written in C and hence is a compiled package. It therefore is different for each type of CPU and OS. On my MS Windows computer, the "Tktable2.9" directory is located in "C:\Tcl\lib". It contains the dynamic link library "Tktable29.dll". On my Mac OSX computer (PPC G4 CPU, OSX 10.4.8) the folder "Tktable2.9" is located in "/usr/local/lib". The folder "Tktable2.9" contains a dynamic library called "libTktable2.9.dylib". It is 136,708 bytes in size. This file is available from: http://bioinf.wehi.edu.au/affylmGUI/Tktable2.9MacOSX_X11.ppc.zip. The dynamic library suitable for an Intel based Mac is 143312 bytes in size. This version is needed for the recently released Intel duo core based Macs. This file is available from: http://bioinf.wehi.edu.au/affylmGUI/Tktable2.9MacOSX_X11.intel.tar.gz. On my unix server (i686 i386 GNU/Linux) the "Tktable2.9" folder is in "/usr/lib". It contains a "libTktable2.9.so" shared object file. This would be created when the package was installed from source files. Note that the *.tcl files on the Mac OSX versions of TkTable2.9 are different (slightly) from the MS Windows versions of these files. For example, pkgIndex.tcl refers to the dynamic link library by name, which differs from Mac to Windows. Note also that the *.tcl files on the Mac OSX versions of TkTable2.9 are different (slightly) from the Linux versions of these files. For example, pkgIndex.tcl refers to the dynamic link library by name, which differs from Mac to Linux. To find if these files, are installed on unix based computers( including Mac OSX), use the command: %find / -name "Tkt*" -print 2>/dev/null (Use man on the find command for more detail). This will list all files on your computer (that you have permission to read) for files beginning with "Tkt". ************************************************ Hope this helps. PS. I've made an educated guess with one or two of the statements above about Linux and MacOSX, if others, more knowledgeable than I, see anything I should correct, would you please email me and I'll publish my complete note soon on the list, cheers, Keith Angel Reyes wrote: > Hello, > > I am getting the following message when I try to run The R Project for > Statistical Computing. > > Cannot find Tcl/TK pckage "Bwidget" limmaGUI cannot continue. > > How can I correct this. > > > Thank You > Angel L. Reyes > Senior Computer Support Specialist > Information Technology > 212-327-8984 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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