[BioC] tcltk problem under Linux (both 32 and 64 bits)

[Robert Gentleman]

Start up your R and look at the output of
capabilities()

On my system I get:
     jpeg      png    tcltk      X11 http/ftp  sockets   libxml     fifo
     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE
   cledit    iconv      NLS
     TRUE     TRUE     TRUE

anything that is FALSE indicates functionality you will not be able to 
access.

Does it say tcltk is TRUE or FALSE

the problem below is clearly a problem with the tcltk library which is 
part of R and NOT part of Bioconductor. So, I am doubting that it is 
properly installed.  Probably you have tcl/tk in some odd spot. You can 
find out what is happening by closely examining the output of configure 
(which would have run when you first installed R, if done from source)

best wishes
   Robert


Groot, Philip de wrote:
> Hello all,
>  
> Currently, I am compiling the latest R-release and find that there is a problem with the tcltk library. When compiling R (using SuSE Linux 9.3 professional and gcc version (GCC) 3.3.3 (SuSE Linux) (64 bit support enabled)).
>  
> Compiling a 64-bits (and 32 bits) R works fine. R executes properly and the 64 bits R can address memory > 4GB, so this is all OK.
>  
> However, when installing BioConductor I also need to install the tkWidgets library. And this fails: it claims that Tcl/Tk is not installed on the system. However, both the normal and development packages for both tcl and tk are properly installed. tclsh and wish can be executed properly. No problem at all! 
>  
> So, I am confused. Where does the problem originate from? It turns out that - during compiling R - the tcltk library is also compiled and installed. No error messages are showed / generated (the library IS actually installed) but when try to load it gives an error message:
>  
>> library(tcltk)
> Error in firstlib(which.lib.loc, package) : 
>         Tcl/Tk support is not available on this system
> Error in library(tcltk) : .First.lib failed for 'tcltk'
> 
> Again: Tck/Tk support IS available on the system (running a 64 bits version of SuSE). It is also available on a 32 bits Linux distribution and the problems on this system remain the same.
>  
> I cannot get any information on the cause of the problem. Even strace does not point me in some direction. So I have some questions:
>  
> 1. If you are running R-2.4.0 under Linux, does library(tcltk) work (to find out whether it is a general problem or not)?
> 2. Any idea what causes this problem?
> 3. How does the library check whether tcltk is available anyway?
>  
> Any help is greatly appreciated. If someone can make a working tcltk library available (e.g. when using the same Linux distribution), this would be great!
>  
> Regards,
>  
> Dr. Philip de Groot
> Wageningen University
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org