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

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 > > _______________________________________________ > 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 > -- 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

Hello Robert, tcltk is FALSE (but I allready knew this): > capabilities() jpeg png tcltk X11 http/ftp sockets libxml fifo TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE cledit iconv NLS TRUE TRUE TRUE The corresponding output of the configure script is as follows (after unpacking R again and running the configure script for the first time again): checking for tclConfig.sh... no checking for tclConfig.sh in library (sub)directories... /usr/lib64/tclConfig.sh checking for tkConfig.sh... no checking for tkConfig.sh in library (sub)directories... no checking /usr/include/tcl8.4/generic/tcl.h usability... no checking /usr/include/tcl8.4/generic/tcl.h presence... no checking for /usr/include/tcl8.4/generic/tcl.h... no checking /usr/include/tcl8.4/tcl.h usability... no checking /usr/include/tcl8.4/tcl.h presence... no checking for /usr/include/tcl8.4/tcl.h... no checking /usr/include/tcl.h usability... yes checking /usr/include/tcl.h presence... yes checking for /usr/include/tcl.h... yes checking for tk.h... no Thanks for your help (the tip to look at the configure-output). Apparently, the tcltk-devel rpm-package is installed instead of the tk-devel rpm-package (confusing names anyway). The problem is corrected, the compilation is fine, and the tcltk library works properly now. Thanks! Philip ________________________________ From: Robert Gentleman [mailto:rgentlem@fhcrc.org] Sent: Tue 10-10-2006 18:06 To: Groot, Philip de Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] tcltk problem under Linux (both 32 and 64 bits) 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 > > _______________________________________________ > 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 > -- 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