Hello, I was wondering if anyone can help me with a problem trying to use library(tcltk) - I'm getting an error "error: unable to load shared library '/usr/local/lib64/R/library/tcltk/libs/tcltk.so' /usr/local/lib64/R/library/tcltk/libs/tcltk.so: undefined symbol: Tcl_DoOneEvent" I installed R version 2.11.1 on a 64 bit version of CentOS [sml at localhost ~]$ uname -a Linux localhost.localdomain 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux and after yum install tcltk-devel, I used the R configure flags to include tcltk (64 bit version): ./configure --with-tcltk --with-tcl-config=/usr/lib64/tclConfig.sh --with-tcl-config=/usr/lib64/tkConfig.sh And you can see that tcltk is TRUE within R using capabilities() below. [sml at localhost ~]$ R R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > capabilities() ? ?jpeg ? ? ?png ? ? tiff ? ?tcltk ? ? ?X11 ? ? aqua http/ftp ?sockets ? FALSE ? ?FALSE ? ?FALSE ? ? TRUE ? ? TRUE ? ?FALSE ? ? TRUE ? ? TRUE ?libxml ? ? fifo ? cledit ? ?iconv ? ? ?NLS ?profmem ? ?cairo ? ?TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ? TRUE ? ?FALSE ? ?FALSE > library(tcltk) Loading Tcl/Tk interface ... Error : .onLoad failed in loadNamespace() for 'tcltk', details: ?call: dyn.load(file, DLLpath = DLLpath, ...) ?error: unable to load shared library '/usr/local/lib64/R/library/tcltk/libs/tcltk.so': ?/usr/local/lib64/R/library/tcltk/libs/tcltk.so: undefined symbol: Tcl_DoOneEvent Error: package/namespace load failed for 'tcltk' > > To be certain, I checked whether the tcltk.so library existed and where it was [root at localhost /]# find . -name tcltk.so -print ./usr/local/lib64/R/library/tcltk/libs/tcltk.so ./home/sml/Installed/R-2.11.1/src/library/tcltk/src/tcltk.so ./home/sml/Installed/R-2.11.1/library/tcltk/libs/tcltk.so [root at localhost /]# Any advice would be appreciated. Sonia

On 06/15/2010 09:51 PM, Sonia Leach wrote: > Hello, > > I was wondering if anyone can help me with a problem trying to use > library(tcltk) - I'm getting an error > > "error: unable to load shared library > '/usr/local/lib64/R/library/tcltk/libs/tcltk.so' > /usr/local/lib64/R/library/tcltk/libs/tcltk.so: undefined symbol: > Tcl_DoOneEvent" > > I installed R version 2.11.1 on a 64 bit version of CentOS > > [sml at localhost ~]$ uname -a > Linux localhost.localdomain 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 > EST 2009 x86_64 x86_64 x86_64 GNU/Linux > > and after yum install tcltk-devel, I used the R configure flags to > include tcltk (64 bit version): > > ./configure --with-tcltk --with-tcl-config=/usr/lib64/tclConfig.sh > --with-tcl-config=/usr/lib64/tkConfig.sh > > And you can see that tcltk is TRUE within R using capabilities() below. > > [sml at localhost ~]$ R > > R version 2.11.1 (2010-05-31) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> capabilities() > jpeg png tiff tcltk X11 aqua http/ftp sockets > FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE > libxml fifo cledit iconv NLS profmem cairo > TRUE TRUE TRUE TRUE TRUE FALSE FALSE >> library(tcltk) > Loading Tcl/Tk interface ... Error : .onLoad failed in loadNamespace() > for 'tcltk', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared library > '/usr/local/lib64/R/library/tcltk/libs/tcltk.so': > /usr/local/lib64/R/library/tcltk/libs/tcltk.so: undefined symbol: > Tcl_DoOneEvent > Error: package/namespace load failed for 'tcltk' Hi Sonia -- this likely means that a library that tcltk.so requires is not being found, and not that there is something wrong with the tcltk.so library per se. You can R CMD ldd /usr/local/lib64/R/library/tcltk/libs/tcltk.so and look for a link to libtcl, which for me is libtcl8.5.so => /usr/lib64/libtcl8.5.so (0x00007f6edb5ae000) This tells me that the OS and R knows where to find libtcl. If this fails you likely need (as root) to use ldconfig to update where your system looks for libraries. (I am not a cent OS user, so I'd proceed with caution in following instructions from me here...); as a workaround you can set the environment variable LD_LIBRARY_PATH=/path/to/libtclX.X.so (where X.X is the appropriate version number for your libtcl). After this step, I objdump -T /usr/lib64/libtcl8.5.so | grep Tcl_DoOneEvent and get 00000000000b1670 g DF .text 00000000000001d8 Base Tcl_DoOneEvent Which tells me that the symbol I'm looking for is actually exported from libtcl8.5.so; if this isn't the case for you then I'd guess it was a version incompatibility between tcl and R. The right place for this question is probably the R-devel mailing list. Martin >> >> > > > To be certain, I checked whether the tcltk.so library existed and where it was > > [root at localhost /]# find . -name tcltk.so -print > ./usr/local/lib64/R/library/tcltk/libs/tcltk.so > ./home/sml/Installed/R-2.11.1/src/library/tcltk/src/tcltk.so > ./home/sml/Installed/R-2.11.1/library/tcltk/libs/tcltk.so > [root at localhost /]# > > Any advice would be appreciated. > > Sonia > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793