Re: [R] tcltk error on Linux
On Thu, 9 Aug 2007, Mark W Kimpel wrote: I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Whether Tcl/Tk would available was determined when you installed R. The relevant information was in the configure output and log, which we don't have. You are not running a released version of R: please don't use the development version unless you are familiar with the build process and know how to debug such things yourself. The rule is that questions about development versions of R should not be asked here but on R-devel (and not to R-core which I have deleted from the recipients). I suggest reinstalling R (preferably R-patched) and if tcltk still is not available sending the relevant configure information to the R-devel list. Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Those are coming from a Bioconductor package: again you must be using development versions with R-devel and those are not stable (last time I looked even Biobase would not install, and the packages change daily). If you have all those packages in your startup, please don't -- there will be a considerable performance hit so only load them when you need them. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for conditional, package Category may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic conditional not found require(tcltk) Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.3annaffy_1.9.1 xtable_1.5-0 [4] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [7] RCurl_0.8-1XML_1.9-0 GOstats_2.3.8 [10] Category_2.3.19genefilter_1.15.9 survival_2.32 [13] KEGG_1.17.0RBGL_1.13.3annotate_1.15.3 [16] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 [19] GO_1.17.0 limma_2.11.9 affy_1.15.7 [22] preprocessCore_0.99.12 affyio_1.5.6 Biobase_1.15.23 [25] graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 rcompgen_0.1-15 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tcltk error on Linux
Hi Mark, Prof Brian Ripley [EMAIL PROTECTED] writes: On Thu, 9 Aug 2007, Mark W Kimpel wrote: I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Any chance you are running R on a remote server using an ssh session? If that is the case, you may have an ssh/X11 config issue that prevents using tcl/tk from such a session. Rerun the configure script for R and verify that tcl/tk support is listed in the summary. Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Those are coming from a Bioconductor package: again you must be using development versions with R-devel and those are not stable (last time I looked even Biobase would not install, and the packages change daily). BioC devel tracks R-devel, but not on a daily basis -- because R changes daily. The recent issues with Biobase are a result of changes to R and have already been fixed. If you have all those packages in your startup, please don't -- there will be a considerable performance hit so only load them when you need them. Presumably, that's why they are there in the first place. The warning messages are a problem and suggest some needed improvements to the methods packages. These are being worked on. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tcltk error on Linux
Seth and Brian, Today and downloaded and installed the latest R-devel and tcltk now works. My suspicion is that Tcl was not on my path when R-devel was installed previously. BTW, I had though that is was a courtesy to cc: the maintainers of a package when writing either R-devel or R-help about a specific package. For tcltk, I see: Maintainer:R Core Team [EMAIL PROTECTED] If it is not appropriate to write R-core regarding packages they maintain, would it perhaps not be better to remove them as maintainers or, not suggest that people cc: maintainers of packages? Just an idea. As for the suggestion that I not use R-devel, I do that because I sometimes use BioC packages that have just been published and are only available in the devel versions of BioC. Are you suggesting that only people who can debug things themselves, and thus who do not need to write to R-devel, use R-devel? As an open-source user, I thought the philosophy was that it was useful to have users willing to test beta versions of software and have those users report problems to developers. If that is not the case, please put a stronger warning on R-devel and warn users not to use it unless they are willing to debug and take care of all problems themselves. Thanks, Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** Seth Falcon wrote: Hi Mark, Prof Brian Ripley [EMAIL PROTECTED] writes: On Thu, 9 Aug 2007, Mark W Kimpel wrote: I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Any chance you are running R on a remote server using an ssh session? If that is the case, you may have an ssh/X11 config issue that prevents using tcl/tk from such a session. Rerun the configure script for R and verify that tcl/tk support is listed in the summary. Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Those are coming from a Bioconductor package: again you must be using development versions with R-devel and those are not stable (last time I looked even Biobase would not install, and the packages change daily). BioC devel tracks R-devel, but not on a daily basis -- because R changes daily. The recent issues with Biobase are a result of changes to R and have already been fixed. If you have all those packages in your startup, please don't -- there will be a considerable performance hit so only load them when you need them. Presumably, that's why they are there in the first place. The warning messages are a problem and suggest some needed improvements to the methods packages. These are being worked on. + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tcltk error on Linux
I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Also, note that I have some warning messages on starting up R, not sure what they mean or if they are pertinent. Thanks, Mark Warning messages: 1: In .updateMethodsInTable(fdef, where, attach) : Couldn't find methods table for conditional, package Category may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic conditional not found require(tcltk) Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.3annaffy_1.9.1 xtable_1.5-0 [4] gcrma_2.9.1matchprobes_1.9.10 biomaRt_1.11.4 [7] RCurl_0.8-1XML_1.9-0 GOstats_2.3.8 [10] Category_2.3.19genefilter_1.15.9 survival_2.32 [13] KEGG_1.17.0RBGL_1.13.3annotate_1.15.3 [16] AnnotationDbi_0.0.88 RSQLite_0.6-0 DBI_0.2-3 [19] GO_1.17.0 limma_2.11.9 affy_1.15.7 [22] preprocessCore_0.99.12 affyio_1.5.6 Biobase_1.15.23 [25] graph_1.15.10 loaded via a namespace (and not attached): [1] cluster_1.11.7 rcompgen_0.1-15 -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
