[R] tcltk error on Linux

[Prof Brian Ripley]

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 be out of date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_1.9.3    annaffy_1.9.1          xtable_1.5-0
>  [4] gcrma_2.9.1            matchprobes_1.9.10     biomaRt_1.11.4
>  [7] RCurl_0.8-1            XML_1.9-0              GOstats_2.3.8
> [10] Category_2.3.19        genefilter_1.15.9      survival_2.32
> [13] KEGG_1.17.0            RBGL_1.13.3            annotate_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,                  ripley at stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595