[R-sig-Fedora] tcktk problem with custom R 2.15.0 build on RHEL5

peter dalgaard pdalgd at gmail.com
Tue May 22 08:56:11 CEST 2012


On May 21, 2012, at 22:54 , Marc Schwartz wrote:

> On May 21, 2012, at 3:30 PM, Bruce Pennypacker wrote:
> 
>> Hi all,
>> 
>> Please bear with me because I'm not all that familiar with R. I manage a research cluster that's running Red Hat 5.6 (64-bit), and we recently installed version 2.15.0 of R for some users.  Here's how we built it:
>> 
>> ./configure --prefix=/opt/shared/R/2.15.0 --with-tcltk --with-system-zlib --with-system-bzlib --with-system-pcre --with-lapack --enable-R-shlib
>> 
>> 
>> 
>> When we ran "make check-all" it didn't report any obvious problems, and we successfully installed a number of add-on's from CRAN.  But when one of our users tries to use R with tcltk he runs into a problem:
>> 
>> R version 2.15.0 (2012-03-30)
>> Copyright (C) 2012 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> ...
>> 
>>> library("sqldf")
>> Loading required package: DBI
>> Loading required package: gsubfn
>> Loading required package: proto
>> Loading required namespace: tcltk
>> Loading Tcl/Tk interface ... done
>> Loading required package: chron
>> Loading required package: RSQLite
>> Loading required package: RSQLite.extfuns
>>> result<-sqldf("select data.*, meth450part.chromStart as MethChromStart, meth450part.chromEnd as MethChromEnd, meth450part.strand as MethStrand, meth450part.name as MethName, meth450part.score as MethScore from data join meth450part where data.V1=meth450part.chrom and data.V2<=meth450part.chromStart and data.V3>=meth450part.chromEnd")
>> Loading required package: tcltk
>> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = "tclObj") :
>> [tcl] unknown math function "min".
>> 
>> Can anybody tell me why we're getting this tcl error about the function "min" not being found?  I've been unable to find anything on the web that relates to this.  We're using version 8.14.3 of tcltk (the RedHat supplied packages).
>> 
>> Thanks,
>> 
>> -Bruce
> 
> 
> What does:
> 
>  capabilities("tcltk")
> 
> show? 

As I read the error message, Tcl as such is working fine. However, the min function seems to be new in Tcl 8.5, and it is unclear which version is in RH 5.6. There's certainly no Tcl 8.14.3. (library(tcltk); tcl("info", "tclversion") will tell you which one is really loaded.)

Google suggests that in earlier versions, there was an add-on called "TclX" that defined min and max functions (among other things, I presume). If it is in RH5.6, I would guess that you could load it with tclRequire("TclX") (or however it might be capiTaLized) before trying to do anything with sqldf().

> 
> It should return TRUE if all is generally well. If it does come back TRUE, check the output of:
> 
>  capabilities()
> 
> to see if anything else comes back as FALSE.
> 
> Since you installed from source rather than using the pre-built binary R RPM available for RHEL from the EPEL (http://fedoraproject.org/wiki/EPEL):
> 
>  http://dl.fedoraproject.org/pub/epel/5/x86_64/repoview/R.html
> 
> you may be missing the required '-devel' RPMs that contain the header files for tcl/tk. I would have thought that you might have gotten errors from 'config' if that were the case, but perhaps they were missed?
> 
> Regards,
> 
> Marc Schwartz
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



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