[R] Broken tkrplot on Mac OS X

Tue Aug 16 21:35:48 CEST 2005

Because of the way Tcl works the C code needs to be linked into a
dylib rather than the other thing.  I keep meaning to either put in a
README.MacOSX or figure out a way to get configure to deal with this
but never get around to it.  Here is the strategy that works for me
(from notes and memory--I may have got a detail wrong):

      Download, untar, and run R CMD INSTALL

      cd to the src directory and repeat the final link command with
      -bundle replaced by -dynamiclib

      Then move the new trkplot.so by hand to the lib directory of the
      installed package

If you are offended by a .so extension on a dylib you can change the
extension and the R code that load it.

If you figure out a better way to do this please let me know,

Best,

luke

On Thu, 12 May 2005, stefano iacus wrote:

> It seems it doesn't work for me either
>
> http://159.149.213.137/R/bin/2.1/check/checkSummaryOSX.html
>
> Will forward to Luke, hopefully he could help
> stefano
>
> On 12/mag/05, at 23:13, Simon Urbanek wrote:
>
>> Hi Robert,
>> 
>> On May 12, 2005, at 4:48 PM, Robert Gentleman wrote:
>>
>>>   I am getting something a bit weird when I do an install.packages on 
>>> tkrplot,
>>> > library(tkrplot)
>>> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = 
>>> "tclObj") :
>>>         [tcl] dyld: /Users/rgentlem/R/R-devel/bin/exec/R malformed 
>>> library: /Users/rgentlem/R/R-devel/library/tkrplot/libs/tkrplot.so (not a 
>>> Mach-O library file, bad filetype value)
>>> .
>>> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
>>> >
>>> 
>>> can either of you confirm - or point me towards what is wrong with my 
>>> installation -
>> 
>> It's rather a problem with tkrplot than with your installation - it 
>> compiles tkrplot.so as if it was a library to be loaded into R (via 
>> dyn.load - more precisely it creates a bundle for R), but then tries to 
>> load it as dylib using Tcl/Tk. I don't know the exact system how to load 
>> plug-ins into Tcl/Tk, but I suspect that the tkrplot code needs to be split 
>> into R part bundle and dylib that is loaded into Tcl/Tk. Chances are that 
>> the bundle is actually not needed at all, because I don't see any .C/.Call 
>> in the tkrplot R code. I have to run now, but I can have a closer look 
>> later this week if it's of interest.
>> 
>> Cheers,
>> Simon
>> 
>
>

-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
     Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
On Fri, 12 Aug 2005, Marco Blanchette wrote:

> Dear all--
>
> I have been trying to get the tkrplot package to work in order to use the
> bioconductor package genArise.
>
> I am trying to build it on a Mac running OS 10.4.1 with R 2.1.1. Following a
> stanadard install from R here the error I get when I try to load tkrplot
>
>> library(tkrplot)
> Loading required package: tcltk
> Loading Tcl/Tk interface ... done
> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
> "tclObj") :
>         [tcl] no suitable image found.  Did find:
>
> /Library/Frameworks/R.framework/Versions/2.1.1/Resources/library/tkrplot/li
> b
> s/tkrplot.so: not a dylib.
> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
>
> Gustavo Corral suggestion was to rebuild the tkrplot.so bundle as a library
> by doing:
>
>> It can be rather tricky to make it work. You have to download it, then
>> install it with R CMD INSTALL, then you may need to edit the file Makeconf in
>> the RHOME/etc directory (the command R RHOME says the path to RHOME
>> directory).
>> In this file you must change:
>>
>> (line 41 in my case)
>> SHLIB_CXXLDFLAGS = -bundle -flat_namespace -undefined suppress
>> replaced by:
>> SHLIB_CXXLDFLAGS = -dynamiclib -flat_namespace -undefined suppress
>>
>> (line 45 ...)
>> SHLIB_LDFLAGS = -bundle -flat_namespace -undefined suppress
>> replaced by:
>> SHLIB_LDFLAGS = -dynamiclib -flat_namespace -undefined suppress
>>
>> then move to the src directory in the tkrplot you just download and link
>> tkrplot
>> with the statement: R CMD SHLIB -o tkrplot.so. Then move tkrplot.so by hand to
>>
>> the libs directory of the tkrplot installation (RHOME/library/tkrplot/libs).
>
> That what I did. Now I am having a different error when I try to load
> tkrplot...
>
>> library(tkrplot)
> Loading required package: tcltk
> Loading Tcl/Tk interface ... done
> Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class =
> "tclObj") :
>        [tcl] couldn't find procedure Rplot_Init.
> Error in library(tkrplot) : .First.lib failed for 'tkrplot'
>
> Any clue as how to fix tkrplot?
>
> Why is this package so difficult to install???
>
> Anyway, I would appreciate any help/suggestions.
>
> Many tx
>
> Marco
>
> Marco Blanchette, Ph.D.
>
> mblanche at uclink.berkeley.edu
>
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
>
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062
>
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-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu