[R-sig-Geo] Adehabitat crashed R on MacOS 2.15.2

Tue Nov 27 17:10:18 CET 2012

yes is my guess that R binary is looking for the tcltk installed as framework

as suggested here :  http://cran.r-project.org/bin/macosx/tools/

do you have it installed ?

i didn't checked if it works on m. lion because i'm giving a try to there home-brew installation (it uses it's own gfortran and X system from the XQuarts installed in /opt/   as a standard unix library not as framework)

Massimo.

Il giorno 27/nov/2012, alle ore 10:57, Els Ducheyne <educheyne at avia-gis.be> ha scritto:

> Dear Massimo
> yes it works from command line, I do get a warning about the tcl tk though, so indeed this must be the source of the problem (see below)
> The good news is that at least I can carry out the code via the terminal if necessary (even it is not with the R Gui) 
> Still hoping for a fix though
> Els
> 
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> 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.
> 
> [Previously saved workspace restored]
> 
>> library(adehabitat)
> Loading required package: ade4
> 
> Attaching package: ‘ade4’
> 
> The following object(s) are masked from ‘package:base’:
> 
>    within
> 
> Loading required package: tkrplot
> Loading required package: tcltk
> Loading Tcl/Tk interface ... done
> Loading required package: shapefiles
> Loading required package: foreign
> 
> Attaching package: ‘shapefiles’
> 
> The following object(s) are masked from ‘package:foreign’:
> 
>    read.dbf, write.dbf
> 
> Be careful: it is now recommended to use the newpackages adehabitatMA, adehabitatLT, adehabitatHR, and adehabitatHS.
> These 4 packages are intended to become the future of adehabitat.
> The "classical" version of adehabitat will still be maintained for some
> time, but no new method will be added to the package.
> 
> Warning message:
> In fun(libname, pkgname) :
>  Can't find a usable tk.tcl in the following directories: 
>    /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5/Resources/Scripts /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5/Resources/Scripts ./lib/tk8.5 ./lib/tk8.5/Resources/Scripts ~/Library/Tcl/tk8.5 ~/Library/Tcl/tk8.5/Resources/Scripts /Library/Tcl/tk8.5 /Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/tk8.5 /System/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/8.5/tk8.5 /System/Library/Tcl/8.5/tk8.5/Resources/Scripts ~/Library/Frameworks/tk8.5 ~/Library/Frameworks/tk8.5/Resources/Scripts /Library/Frameworks/tk8.5 /Library/Frameworks/tk8.5/Resources/Scripts /System/Library/Frameworks/tk8.5 /System/Library/Frameworks/tk8.5/Resources/Scripts ./library
> 
> 
> 
> This probably means that tk wasn't installed properly.
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
> [1] adehabitat_1.8.11 shapefiles_0.6    foreign_0.8-51    tkrplot_0.0-23   
> [5] ade4_1.4-17      
>> 
> 
> On 27 Nov 2012, at 16:42, rpi <distem at rpi.edu> wrote:
> 
>> Els,
>> 
>> i tried to run adehabitat form inside the Gui.app (64 bit) using R 
>> (installed from Homebrew )
>> 
>> .. and i got the same problem you had
>> 
>> i tried to rebuild the  gui.app using Xcode but no lucky .. same crash.
>> 
>> trying to run R from the command line … it is able to load adehabitat.
>> 
>> seems to me a GUI.app problem 
>> 
>> ..  can you check if your adehabitat code runs fine starting R from command line ?
>> 
>> thanks,
>> 
>> Massimo.
>> 
>> 
>> Il giorno 27/nov/2012, alle ore 09:34, Els Ducheyne <educheyne at avia-gis.be> ha scritto:
>> 
>>> Dear Massimo
>>> I've just tried and it is still the same problem. Should I put it somewhere for R to find this?
>>> 
>>> Best
>>> Els
>>> 
>>> On 27 Nov 2012, at 15:03, epi <massimodisasha at gmail.com> wrote:
>>> 
>>>> did you tried to install XQuartz ?
>>>> 
>>>> http://xquartz.macosforge.org/landing/
>>>> 
>>>> --Massimo.
>>>> 
>>>> 
>>>> Il giorno 27/nov/2012, alle ore 09:00, Els Ducheyne <educheyne at avia-gis.be> ha scritto:
>>>> 
>>>>> Dear list
>>>>> I am trying to run ENFA for presence only records. I have installed adehabitat v1.18.11 on R2.15.2 on MacOS 10.8.2. I
>>>>> Whilst the library is successfully installed and loaded, it crashed R when I am trying to run other commands after loading the library.
>>>>> Did anyone experience this before? 
>>>>> Is it the Tcl/Tk that causes the problem, could I load the package without the Tcl/Tk?
>>>>> I have tested under windows too with same version of adehabitat and R and there it works fine. Unfortunately, I will use the package for teaching and some students use MacOS so therefore I would like to find a solution.
>>>>> 
>>>>>> sessionInfo()
>>>>> R version 2.15.2 (2012-10-26)
>>>>> Platform: i386-apple-darwin9.8.0/i386 (32 bit)
>>>>> 
>>>>> locale
>>>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>>>> 
>>>>> attached base packages:
>>>>> stats graphics grDevices utils datasets methods base
>>>>>> library(adehabitat)
>>>>> Loading required package: ade4
>>>>> Attaching package: 'ade4'
>>>>> The following objects are masked from 'package:base'
>>>>> within
>>>>> loading required package:tkrplot
>>>>> loading required package: tcltk
>>>>> Loading Tcl/Tk interface
>>>>>> sessionInfo()
>>>>> 
>>>>> After the second sessionInfo() R does not respond, nor with any other command. The only option is Force quit and reboot.
>>>>> 
>>>>> Thanks for any help
>>>>> Els
>>>>> 
>>>>> _______________________________________________
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>>>>> R-sig-Geo at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>> 
>>> 
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>> 
> 
> 
> 