[R-sig-Geo] Adehabitat crashed R on MacOS 2.15.2
Mathieu Basille
basille at ase-research.org
Tue Nov 27 17:25:31 CET 2012
Dear Els,
I can't really help on the Mac OS issue with tcl/tk since I'm using Linux.
However, as the command line warning tells you, you'd better use
'adehabitatHS' [1] now, instead of the old 'adehabitat', which is no longer
developed (bug fixes are added, but no new methods). I don't think it will
solve your problem, though, but I really recommend to upgrade. Besides, you
might want to have a look at the MADIFA instead of the ENFA. See [2] for
further details.
Best,
Mathieu Basille.
[1] http://cran.r-project.org/web/packages/adehabitatHS/index.html
[2] Calenge, C.; Darmon, G.; Basille, M.; Loison, A. & Jullien, J.-M.
(2008) The factorial decomposition of the Mahalanobis distances in habitat
selection studies. Ecology, 89: 555-566 doi 10.1890/06-1750.1
Le 27/11/2012 10:57, Els Ducheyne a écrit :
> 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
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-Geo mailing list
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>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>
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>>
>
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--
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Mathieu Basille, PhD
~$ locate --details
University of Florida \\
Fort Lauderdale Research and Education Center
(+1) 954-577-6314
http://ase-research.org/basille
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« Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. »
-- Paul Éluard
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