[AniMov] problem with instalation of adehabitat

Anne Ghisla a.ghisla at gmail.com
Wed Oct 6 23:22:09 CEST 2010


sorry,  I forgot the quotes. The correct code is:

import rpy2 as rpy2
import rpy2.robjects as ro
print ro.r.require("adehabitat")

If the module can't load ade4 package, please then open a ticket on the trac.
It is also worth mentioning the rpy2 bugtracker, the actual place
where to report rpy2 problems, as I don't have the skills to fix them
myself. Sadly I saw this error only occurring on Windows. In the
Animov mailing list archives you can find several mails about it, and
the related links.

hope this shades some light on the problem.

ps. it is considered not polite to hijack threads [0,1] - the mail you
posted in the OpenSUSE thread is not related to that discussion. If I
take longer to answer, is that this week I'm attending a course and
come back online at late night. In the very need of an answer, please
respond to the same thread. Thanks :)

regards
Anne

[0] http://www.catb.org/esr/faqs/smart-questions.html
[1] http://schools-at-the-centre.ning.com/forum/topics/online-discussion-netiquette
On Sun, Oct 3, 2010 at 6:13 PM,  <blackdaysvk at gmail.com> wrote:
> Plugin ManageR was uninstalled and then I wrote command import rpy2 as rpy2,
> answer:
>
> import rpy2 as rpy2
>>>>
>>>> import rpy2 as rpy2
>>>> import rpy2.robjects as ro
>>>> print ro.r.require(adehabitat)
>
> Traceback (most recent call last):
>  File "<input>", line 1, in <module>
> NameError: name 'adehabitat' is not defined
>
>
>
>
>
> ----- Original Message ----- From: "Anne Ghisla" <a.ghisla at gmail.com>
> To: <blackdaysvk at gmail.com>
> Cc: "Animal Movement" <animov at faunalia.it>
> Sent: Sunday, October 03, 2010 5:17 PM
> Subject: Re: [AniMov] problem with instalation of adehabitat
>
>
> On Sun, Oct 3, 2010 at 4:55 PM,  <blackdaysvk at gmail.com> claviota:
>>
>> Ok,
>>
>> I wrote the command: require(adehabitat), then I obtained message: >
>> require(adehabitat)
>> Loading required package: adehabitat
>> Loading required package: ade4
>>
>> Attaching package: 'ade4'
>>
>> The following object(s) are masked from 'package:base':
>>
>> within
>>
>> This package requires ade4 to be installed
>>
>> Type:
>> demo(rastermaps) for demonstration of raster map analysis
>> demo(homerange) for demonstration of home-range estimation
>> demo(managltraj) for demonstration of animals trajectory management
>> demo(analysisltraj) for demonstration of animals trajectory analysis
>> demo(nichehs) for demonstration of niche/habitat selection analysis
>>
>> Loading required package: gpclib
>> General Polygon Clipper Library for R (version 1.5-1)
>> Type 'class ? gpc.poly' for help
>
> great, so it works in R.
>
>>
>> Then I wrote command to the Python console:
>>
>> import rpy2 as rpy2
>>
>> answer from Python:
>>
>> Pri súšťaní kódu v Pythone nastala chyba:
>>
>> Traceback (most recent call last):
>> File "C:\Users\Vlado/.qgis/python/plugins\manageR\manageR.py", line 2110,
>> in commandOutput
>> self.appendText(unicode(output))
>> File "C:\Users\Vlado/.qgis/python/plugins\manageR\manageR.py", line 2057,
>> in appendText
>> cursor = self.textCursor()
>> RuntimeError: underlying C/C++ object has been deleted
>
> Puzzling. Why is manageR interfering? Try to disable it via Manage
> Plugins and rerun the command.
> There are already a lot of variables in the problem...
>
> thanks for testing,
>
> regards,
> Anne
>
>> Verzia Pythonu:
>> 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)]
>> QGIS version:
>> 1.5.0-Tethys Tethys, 13923M
>>
>> Cesta k Pythonu: ['C:/PROGRA~1/QUANTU~1/apps/qgis/./python',
>> 'C:\\Users\\Vlado/.qgis/python', 'C:\\Users\\Vlado/.qgis/python/plugins',
>> 'C:/PROGRA~1/QUANTU~1/apps/qgis/./python/plugins',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\gdal-16\\pymod', 'C:\\Program
>> Files\\Quantum
>> GIS Tethys', 'C:\\PROGRA~1\\QUANTU~1\\bin\\python25.zip',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\DLLs',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\plat-win',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\lib-tk',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\qgis\\bin',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\win32',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\win32\\lib',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\Pythonwin',
>>
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode',
>> u'C:/Users/Vlado/.qgis//python/plugins',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\qgis\\python\\plugins\\fTools\\tools',
>> '/usr/share/qgis/python', '.']
>>
>> command import rpy2.robjects as ro
>>
>> answer:
>>
>> Pri súšťaní kódu v Pythone nastala chyba:
>>
>> Traceback (most recent call last):
>> File "C:\Users\Vlado/.qgis/python/plugins\manageR\manageR.py", line 2110,
>> in commandOutput
>> self.appendText(unicode(output))
>> File "C:\Users\Vlado/.qgis/python/plugins\manageR\manageR.py", line 2057,
>> in appendText
>> cursor = self.textCursor()
>> RuntimeError: underlying C/C++ object has been deleted
>>
>> Verzia Pythonu:
>> 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)]
>>
>>
>> QGIS version:
>> 1.5.0-Tethys Tethys, 13923M
>>
>> Cesta k Pythonu: ['C:/PROGRA~1/QUANTU~1/apps/qgis/./python',
>> 'C:\\Users\\Vlado/.qgis/python', 'C:\\Users\\Vlado/.qgis/python/plugins',
>> 'C:/PROGRA~1/QUANTU~1/apps/qgis/./python/plugins',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\gdal-16\\pymod', 'C:\\Program
>> Files\\Quantum
>> GIS Tethys', 'C:\\PROGRA~1\\QUANTU~1\\bin\\python25.zip',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\DLLs',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\plat-win',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\lib-tk',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\qgis\\bin',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\win32',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\win32\\lib',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\Pythonwin',
>>
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode',
>> u'C:/Users/Vlado/.qgis//python/plugins',
>> 'C:\\PROGRA~1\\QUANTU~1\\apps\\qgis\\python\\plugins\\fTools\\tools',
>> '/usr/share/qgis/python', '.']
>>
>>
>> Vlado
>>
>> ----- Original Message ----- From: "Anne Ghisla" <a.ghisla at gmail.com>
>> To: <blackdaysvk at gmail.com>
>> Cc: "Animal Movement" <animov at faunalia.it>
>> Sent: Sunday, October 03, 2010 4:14 PM
>> Subject: Re: [AniMov] problem with instalation of adehabitat
>>
>>
>>> On Sun, Oct 3, 2010 at 3:50 PM, <blackdaysvk at gmail.com> wrote:
>>>>
>>>> Hi Anne,
>>>>
>>>> sorry, but I forgot send information about my system... System:
>>>>
>>>> - Windows Vista - OS
>>>>>
>>>>> - QGIS version - 1.5.0 Tethys
>>>>> - how did you install QGIS - standalone installer
>>>>> - R version - 2.11.1
>>>>> - adehabitat version: see - I dont know... But I install adehabitat
>>>>> from
>>>>> Slovakia server via R - install packages
>>>>> - Python version - I installed Python 3.1.2 program
>>>>
>>>> Please help me with this installation, I use Arcview 3 with Animal
>>>> Movement
>>>> extension for analyses, but I prefer opensource solution ... :-)
>>>
>>> R 2.11 and Python 3. are untested so far; actually, the standalone
>>> QGIS carries its own Python so there is no problem on this side.
>>>
>>> you can test this code into R console:
>>>
>>> require(adehabitat)
>>>
>>> and see if it loads the package correctly.
>>>
>>> If it doesn't, it's a R/adehabitat issue. Please post details (see
>>> sessionInfo() function )
>>> If R loads adehabitat, pass to QGIS Python Console (last item in
>>> Plugins menu) and type:
>>>
>>> import rpy2 as rpy2
>>> import rpy2.robjects as ro
>>> print ro.r.require('adehabitat')
>>>
>>> let us know if there are any errors there. If so, please post the
>>> error messages.
>>>
>>> regards,
>>> Anne
>>>
>>>> Best wishes,
>>>>
>>>> Vlado Nemcek
>>>>
>>>>
>>>> ----- Original Message ----- From: "Anne Ghisla" <a.ghisla at gmail.com>
>>>> To: <blackdaysvk at gmail.com>; "Animal Movement" <animov at faunalia.it>
>>>> Sent: Sunday, October 03, 2010 12:15 PM
>>>> Subject: Re: [AniMov] problem with instalation of adehabitat
>>>>
>>>>
>>>>> On Sat, 2010-10-02 at 17:06 +0200, blackdaysvk at gmail.com wrote:
>>>>>>
>>>>>> Dear users of quantum GIS,
>>>>>>
>>>>>> I have a problem with installation of adehabitat on my computer. I
>>>>>> download and install animove and R to the PC. But when I want
>>>>>> calculate the MCP or kernel polygon, then my PC put up the message -
>>>>>>
>>>>>> R error (please consult its documentation) is:
>>>>>>
>>>>>> Error in function (x, method = c("mcp", "href", "lscv", "hadj",
>>>>>> "clusthr", :
>>>>>>
>>>>>> This procedure requires adehabitat to be installed
>>>>>>
>>>>>>
>>>>>>
>>>>>> But I have R and adehabitat - I install and download adehabitat from
>>>>>> server with R... Please can you write me detailed installation of
>>>>>> adehabitat - step by step...
>>>>>
>>>>> Hi Vlado,
>>>>>
>>>>> we would help you right now but you didn't tell us:
>>>>> - your operating system
>>>>> - QGIS version
>>>>> - how did you install QGIS (source, binary package, OSGeo4W,
>>>>> standalone)
>>>>> - R version
>>>>> - adehabitat version: see
>>>>> http://lists.faunalia.it/pipermail/animov/2010-September/000674.html
>>>>> - Python version
>>>>>
>>>>> that is important, each platform has its own answers:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> http://www.qgis.org/wiki/HomeRange_plugin#Installation_requirements_and_tested_platforms
>>>>>
>>>>> There are plenty of installation notes in the wiki and in the archives
>>>>> of this mailing list. Of course if your problem is not covered, send
>>>>> the
>>>>> list a mail with the details listed above, or better fill a ticket into
>>>>>
>>>>> https://www.faunalia.it/animove/trac/
>>>>>
>>>>> regards,
>>>>> anne
>>>>> --
>>>>> http://wiki.osgeo.org/wiki/Anne_Ghisla
>>>>
>>>>
>>> --
>>> http://gis.fem-environment.eu/anne-ghisla/
>>
>>
>
>
>
> --
> http://gis.fem-environment.eu/anne-ghisla/
>



-- 
http://gis.fem-environment.eu/anne-ghisla/


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