[Qgis-developer] Re: [Qgis-user] delimited text-rgdal-HR

John C. Tull john.tull at wildnevada.org
Wed Feb 25 14:13:18 EST 2009 

I think my version that worked was with rpy1, not 2. You should be  
able to do library(rgdal) in R to see if it is loading properly.  
Something like this should show up in the R console:
 > library(rgdal)
Loading required package: sp
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.6.0, released 2008/12/04
Path to GDAL shared files: /Library/Frameworks/GDAL.framework/Versions/ 
1.6/Resources/gdal
Loaded PROJ.4 runtime: Rel. 4.6.1, 21 August 2008
Path to PROJ.4 shared files: (autodetected)

It might be worth trying an older R binary, not 2.8.x. Perhaps the R  
update breaks something.

Cheers,
John


On Feb 25, 2009, at 10:14 AM, Declan Troy wrote:

> Roger that. I reinstalled HR and it caused Qgis to freeze up again  
> necessitating a forced quit. I'm getting practiced at uninstalling  
> this! Here's the error:
>
>
> Couldn't load plugin "HomeRange_plugin" from ['/Applications/ 
> qgis-1.0.0/qgis1.0.0.app/Contents/MacOS/share/qgis/python', '/Users/ 
> declantroy/.qgis//python/plugins', '/Applications/qgis-1.0.0/ 
> qgis1.0.0.app/Contents/MacOS/share/qgis/python/plugins', '/Library/ 
> Frameworks/GDAL.framework/Versions/1.6/Python/site-packages', '/ 
> Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip',  
> '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5', '/ 
> Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat- 
> darwin', '/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/plat-mac', '/Library/Frameworks/Python.framework/Versions/ 
> 2.5/lib/python2.5/plat-mac/lib-scriptpackages', '/Library/Frameworks/ 
> Python.framework/Versions/2.5/lib/python2.5/lib-tk', '/Library/ 
> Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload',  
> '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
> site-packages', '/Users/declantroy/.qgis/python/plugins/fTools/tools']
>
> Traceback (most recent call last):
>   File "", line 2, in
>   File "/Users/declantroy/.qgis//python/plugins/HomeRange_plugin/ 
> __init__.py", line 32, in
>     from plugin import HRPlugin
>   File "/Users/declantroy/.qgis//python/plugins/HomeRange_plugin/ 
> plugin.py", line 108, in
>     import rpy2.robjects as robjects
>   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/rpy2/robjects/__init__.py", line 12, in
>     import rpy2.rinterface as rinterface
>   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
> python2.5/site-packages/rpy2/rinterface/__init__.py", line 6, in
>     R_HOME = os.popen("R RHOME").readlines()
> IOError: [Errno 4] Interrupted system call
>
> Python version:
> 2.5 (r25:51918, Sep 19 2006, 08:49:13)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)]
>
>
> I imagine most versions are hidden in there somewhere but just in  
> case: Qgis 1.0.0; OS X 10.5.6; R 2.8.0.
>
> I suspect that rgdal isn't properly installed but then again, I  
> think that will be a problem yet to come. The near penultimate line  
> references rpy2. Does that indicate it is installed correctly or the  
> source of the problem?
>
> Yeah, I should figure out how to do this directly via adehabitat and  
> ultimately I will. This would be nice to figure out all the same.
>
> Declan
>
>
> On Feb 24, 2009, at 11:50 AM, John C. Tull wrote:
>
>> Well, you might try the plugin again. I'm using a qgis build from  
>> the developer trunk, so things might be unstable because it's  
>> bleeding edge.
>>
>> The weird thing is that one run worked, at least partially. I  
>> noticed that it failed on the kernel methods (or one of them at  
>> least). I've tried a few more times today to no avail. Give it a  
>> try on your end and let me know if it works, what versions of  
>> everything you're using, etc.
>>
>> The alternative is to do the calculations in R with the adehabitat  
>> package (I think that's the one with home range analyses).
>>
>> John
>>
>> On Feb 24, 2009, at 12:12 PM, Declan Troy wrote:
>>
>>> Wow, thanks for the quick response and follow-ups.
>>>
>>> The mention of problem with R 2.8 was most useful as that is what  
>>> I have. Oddly, on my first attempt to install HR all went  
>>> smoothly, no errors, menus appeared and such. It was in trying to  
>>> get some data to test that I discovered the delimited text issue.  
>>> However, at some point during start-up of Qgis errors associated  
>>> with HR appeared and proved rather troublesome (selecting the  
>>> plugin menu to uninstall HR would cause the application to  
>>> freeze). Eventually during a freak error free start I uninstalled  
>>> it. That is when I realized I needed rgdal. I guess that won't be  
>>> the final solution!
>>>
>>> At this point I'll wait for an update of HR rather than risk more  
>>> incompatibilities by stepping backward. This will give me a chance  
>>> to try to figure out installing rgdal. I'm missing something in  
>>> the proper command.
>>>
>>> Thanks again for your help and advice. Hard to believe it but  
>>> there a couple of other newbies after me for advice!
>>>
>>> Declan
>>>
>>>
>>> On Feb 23, 2009, at 2:54 PM, John C. Tull wrote:
>>>
>>>> I'm on my phone. Sorry for brevity.
>>>>
>>>> I think I ended up doing the source install through R. The HR  
>>>> plugin is currently not working with R 2.8. If you need it, grab  
>>>> an older version or wait until it's fixed.
>>>>
>>>> John C. Tull, Ph.D.
>>>> Conservation Director
>>>> Nevada Wilderness Project
>>>> 8550 White Fir St.
>>>> Reno, NV 89523 USA
>>>> 775-746-7851 (office)
>>>> 775-224-2947 (mobile)
>>>> www.wildnevada.org
>>>>
>>>> On Feb 23, 2009, at 15:28, Declan Troy <declan.troy at gmail.com>  
>>>> wrote:
>>>>
>>>>> Hey John,
>>>>>
>>>>> Indeed. I was crawling up the GRASS learning curve and then  
>>>>> along came Qgis which seems to be a gentler way into the GRASS  
>>>>> way of doing things (and even allows access to at least some of  
>>>>> the power of GRASS).
>>>>>
>>>>> Do you have any hints as to how to install rgdal (OS X)? I'm  
>>>>> trying to install the Home Range plugin into Qgis and this seems  
>>>>> to be the primary thing I'm missing. I can get the source  
>>>>> through the R package installer (no binary) or the framework  
>>>>> from  http://www.kyngchaos.com/ but I'm not really sure of what  
>>>>> to do from there. I suspect I can eventually sort it out (I  
>>>>> think rpy2 installed ok) but I get a bit nervous experimenting  
>>>>> in the monitor window. Tips would be welcome!
>>>>>
>>>>> Declan
>>>>>
>>>>>
>>>>> On Feb 20, 2009, at 8:01 PM, John C. Tull wrote:
>>>>>
>>>>>> The devs are quite great (I'm just a user, myself). Stick with  
>>>>>> it and you should be quite productive. I use Qgis and GRASS,  
>>>>>> the latter for heavy crunching of analytical maps. I'm quite  
>>>>>> pleased with both.
>>>>>>
>>>>>> John
>>>>>>
>>>>>>
>>
>

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