[R-sig-Geo] rPython installation problem
Javier Martínez López
javier.martinez at um.es
Fri Feb 28 09:08:40 CET 2014
I will try it! Thanks! Cheers, Javier
Quoting Jonathan Greenberg <jgrn at illinois.edu>:
> Javier:
>
> I guess my first suggestion is to try out my rasterEngine function in
> the spatial.tools package -- it is designed to perform parallel
> processing of raster images entirely within R. I have a tutorial
> here:
>
> http://www.geog.illinois.edu/~jgrn/software-and-datasets/rasterengine-tutorial/
>
> You might want to look at the more complex randomForest example. I
> have a bunch of updates to rasterEngine that haven't made it into the
> tutorial yet, that might also be useful, including having > 1 output
> file. The help for rasterEngine has some of these updates.
>
> Let me know how it goes!
>
> --j
>
> On Thu, Feb 27, 2014 at 11:55 AM, Javier Martínez López
> <javier.martinez at um.es> wrote:
>> Dear Jonathan,
>>
>> That is a nice question! I need to repetitively apply the Mahalanobis
>> distance to a stack of eleven raster maps comprising very large areas in
>> order to compare the similarity of different areas (see the eHabitat R
>> library [1] which is used for the DOPA explorer [2]). I am just trying to
>> speed up the processing by hosting the maps in GRASS GIS, using the Pygrass
>> module for importing them as numpy arrays, using a parallel processing
>> script for calculating the mahalanobis distance which also benefits from MKL
>> enhancements, and eventually continue some processing in R, if I find a fast
>> way, in combination with the existent eHabitat library, or directly
>> producing the resulting tiff and csv files... Does it make sense to you at
>> all? I plan to upload a first working version of the code to github [3] this
>> or next week, as soon as I solve some errors.
>>
>> Thank you for your interest!
>>
>> Cheers,
>>
>> Javier
>>
>>
>> [1](https://github.com/javimarlop/eHabitat)
>> [2](http://ehabitat-wps.jrc.ec.europa.eu/dopa_explorer/)
>> [3](https://github.com/javimarlop/eHab_grasspy)
>>
>>
>> Quoting Jonathan Greenberg <jgrn at illinois.edu>:
>>
>>> Javier:
>>>
>>> If you don't mind me asking -- when you said "I need to combine R and
>>> Python to process large raster files" is there a particular function
>>> in python you need to apply to the rasters, or are you specifically
>>> referring to some benefit in python of working with arbitrarily large
>>> raster files?
>>>
>>> --j
>>>
>>> On Thu, Feb 27, 2014 at 4:24 AM, Javier Martínez López
>>> <javier.martinez at um.es> wrote:
>>>>
>>>> Dear Roger,
>>>>
>>>> your help is very much appreciated! When I try to locate libpython2.7 is
>>>> does not come up, but the file is present in my $HOME/anaconda/lib.
>>>> Systemwide only python 2.6 is present due to a conflict with 2.7 in
>>>> CentOS.
>>>>
>>>> I tried something like:
>>>>
>>>> R CMD INSTALL rPython_0.0-4.tar.gz
>>>> --configure-args='LD_LIBRARY_PATH=/home/majavie/anaconda/lib/'
>>>>
>>>> and
>>>>
>>>> R CMD INSTALL rPython_0.0-4.tar.gz
>>>>
>>>> --configure-args='PYTHONLIBFILE=/home/majavie/anaconda/lib/libpython2.7.so'
>>>>
>>>> but still getting the same error, and when try:
>>>>
>>>> export LD_LIBRARY_PATH=/home/majavie/anaconda/lib/:$PATH
>>>>
>>>> then I cannot even start R!... so, I might try to install a local version
>>>> of
>>>> R from source, just to try if this one works!
>>>>
>>>> Thank you again and cheers,
>>>>
>>>> Javier
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Quoting Roger Bivand <Roger.Bivand at nhh.no>:
>>>>
>>>>> On Wed, 26 Feb 2014, Javier Martínez López wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I need to combine R and Python to process large raster files and I
>>>>>> would
>>>>>> like to use the "rPython" library for direct transformation of the data
>>>>>> objects created using those environments. However, when I try to
>>>>>> install it,
>>>>>> it produces the following error related to the python libraries (see
>>>>>> below).
>>>>>> I just installed the Anaconda python distribution locally (no admin
>>>>>> rights)
>>>>>> in my home folder (Linux CentOS), which might be causing the problem,
>>>>>> but I
>>>>>> do not know how to deal with this issue, so any help is welcome!
>>>>>
>>>>>
>>>>>
>>>>> This is not a specific question for this list, but there may be interest
>>>>> in this fresh and as yet unproven package. What does:
>>>>>
>>>>> locate libpython2.7
>>>>>
>>>>> say on your system? On current Fedora, I see:
>>>>>
>>>>> /usr/lib64/libpython2.7.so
>>>>>
>>>>> with:
>>>>>
>>>>> $ python --version
>>>>> Python 2.7.5
>>>>>
>>>>> as per the advice in:
>>>>>
>>>>> http://cran.r-project.org/web/packages/rPython/INSTALL
>>>>>
>>>>> Your system should provide python, but may have only the python, not
>>>>> both
>>>>> that and the python-devel RPMs installed. If you have installed
>>>>> libpython2.7.so locally, you may need to adjust your LD_LIBRARY_PATH so
>>>>> that
>>>>> the library is visible. If you can get your sysadmin to add the
>>>>> python-devel
>>>>> RPM, life may be easier. Also, write to the package maintainer
>>>>> suggesting
>>>>> that libpython be checked in configure.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> Roger
>>>>>
>>>>>>
>>>>>> Thank you very much and cheers,
>>>>>>
>>>>>> Javier
>>>>>>
>>>>>>> install.packages('rPython')
>>>>>>
>>>>>>
>>>>>> Installing package into
>>>>>> /home/majavie/R/x86_64-redhat-linux-gnu-library/3.0
>>>>>> (as lib is unspecified)
>>>>>> trying URL
>>>>>>
>>>>>> 'http://cran.mirror.garr.it/mirrors/CRAN/src/contrib/rPython_0.0-4.tar.gz'
>>>>>> Content type 'text/plain' length 37034 bytes (36 Kb)
>>>>>> opened URL
>>>>>> ==================================================
>>>>>> downloaded 36 Kb
>>>>>>
>>>>>> * installing *source* package rPython ...
>>>>>> ** package rPython successfully unpacked and MD5 sums checked
>>>>>> a specific python version to use was not provided
>>>>>> defaulting to the standard python in the system
>>>>>> checking for gcc... gcc -m64 -std=gnu99
>>>>>> checking whether the C compiler works... yes
>>>>>> checking for C compiler default output file name... a.out
>>>>>> checking for suffix of executables...
>>>>>> checking whether we are cross compiling... no
>>>>>> checking for suffix of object files... o
>>>>>> checking whether we are using the GNU C compiler... yes
>>>>>> checking whether gcc -m64 -std=gnu99 accepts -g... yes
>>>>>> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none
>>>>>> needed
>>>>>> configure: creating ./config.status
>>>>>> config.status: creating src/Makevars
>>>>>> ** libs
>>>>>> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include
>>>>>> -I/home/majavie/anaconda/include/python2.7
>>>>>> -I/home/majavie/anaconda/include/python2.7 -D
>>>>>> PYTHONLIBFILE=libpython2.7.so -fpic -O2 -g -pipe -Wall
>>>>>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>>>>>> --param=ssp-buffer-size=4 -m64 -mtune=generic -c pycall.c -o pycall.o
>>>>>> gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o rPython.so pycall.o
>>>>>> -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
>>>>>> -L/usr/lib64/R/lib -lR
>>>>>> /usr/bin/ld: cannot find -lpython2.7
>>>>>> collect2: ld returned 1 exit status
>>>>>> make: *** [rPython.so] Error 1
>>>>>> ERROR: compilation failed for package rPython
>>>>>> * removing /home/majavie/R/x86_64-redhat-linux-gnu-library/3.0/rPython
>>>>>> * restoring previous
>>>>>> /home/majavie/R/x86_64-redhat-linux-gnu-library/3.0/rPython
>>>>>>
>>>>>> The downloaded source packages are in
>>>>>> /tmp/RtmpfPBtPF/downloaded_packages
>>>>>> Warning message:
>>>>>> In install.packages("rPython") :
>>>>>> installation of package rPython had non-zero exit status
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-Geo mailing list
>>>>>> R-sig-Geo at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Roger Bivand
>>>>> Department of Economics, Norwegian School of Economics,
>>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>>> voice: +47 55 95 93 55; fax +47 55 95 95 43
>>>>> e-mail: Roger.Bivand at nhh.no
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Javier Martínez-López
>>>> Ecology and Hydrology Department
>>>> Biology Faculty
>>>> University of Murcia
>>>> Espinardo E-30100
>>>> Murcia - Spain
>>>>
>>>> E-mail: javier.martinez at um.es
>>>> web: http://webs.um.es/javier.martinez
>>>>
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>>
>>> --
>>> Jonathan A. Greenberg, PhD
>>> Assistant Professor
>>> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
>>> Department of Geography and Geographic Information Science
>>> University of Illinois at Urbana-Champaign
>>> 259 Computing Applications Building, MC-150
>>> 605 East Springfield Avenue
>>> Champaign, IL 61820-6371
>>> Phone: 217-300-1924
>>> http://www.geog.illinois.edu/~jgrn/
>>> AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
>>>
>>
>>
>>
>> --
>> Javier Martínez-López
>> Ecology and Hydrology Department
>> Biology Faculty
>> University of Murcia
>> Espinardo E-30100
>> Murcia - Spain
>>
>> E-mail: javier.martinez at um.es
>> web: http://webs.um.es/javier.martinez
>>
>
>
>
> --
> Jonathan A. Greenberg, PhD
> Assistant Professor
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Department of Geography and Geographic Information Science
> University of Illinois at Urbana-Champaign
> 259 Computing Applications Building, MC-150
> 605 East Springfield Avenue
> Champaign, IL 61820-6371
> Phone: 217-300-1924
> http://www.geog.illinois.edu/~jgrn/
> AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
>
--
Javier Martínez-López
Ecology and Hydrology Department
Biology Faculty
University of Murcia
Espinardo E-30100
Murcia - Spain
E-mail: javier.martinez at um.es
web: http://webs.um.es/javier.martinez
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