[R-sig-Geo] rPython installation problem
Javier Martínez López
javier.martinez at um.es
Thu Feb 27 18:55:32 CET 2014
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
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