[R-sig-Geo] rPython installation problem

Thu Feb 27 16:41:17 CET 2014

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
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>>
>>
>> --
>> 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
>
>
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-- 
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/
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