rPython installation problem
On Wed, 26 Feb 2014, Javier Mart?nez L?pez 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
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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