Prepare the environment
Before configure and compile R source code, I did the following updating of CentOS in order to support R capabilities by installing these packages:
[sourcecode language=""]
libtiff libtiff-devel
libpng libpng-devel
libjpeg libjpeg-devel
cairo cairo-devel
libX11 libX11-devel
libXt ibXt-devel
readline readline-devel
[/sourcecode]
and in order to produce the pdf version of the R-manual, I also installed all search results of
[sourcecode language="bash"]
yum search tetex except tetex-doc
[/sourcecode]
The RPy2 requires that you enabling R-shlib when you install R package. To do so you can build your own R package from source code.
1. donwload R source code: from http://cran.r-project.org/src/base/R-2/
[sourcecode language="bash"]
./configure --enable-R-shlib
[/sourcecode]
Here are my configuration results:
[sourcecode language=""]
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -std=gnu99 -g -O2
Fortran 77 compiler: gfortran -g -O2
C++ compiler: g++ -g -O2
Fortran 90/95 compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: readline
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
Options enabled: shared R library, shared BLAS, R profiling, Java
Recommended packages: yes
configure: WARNING: inconsolata.sty not found: PDF vignettes and package manuals will not be rendered optimally (as for this warning, specific fonts is not found.)
[/sourcecode]
2. Continue the following steps to complete installing R
[sourcecode language="bash"]
make
make check
make install
[/sourcecode]
some other errors you may encounter:
[sourcecode language=""]
configure: error: no acceptable C compiler found in $PATH --install gcc gcc-c++
configure: error: No F77 compiler found --install compat-gcc-34-g77 gcc-gfortran
configure: error: --with-x=yes (default) and X11 headers/libs are not available --install libXt-devel
[/sourcecode]
3. Install RPy2:
[sourcecode language="bash"]
/opt/python2.7/bin/easy_install rpy2
[/sourcecode]
You could use python2.7 if you have made a symbolic link in /usr/bin/python2.7 by
[sourcecode language="bash"]
ln -s /opt/python2.7/bin/python /usr/bin/python2.7
[/sourcecode]
** I had encountered a problem showing that lpython2.7 cannot be found, to solve this problem I created a symbolic link
[sourcecode language="bash"]
cd /usr/lib64
ln -s /opt/python2.7/lib/libpython2.7.so.1.0 libpython2.7.so.1.0
ln -s libpython2.7.so.1.0 libpython2.7.so
[/sourcecode]
If you have more than one R package installed on your system you may encounter some errors, like "rpy2.rinterface.baseenv.get("show") show not found" when you try to use the rpy2 package.
solution:
configure the /etc/ld.so.conf.d/R-x86_64.conf file, create the file if the file does not exist Put the path of the R package whic you used to build your rpy2 into this file. Mine is /usr/local/lib64/R/lib.
Run /sbin/ldconfig
You may solve the problem by now.
3. install libraries in R
[sourcecode language="bash"]
sudo R
install.packages('package_name')
[/sourcecode]
pay attention to the location of the installation of new packages "/usr/local/lib64/R/library/e1071/libs"
Sometimes when you install a package and it requires at least certain version of the R, you could download the source code of the package and do the following installation:
[sourcecode language="bash"]
install.packages("/path/to/the/packages/source/file", repos=NULL, type="source")
[/sourcecode]
How to find the procss using specific port and kill it
I am using PyDev in Eclipse on CentOS. Eclipse crashes sometimes and leaves python still using port 8000. Before you can restart the development server, you have to kill the previous process, to do so,
$ sudo /usr/sbin/lsof -w -n -i tcp:8000
which will list the process pid using port 8000
COMMAND PID USER FD TYPE DEVICE SIZE NODE NAME
python2.7 6211 htang 3u IPv4 157102 TCP 127.0.0.1:irdmi (LISTEN)
$ sudo kill 6211
which will kill process 6211.
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