72.3 Installing RSPython
Then install RSPython in R:
This command, executed as the root user has then installed the
required files into /usr/lib/R/library/RSPython. To
communicate where the files are installed to Python we need to set up
three environment variables (a Debian package would probably set this
up so that these extra environment variables are not required), and
then run Python and try out some RSPython calls:
$ export R_HOME=/usr/lib/R
$ export PYTHONPATH=${R_HOME}/library/RSPython/Python
$ export PYTHONPATH=${PYTHONPATH}:${R_HOME}/library/RSPython/libs
$ export LD_LIBRARY_PATH=${R_HOME}/bin
$ python
Python 2.2.1 (#2, Sep 13 2002, 23:25:07)
[GCC 2.95.4 20011002 (Debian prerelease)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import RS
Initialized R-Python interface package.
>>> RS.call("rnorm", 10)
[-0.65567988872831473, 0.67905969371540564, -1.1444361954473865,
0.81452303045337249, 0.72703311800839554, 0.86401079894005484,
-2.0267500136837922, 1.3879521193129922, -0.59819064121768595,
1.1045450495203162]
>>> RS.call("plot", [1,2,3,4])
>>> RS.call("plot", RS.call("rnorm",10))
>>> ^DIf you get:
$ python
>>> import RS
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/R/library/RSPython/Python/RS.py", line 1, in ?
import RSInternal
ImportError: /usr/lib/atlas/libblas.so.2: undefined symbol: e_wsfe
>>> Then be sure that you don’t have atlas2-base installed:
72.3.1 Installing RPy
For sophisticated plotting using the R package see Chapter ??.
Install python-rpy.
Older approaches did:
Then test it with:
$ python
Python 2.3.1 (#2, Sep 24 2003, 11:39:14)
[GCC 3.3.2 20030908 (Debian prerelease)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rpy import *
>>> l = [r.dchisq(x, 4) for x in r.seq(0, 10, by=0.1)]
>>> r.par(ask=1, ann=0)
{'ask': 0, 'ann': 1}
>>> r.plot(l, type='lines')
Hit <Return> to see next plot:
>>> r.dev_off()
{'null device': 1}
>>> ^DTo install it by hand until rpy debian package is released:
$ cd /tmp
$ wget http://easynews.dl.sourceforge.net/sourceforge/rpy/rpy-0.2.tar.gz
$ tar zxvf rpy-0.2.tar.gz
$ cd rpy-0.2
$ sudo python setup.py install
$ sudo emacs -nw /etc/ld.so.conf
Add the line:
/usr/lib/R/bin
$ sudo ldconfig
$ python
Python 2.2.1 (#2, Sep 7 2002, 15:35:22)
[GCC 2.95.4 20011002 (Debian prerelease)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rpy import *
>>> l = [r.dchisq(x, 4) for x in r.seq(0, 10, by=0.1)]
>>> r.par(ask=1, ann=0)
>>> r.plot(l, type='lines')
>>> ^D
$ cd ..
$ sudo rm -rf rpy-0.2*For earlier versions of rpy I used to get:
$ python
>>> from rpy imprt *
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "rpy.py", line 24, in ?
import _rpy
ImportError: /usr/lib/atlas/libblas.so.2: undefined symbol: e_wsfe
>>> then you needed to remove atlas2-base:
However, more recently this packages is actually required to run R and rpy!
With version 0.3.1 of rpy I get the following (11 Aug 03):
$ python2.2
Python 2.2.3+ (#1, Aug 10 2003, 10:11:23)
[GCC 3.3.1 (Debian)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.2/site-packages/rpy.py", line 24, in ?
import _rpy
ImportError: /usr/lib/python2.2/site-packages/_rpymodule.so:
undefined symbol: jump_now
>>>Also happens for python2.3 (11 Aug 2003).
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