On 14/01/10 04:04, Guozhu.Wen wrote:
Hi, I use rpy2 2.0.6, I encountered some errors when I
load('mypackage') within rpy2 by r.source(rfile). Woudl you help me?
The environment variable R_LD_LIBRARY_PATH defined in my
$RHOME/etc/ldpaths is :
${R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/local/lib:}
I added the path "/usr/local/lib" because when I use
library('mypackage') in the R console, my R package must link some
*.so located in "/usr/local/lib". Now It worked in R console, but not
in rpy2. When I load "mypackage" in rpy2, it raise Exception telling
me cannot find some *.so which actually localed in "/usr/local/lib".
So I think maybe rpy2 don't use the configuration defined in
$RHOME/etc/ldpaths.
I think that there are two possible reasons for this, and two ways to
solve it.
- $RHOME/etc/ldpaths is ignored when an embedded R is started with the
option "--vanilla" (and this is what rpy2 has by default - may be not
such a good thing). Try if the following helps:
#do this *before* your import anything from rpy2
import rpy2.rinterface as ri
ri.set_initoptions(('--quiet', '--no-save'))
# now import whatever from rpy2 as usual
Documentation for that at:
http://rpy.sourceforge.net/rpy2/doc-2.1/html/rinterface.html#initialization
- $RHOME/etc/ldpaths is only used by the R console (and rpy/rpy2 have
use an embedded R that can't know about it). In that case, you should
define your LD_LIBRARY_PATH *before* starting python.
For example:
source $RHOME/etc/ldpaths
python
L.
PS: rpy2-2.0.8 is out, and 2.1.0 is almost there.
Would you plan to add R's ldpaths in rpy2? Thanks.
--
Guozhu. Wen
mail: guozhu...@gmail.com <mailto:guozhu...@gmail.com>
douban: http://www.douban.com/people/wentrue/
blog: http://www.wentrue.net/blog/
twitter: https://twitter.com/wentrue
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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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