On 2 September 2008 at 18:26, Robert Nuske wrote:
| > I may have seen that one problem mentioned earlier to the list.
| me to, but can't find it now
|
| > The location of R's include files is seemingly a bit too exotic for the
| > disutils script.
| they were placed there by the debian package
Yes, as we were once asked / forced to place architecture-independent files
below /usr/share/
| > The setup.py script expects them to be in ${RHOME}/include
| > (RHOME being the outcome of running 'R RHOME').
|
| by googeling R_INCLUDE_DIR I found that it is not recommended to rely on
| ${RHOME}/include
|
| eg.
|
http://www.nabble.com/Bug-354775%3A-r-base-core%3A-R-CMD-config-doesn%27t-reflect-new-file-locations-tp3175446p3175720.html
It works always everywhere but alas not on Debian.
| > There is currently no other way around that than either
| > - edit setup.py
| > - copy or link the headers.
|
| one way to get the include dirs
| R CMD echo $R_INCLUDE_DIR
For rpy (v1) it works out-of-the-box on all Debian systems. But as I recall
that may have taken Greg and myself a few iterations over setup.py.
I'm sure we can achieve the same for rpy v2, I just haven't gotten to it yet.
| but the recommed way of finding the include dirs seems to be:
| R CMD config --cppflags
|
| on my system this returns
| -I/usr/share/R/include -I/usr/share/R/include
|
| but I can't use it with get_rconfig, since get_rconfig checks for -l/-L and
| raises an ecxecption otherwise, more or less
|
|
| If I hardcode the include dir in setup.py it finds the headers, but stops
| with:
|
| [EMAIL PROTECTED]:/usr/local/src/rpy_nextgen$ python setup.py install
| running install
| running build
| running build_py
| running build_ext
| building 'rpy2.rinterface.rinterface' extension
| gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
| build/temp.linux-i686-2.5/rpy/rinterface/array.o
| build/temp.linux-i686-2.5/rpy/rinterface/r_utils.o
| build/temp.linux-i686-2.5/rpy/rinterface/rinterface.o -L/usr/lib/R/lib
-L/usr/lib/R/modules -Wl,-R/usr/lib/R/lib -Wl,-R/usr/lib/R/modules -lR
-lRlapack -lRblas -o
| build/lib.linux-i686-2.5/rpy2/rinterface/rinterface.so -L/usr/lib/R/lib -lR
-llapack -lblas
| /usr/bin/ld: cannot find -lRlapack
| collect2: ld returned 1 exit status
| error: command 'gcc' failed with exit status 1
Similarly, prior to the new gfortran-built liblapack / libblas / libatlas
packages, we used to build R with its copy of Lapack --- hence -lRlapack.
Since last winter, however, we have newer / better lapack libs and no longer
use R's lapack source --- hence now
[EMAIL PROTECTED]:~> R CMD config --ldflags
-L/usr/lib/R/lib -lR
[EMAIL PROTECTED]:~> R CMD config LAPACK_LIBS
-llapack
[EMAIL PROTECTED]:~>
Hth, Dirk
--
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