Hello,
I want to try rpy on my linux CentOS5.4 x86_64 operating system.
I try to compile R with -shlibs option in configure command but it did not
work. I had the same error as this thread :
https://stat.ethz.ch/pipermail/r-sig-fedora/2011-March/000173.html
So I decided to use RPMs like suggested in this previous thred (...see the
solution in the previous link)
Here is what I did :
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/xdg-utils-1.0.2-4.el5.noarch.rpm
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/R-core-2.13.1-4.el5.x86_64.rpm
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/R-devel-2.13.1-4.el5.x86_64.rpm
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/libRmath-2.13.1-4.el5.x86_64.rpm
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/libRmath-devel-2.13.1-4.el5.x86_64.rpm
wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/R-2.13.1-4.el5.x86_64.rpm
cp xdg-utils-1.0.2-4.el5.noarch.rpm /tmp
cp R-core-2.13.1-4.el5.x86_64.rpm /tmp
cp R-devel-2.13.1-4.el5.x86_64.rpm /tmp
cp libRmath-2.13.1-4.el5.x86_64.rpm /tmp
cp libRmath-devel-2.13.1-4.el5.x86_64.rpm /tmp
cp R-2.13.1-4.el5.x86_64.rpm /tmp
yum install bzip2-devel pcre-devel tcl-devel tetex-latex tk-devel
rpm -Uvh xdg-utils-1.0.2-4.el5.noarch.rpm
rpm -Uvh R-core-2.13.1-4.el5.x86_64.rpm
rpm -Uvh R-devel-2.13.1-4.el5.x86_64.rpm
rpm -Uvh libRmath-2.13.1-4.el5.x86_64.rpm
rpm -Uvh libRmath-devel-2.13.1-4.el5.x86_64.rpm
rpm -Uvh R-2.13.1-4.el5.x86_64.rpm
cd /tmp/
export
LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64:/lib64:/usr/lib64:/usr/local/lib64:/usr/lib/:/usr/local/lib/
export R_HOME=/usr/lib64/R/
export RHOME=/usr/lib64/R/
cp /usr/lib64/R/lib/libR.so /usr/lib64/R/bin
ln -s /usr/lib64/R/lib/libR.so /lib64/libR.so
ln -s /usr/lib64/R/lib/libRblas.so /lib64/libRblas.so
ln -s /usr/lib64/R/lib/libRlapack.so /lib64/libRlapack.so
ldconfig
sh install_rpy.sh
My install_rpy.sh is just :
tar -xzf rpy.tar.gz
cd rpy
python setup.py install
But with all these things install still does not work. Right now, I do not
have the error on libR.so but I still have errors. It is also a gcc error
(due to Rlapack ??) :
# sh install_rpy.sh
RHOMES= []
DEBUG= False
Setting RHOMES to ['/usr/lib64/R/']
### Using R verion 2.13.1 installed at /usr/lib64/R/ ###
RHOME= /usr/lib64/R/
copying src/rpymodule.c -> src/rpymodule2131.c
copying src/R_eval.c -> src/R_eval2131.c
copying src/io.c -> src/io2131.c
running install
running build
running build_py
running build_ext
building '_rpy2131' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DRPY_SHNAME=_rpy2131 -DINIT_RPY=init_rpy2131
-UPRE_2_2 -UWITH_NUMERIC -I/usr/lib64/R/include -Isrc
-I/usr/share/R/include -I/usr/local/include/python2.6 -c
src/rpymodule2131.c -o build/temp.linux-x86_64-2.6/src/rpymodule2131.o
-shared WARNING: ignoring environment value of R_HOME
-L/usr/lib64/R/lib -lRlapack
gcc: WARNING: ignoring environment value of R_HOME
-L/usr/lib64/R/lib -lRlapack: No such file or directory
In file included from /usr/lib64/R/include/Rdefines.h:29,
from src/RPy.h:52,
from src/rpymodule2131.c:51:
/usr/lib64/R/include/Rinternals.h:657: warning: function declaration isn't
a prototype
In file included from src/RPy.h:64,
from src/rpymodule2131.c:51:
/usr/lib64/R/include/R_ext/Rdynload.h:26: warning: function declaration
isn't a prototype
src/rpymodule2131.c:1565: warning: initialization from incompatible pointer
type
src/rpymodule2131.c:1568: warning: 'intargfunc' is deprecated
src/rpymodule2131.c:1568: warning: initialization from incompatible pointer
type
src/rpymodule2131.c:1569: warning: 'intintargfunc' is deprecated
src/rpymodule2131.c:1569: warning: initialization from incompatible pointer
type
src/rpymodule2131.c:1570: warning: initialization from incompatible pointer
type
error: command 'gcc' failed with exit status 1
More informations :
# lsb_release -a
LSB Version:
:core-3.1-amd64:core-3.1-ia32:core-3.1-noarch:graphics-3.1-amd64:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: CentOS
Description: CentOS release 5.4 (Final)
Release: 5.4
Codename: Final
# uname -a
Linux compute-0-6.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST
2009 x86_64 x86_64 x86_64 GNU/Linux
# ls -l /usr/lib64/R/include/
total 96
-rw-r--r-- 1 root root 415 Aug 9 18:22 Rconfig.h
-rw-r--r-- 1 root root 5620 Aug 9 18:22 Rdefines.h
-rw-r--r-- 1 root root 1976 Aug 9 18:22 Rembedded.h
drwxr-xr-x 2 root root 4096 Nov 3 13:53 R_ext
-rw-r--r-- 1 root root 1959 Aug 9 18:22 R.h
-rw-r--r-- 1 root root 4305 Aug 9 18:22 Rinterface.h
-rw-r--r-- 1 root root 35718 Aug 9 18:22 Rinternals.h
-rw-r--r-- 1 root root 16611 Aug 9 18:22 Rmath.h
-rw-r--r-- 1 root root 473 Aug 9 18:22 Rversion.h
-rw-r--r-- 1 root root 2129 Aug 9 18:22 S.h
# ls -l /usr/lib64/R/bin/
total 3288
-rwxr-xr-x 1 root root 1843 Aug 9 18:22 BATCH
-rwxr-xr-x 1 root root 317 Aug 9 18:22 build
-rwxr-xr-x 1 root root 317 Aug 9 18:22 check
-rwxr-xr-x 1 root root 2127 Aug 9 18:22 COMPILE
-rwxr-xr-x 1 root root 7513 Aug 9 18:22 config
drwxr-xr-x 2 root root 4096 Nov 3 13:53 exec
-rwxr-xr-x 1 root root 3627 Aug 9 18:22 f77_f2c
-rwxr-xr-x 1 root root 823 Aug 9 18:22 INSTALL
-rwxr-xr-x 1 root root 11739 Aug 9 18:22 javareconf
-rwxr-xr-x 1 root root 2950688 Nov 3 13:57 libR.so
-rwxr-xr-x 1 root root 274119 Aug 9 18:22 libtool
-rwxr-xr-x 1 root root 1594 Aug 9 18:22 LINK
-rwxr-xr-x 1 root root 3494 Aug 9 18:22 mkinstalldirs
-rwxr-xr-x 1 root root 413 Aug 9 18:22 pager
-rwxr-xr-x 1 root root 8504 Aug 9 18:22 R
-rwxr-xr-x 1 root root 1336 Aug 9 18:22 Rcmd
-rwxr-xr-x 1 root root 316 Aug 9 18:22 Rd2dvi
-rwxr-xr-x 1 root root 359 Aug 9 18:22 Rdconv
-rwxr-xr-x 1 root root 258 Aug 9 18:22 Rdiff
-rwxr-xr-x 1 root root 158 Aug 9 18:22 REMOVE
-rwxr-xr-x 1 root root 310 Aug 9 18:22 Rprof
-rwxr-xr-x 1 root root 8656 Aug 9 18:22 Rscript
-rwxr-xr-x 1 root root 4133 Aug 9 18:22 rtags
-rwxr-xr-x 1 root root 155 Aug 9 18:22 SHLIB
-rwxr-xr-x 1 root root 114 Aug 9 18:22 Stangle
-rwxr-xr-x 1 root root 184 Aug 9 18:22 Sweave
# ls -l /usr/lib64/R/lib/
total 4508
-rwxr-xr-x 1 root root 177176 Aug 9 18:22 libRblas.so
-rwxr-xr-x 1 root root 1470264 Aug 9 18:22 libRlapack.so
-rwxr-xr-x 1 root root 2950688 Aug 9 18:22 libR.so
Any help would be greatly appreciated.
-Regards,
Rem.
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