[R] Rmpi installation problems

Jos Elkink jos at yuliuskitchen.com
Fri Dec 2 10:19:50 CET 2011

Hi all,

I am trying to install the Rmpi package in R and, while the installation
itself works, it breaks down when trying to load the library. I think it
has something to do with shared vs static loading of helper libraries,
or the order in which shared libraries are loaded, but I am not sure.

R version: 2.14.0
Linux version: Gentoo, i686-pc-linux-gnu (32-bit)
GCC version: 4.5.3 (Gentoo 4.5.3-r1 p1.0)
OpenMPI version: 1.5.4

Output from R CMD INSTALL . in Rmpi source directory:

* installing to library ‘/home/jos/R/i686-pc-linux-gnu-library/2.14’
* installing *source* package ‘Rmpi’ ...
checking for gcc... i686-pc-linux-gnu-gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether i686-pc-linux-gnu-gcc -std=gnu99 accepts -g... yes
checking for i686-pc-linux-gnu-gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** Creating default NAMESPACE file
** libs
make: Nothing to be done for `all'.
installing to /home/jos/R/i686-pc-linux-gnu-library/2.14/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
/usr/lib/R/bin/exec/R: symbol lookup error: /usr/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol: mca_base_param_reg_int
ERROR: loading failed
* removing ‘/home/jos/R/i686-pc-linux-gnu-library/2.14/Rmpi’

Any help would be greatly appreciated!


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