Hi,

I was trying to install Rmpi and snow in my local environment on a hpc cluster 
running SGE. I get some errors during the install. I've tried searching the 
errors and recommendations by others on this list, but I still seem unable to 
install the package. Here is what I get (sessionInfo at bottom):

====================
>install.packages("/home/ts/R-2.13.0/Rmpi_0.5-9.tar.gz",configure.args=c("--with-Rmpi-include=/home/ts/openmpi/include","--with-Rmpi-libpath=/home/ts/openmpi/lib","--with-Rmpi-type=OPENMPI"))
>)
inferring 'repos = NULL' from the file name
* installing *source* package ‘Rmpi’ ...
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/ts/R-2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/home/ts/openmpi/include  -DMPI2 -DOPENMPI 
-I/usr/local/include    -fpic  -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/ts/R-2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/home/ts/openmpi/include  -DMPI2 -DOPENMPI 
-I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/ts/R-2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/home/ts/openmpi/include  -DMPI2 -DOPENMPI 
-I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/ts/R-2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -I/home/ts/openmpi/include  -DMPI2 -DOPENMPI 
-I/usr/local/include    -fpic  -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o 
conversion.o internal.o -L/home/ts/openmpi/lib -lmpi
installing to /home/ts/R-2.13.0/lib64/R/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object 
'/home/ts/R-2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so':
  /home/ts/openmpi/lib/libmpi.so.0: undefined symbol: opal_paffinity_alone
Error: loading failed
In addition: Warning message:
.Last.lib failed in detach() for 'Rmpi', details:
  call: dyn.unload(file.path(libpath, "libs", paste("Rmpi", 
.Platform$dynlib.ext, 
  error: shared object '/home/ts/R-2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so' was 
not loaded 
Execution halted
ERROR: loading failed
* removing ‘/home/ts/R-2.13.0/lib64/R/library/Rmpi’
Warning message:
In install.packages("/home/ts/R-2.13.0/Rmpi_0.5-9.tar.gz", configure.args = 
c("--with-Rmpi-include=/home/ts/openmpi/include",  :
  installation of package '/home/ts/R-2.13.0/Rmpi_0.5-9.tar.gz' had non-zero 
exit status
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

======================

Any help would be highly appreciated!

thanks!
	[[alternative HTML version deleted]]

