[R] C compilation error (unknown type R_xlen_t) when installing Rmpi package

Sebastian L sl-research at outlook.com
Wed Apr 8 17:00:02 CEST 2015


I am trying to use the parallel computing cluster of our university. To that end, I would like to install the Rmpi package on the cluster. The R version currently installed on the cluster is 

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Platform: x86_64-redhat-linux-gnu (64-bit)

I am trying to install the Rmpi package from the tar.gz source file, but encounter the following problem during the compilation process:

What I run within R is
install.packages("/home/myusername/Rpackages/Rmpi_0.6-5.tar.gz", repos = NULL, type = "source", lib = "/home/myusername/Rpackages/", 
configure.args=c("--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.6.3/lib64/","--with‌​-Rmpi-type=OPENMPI", "--with-Rmpi-include=/usr/mpi/gcc/openmpi-1.6.3/include/"))

and I get the following output with an error message:

* installing *source* package ‘Rmpi’ ...
** Paket ‘Rmpi’ erfolgreich entpackt und MD5 Summen überprüft
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/mpi/gcc/openmpi-1.6.3/include/  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Rmpi.c -o Rmpi.o
Rmpi.c: In Funktion »mpi_bcast«:
Rmpi.c:605:2: Fehler: unbekannter Typname: »R_xlen_t«
make: *** [Rmpi.o] Fehler 1
ERROR: compilation failed for package ‘Rmpi’

I can not quite figure out what happens here, and what "unknown type name "R_xlen_t"" possibly refers to. 

Thanks in advance


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