Hi,
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 ?berpr?ft
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
C compilation error (unknown type R_xlen_t) when installing Rmpi package
3 messages · Sebastian L, Henrik Bengtsson, Brian Ripley
Support for long vectors (and hence R_xlen_t) was introduced in R 3.0.0. Your version is far outdated. If you wait a teeny but longer (after April 16) to update, you'll get R 3.2.0. Henrik
On Apr 8, 2015 08:00, "Sebastian L" <sl-research at outlook.com> wrote:
Hi,
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 ?berpr?ft
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
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
On 08/04/2015 16:00, Sebastian L wrote:
Hi, 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
This was a matter for the R-devel list as it involves compiled code: see the posting guide.
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 ?berpr?ft
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.
It is a C type introduced in R 3.0.0. Find in the CRAN archives a version of Rmpi as old as your version of R (or at least earlier than 3.0.0) and install that. Note to the maintainer (Cc:ed) -- you need to correct the R version dependence.
Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK