R help - Apr 2015 - C compilation error (unknown type R_xlen_t) when installing Rmpi package

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

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Your version is far outdated.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.
	[[alternative HTML version deleted]]

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