[R] trouble installing Rmpi on 64-bit Ubuntu 8.04 with openmpi

From: Mark Kimpel <mwkimpel_at_gmail.com>
Date: Tue, 06 May 2008 12:52:45 -0400


Subject pretty much says it all. I am running 64-bit Ubuntu 8.04, i.e. Hardy Heron, have openmpi installed, and get the following error message with attempted install of Rmpi. sessionInfo() follows.

Mark

checking for ANSI C header files... yes
checking for sys/types.h... yes

checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes

checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... no
checking mpi.h presence... no

checking for mpi.h... no
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_UNISTD_H=1 -DUNKNOWN -fPIC -I/usr/local/include -fpic -g -O2 -c
conversion.c -o conversion.o
In file included from conversion.c:18:
Rmpi.h:1:17: error: mpi.h: No such file or directory In file included from conversion.c:18:
Rmpi.h:14: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mpitype'
make: *** [conversion.o] Error 1
chmod: cannot access `/home/mkimpel/R_HOME/site-library-2.7.0/Rmpi/libs/*': No such file or directory
ERROR: compilation failed for package 'Rmpi' ** Removing '/home/mkimpel/R_HOME/site-library-2.7.0/Rmpi'

The downloaded packages are in

    /tmp/RtmppcK0FI/downloaded_packages
Warning message:

> sessionInfo()
R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] graph_1.18.0

loaded via a namespace (and not attached): [1] cluster_1.11.10 tcltk_2.7.0 tools_2.7.0

--

Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)


        [[alternative HTML version deleted]]



R-help_at_r-project.org mailing list
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. Received on Tue 06 May 2008 - 17:53:28 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 05 Jun 2008 - 01:30:38 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive