R SIG Debian - May 2010 - Problem installing/updating Rpmi

Hi

I have a few problems installing/updating packages with complicated 
dependencies. For example, the Rmpi package:

update.packages(...)
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package ?Rmpi?

So I tried:

 >install.packages("Rmpi",configure.args="--with-mpi=/usr/lib/openmpi")

Trying to find mpi.h ...
Cannot find mpi.h header file
Please use --with-mpi=/path/to/mpi or specify the environment variable 
MPI_ROOT

As well as:
$sudo R CMD INSTALL Rmpi --configure-args=--with-mpi
=/usr/lib64/openmpi

but get same error message... So it looks it is asking me what I thought 
precisely that I was doing (specifying the library)...

Should I do something more elaborate? I feel this was working before 
when I used the version from r-cran-*, nut now R 2.11 want the latest 
package to be installed... which seems no to be available on r-cran-*

Btw, when are usually the packages on r-cran updated? Are/Will they be 
updated for R 2.11? Thanks a lot for those very useful instalaltion 
facilities!!!

Matthieu


sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-pc-linux-gnu

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

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

loaded via a namespace (and not attached):
[1] tools_2.11.0

On 2 May 2010 at 21:15, mat wrote:
| Hi
| 
| I have a few problems installing/updating packages with complicated 
| dependencies. For example, the Rmpi package:
| 
| update.packages(...)
| checking for mpi.h... no
| configure: error: "Cannot find mpi.h header file"
| ERROR: configuration failed for package ?Rmpi?
| 
| So I tried:
| 
| 
>install.packages("Rmpi",configure.args="--with-mpi=/usr/lib/openmpi")

I recommend

  sudo apt-get install r-cran-rmpi

which gets you Rmpi 0.5-8 (via Debian testing, or via Debian unstable, or via
the cran2dep repository). It is always the same versions 0.5-8.
 
| Trying to find mpi.h ...
| Cannot find mpi.h header file
| Please use --with-mpi=/path/to/mpi or specify the environment variable 
| MPI_ROOT
| 
| As well as:
| $sudo R CMD INSTALL Rmpi --configure-args=--with-mpi
| =/usr/lib64/openmpi
| 
| but get same error message... So it looks it is asking me what I thought 
| precisely that I was doing (specifying the library)...

If you want to install from source, read the README in the sources and
install the relevant packages which are missing here (as indicated by the
missing mpi.h).

Dirk
 
| Should I do something more elaborate? I feel this was working before 
| when I used the version from r-cran-*, nut now R 2.11 want the latest 
| package to be installed... which seems no to be available on r-cran-*
| 
| Btw, when are usually the packages on r-cran updated? Are/Will they be 
| updated for R 2.11? Thanks a lot for those very useful instalaltion 
| facilities!!!
| 
| Matthieu
| 
| 
| sessionInfo()
| R version 2.11.0 (2010-04-22)
| x86_64-pc-linux-gnu
| 
| locale:
| [1] LC_CTYPE=fr_CH.UTF-8 LC_NUMERIC=C
| [3] LC_TIME=fr_CH.UTF-8 LC_COLLATE=fr_CH.UTF-8
| [5] LC_MONETARY=C LC_MESSAGES=fr_CH.UTF-8
| [7] LC_PAPER=fr_CH.UTF-8 LC_NAME=C
| [9] LC_ADDRESS=C LC_TELEPHONE=C
| [11] LC_MEASUREMENT=fr_CH.UTF-8 LC_IDENTIFICATION=C
| 
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
| 
| loaded via a namespace (and not attached):
| [1] tools_2.11.0
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
  Regards, Dirk