[R-sig-Debian] (no subject)

[Michael Rutter]

On 12/12/2011 04:47 PM, Christoph Knapp wrote:
> Hi all,
> I'm trying to get the snow package with mpi working on my linux ubuntu 10.04 machine. When I tried to install it (see below) it already had problems with the dependencies.

I am going to point you to my PPA, c2d4u.  It has a version of Rmpi 
rebuilt that solves the "NAMESPACE" issue.  Once you have added the PPA 
to you system ('sudo add-apt-repository ppa:marutter/c2d4u'), 
update/install r-cran-rmpi and r-cran-snow from apt or synaptic.  They 
should work fine.

Here is the PPA:

https://launchpad.net/~marutter/+archive/c2d4u

Michael

> R version 2.14.0 (2011-10-31)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> install.packages("Rmpi")
> Installing package(s) into ‘/home/christoph/R/x86_64-pc-linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/Rmpi_0.5-9.tar.gz'
> Content type 'application/x-gzip' length 87953 bytes (85 Kb)
> opened URL
> ==================================================
> downloaded 85 Kb
>
> * installing *source* package ‘Rmpi’ ...
> checking for gcc... gcc -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -std=gnu99 -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> 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
> configure: error: "Cannot find mpi.h header file"
> ERROR: configuration failed for package ‘Rmpi’
> * removing ‘/home/christoph/R/x86_64-pc-linux-gnu-library/2.14/Rmpi’
>
> The downloaded packages are in
>      ‘/tmp/RtmplPStE5/downloaded_packages’
> Warning message:
> In install.packages("Rmpi") :
>    installation of package ‘Rmpi’ had non-zero exit status
>> q()
> Save workspace image? [y/n/c]: n
> christoph at dell-desktop:~$ sudo apt-get install r-cran-rmpi
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> r-cran-rmpi is already the newest version.
> The following packages were automatically installed and are no longer required:
>    r-cran-catools r-cran-gdata r-cran-gtools r-cran-gmodels libvpx0
>    r-cran-bitops r-cran-gplots
> Use 'apt-get autoremove' to remove them.
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> christoph at dell-desktop:~$ dpkg -s r-cran-rmpi
> Package: r-cran-rmpi
> Status: install ok installed
> Priority: optional
> Section: gnu-r
> Installed-Size: 408
> Maintainer: Ubuntu Developers<ubuntu-devel-discuss at lists.ubuntu.com>
> Architecture: amd64
> Source: rmpi
> Version: 0.5-8-1
> Depends: libc6 (>= 2.4), libopenmpi1.3, r-base-core (>= 2.10.1), mpi-default-bin
> Suggests: r-cran-rsprng
> Description: GNU R package interfacing MPI libraries for distributed computing
>   This CRAN package provides an interface to the MPI (Message-Passing
>   Interface) API. It also provides an interactive R slave environment
>   in which distributed statistical computing can be carried out.
> Original-Maintainer: Dirk Eddelbuettel<edd at debian.org>
> christoph at dell-desktop:~$ R
>
> R version 2.14.0 (2011-10-31)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> library(Rmpi)
> Error in library(Rmpi) :
>    package ‘Rmpi’ does not have a NAMESPACE and should be re-installed
>>
>> q()
> Save workspace image? [y/n/c]: n
> christoph at dell-desktop:~$ R
>
> R version 2.14.0 (2011-10-31)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> install.packages("snow",dependencies=T)
> Installing package(s) into ‘/home/christoph/R/x86_64-pc-linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> also installing the dependencies ‘rpvm’, ‘rsprng’
>
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/rpvm_1.0-4.tar.gz'
> Content type 'application/x-gzip' length 66497 bytes (64 Kb)
> opened URL
> ==================================================
> downloaded 64 Kb
>
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/rsprng_1.0.tar.gz'
> Content type 'application/x-gzip' length 35916 bytes (35 Kb)
> opened URL
> ==================================================
> downloaded 35 Kb
>
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/snow_0.3-8.tar.gz'
> Content type 'application/x-gzip' length 22893 bytes (22 Kb)
> opened URL
> ==================================================
> downloaded 22 Kb
>
> * installing *source* package ‘rpvm’ ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> Check if PVM_ROOT is defined...
> no
> I'll try to build rpvm but you need set PVM_ROOT
> before use pvm. See pvm_intro(1PVM)
>
> Try to guess if pvm is installed somewhere ...
>   Cannot find pvm.
>   If pvm is installed, set PVM_ROOT to where pvm is.
>   Otherwise, please install pvm first.
> ERROR: configuration failed for package ‘rpvm’
> * removing ‘/home/christoph/R/x86_64-pc-linux-gnu-library/2.14/rpvm’
> * installing *source* package ‘rsprng’ ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> Try to find sprng.h ...
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> 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 sprng.h usability... no
> checking sprng.h presence... no
> checking for sprng.h... no
> Cannot find sprng 2.0 header file.
> ERROR: configuration failed for package ‘rsprng’
> * removing ‘/home/christoph/R/x86_64-pc-linux-gnu-library/2.14/rsprng’
> * installing *source* package ‘snow’ ...
> ** package ‘snow’ successfully unpacked and MD5 sums checked
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>
> * DONE (snow)
>
> The downloaded packages are in
>      ‘/tmp/RtmprRxhVG/downloaded_packages’
> Warning messages:
> 1: In install.packages("snow", dependencies = T) :
>    installation of package ‘rpvm’ had non-zero exit status
> 2: In install.packages("snow", dependencies = T) :
>    installation of package ‘rsprng’ had non-zero exit status
>>
>
> I have installed openmpi and tried to set the MPI_ROOT, but I'm not sure I picked the right path.
>
> christoph at dell-desktop:~$ whereis openmpi
> openmpi: /etc/openmpi /usr/lib/openmpi /usr/lib64/openmpi /usr/share/openmpi
>
> For now I set it to
>
> christoph at dell-desktop:~$ $MPI_ROOT
> bash: /etc/openmpi: is a directory
>
> I tried all of them but without any luck. I also googled the problem and found a lot but nothing really which solved the problem.
>
> Any ideas where I'm going wrong? I'm mainly interested in using snow with mpi.
>
> Thanks in advance
>
> Christoph
>
>
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-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter