[R-sig-Debian] (no subject)

Mon Dec 12 23:57:01 CET 2011

Hi Michael, 
I'm not sure I did exactly what you told me. Here is what I did. Its still not working. did i miss something?

Thanks a lot anyway

Christoph

christoph at dell-desktop:~$ sudo add-apt-repository ppa:marutter/c2d4u
[sudo] password for christoph: 
Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /etc/apt/secring.gpg --trustdb-name /etc/apt/trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv C9A7585B49D51698710F3A115E25F516B04C661B
gpg: requesting key B04C661B from hkp server keyserver.ubuntu.com
gpg: key B04C661B: public key "Launchpad PPA for marutter" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
christoph at dell-desktop:~$ sudo apt-get remove r-cran-rmpi
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  r-cran-catools r-cran-gdata r-cran-gtools blcr-dkms r-cran-gmodels blcr-util
  dkms libvpx0 libopenmpi1.3 openmpi-checkpoint libcr0 libnuma1 openmpi-bin
  libibverbs1 mpi-default-bin r-cran-bitops openmpi-common r-cran-gplots
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
  r-cran-rmpi
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 418kB disk space will be freed.
Do you want to continue [Y/n]? y
(Reading database ... 383303 files and directories currently installed.)
Removing r-cran-rmpi ...
christoph at dell-desktop:~$ sudo apt-get install r-cran-rmpi
Reading package lists... Done
Building dependency tree       
Reading state information... Done
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.
The following NEW packages will be installed:
  r-cran-rmpi
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0B/189kB of archives.
After this operation, 418kB of additional disk space will be used.
Selecting previously deselected package r-cran-rmpi.
(Reading database ... 383264 files and directories currently installed.)
Unpacking r-cran-rmpi (from .../r-cran-rmpi_0.5-8-1_amd64.deb) ...
Setting up r-cran-rmpi (0.5-8-1) ...
christoph at dell-desktop:~$ sudo apt-get remove r-cran-snow
Reading package lists... Done
Building dependency tree       
Reading state information... Done
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.
The following packages will be REMOVED:
  r-cran-snow
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 242kB disk space will be freed.
Do you want to continue [Y/n]? Y
(Reading database ... 383303 files and directories currently installed.)
Removing r-cran-snow ...
christoph at dell-desktop:~$ sudo apt-get install r-cran-snow
Reading package lists... Done
Building dependency tree       
Reading state information... Done
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.
Suggested packages:
  r-cran-rpvm
The following NEW packages will be installed:
  r-cran-snow
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0B/62.7kB of archives.
After this operation, 242kB of additional disk space will be used.
Selecting previously deselected package r-cran-snow.
(Reading database ... 383267 files and directories currently installed.)
Unpacking r-cran-snow (from .../r-cran-snow_1%3a0.3.4~20080824-1_all.deb) ...
Setting up r-cran-snow (1:0.3.4~20080824-1) ...
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(snow)
> library(Rmpi)
Error in library(Rmpi) : 
  package ‘Rmpi’ does not have a NAMESPACE and should be re-installed
> 

________________________________________
From: r-sig-debian-bounces at r-project.org [r-sig-debian-bounces at r-project.org] on behalf of Michael Rutter [mar36 at psu.edu]
Sent: Tuesday, December 13, 2011 11:28
To: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] (no subject)

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
>
>
>       [[alternative HTML version deleted]]
>
>
>
>
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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

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