[R-sig-Debian] (no subject)

Michael Rutter mar36 at psu.edu
Tue Dec 13 00:07:46 CET 2011 


On 12/12/2011 05:57 PM, Christoph Knapp wrote:
> 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,

I don't think you ran an "sudo apt-get update" after installing the PPA. 
  apt doesn't know about the version at the PPA until you do that.

Michael

> 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]]
>>
>>
>>
>>
>> _______________________________________________
>> R-SIG-Debian mailing list
>> R-SIG-Debian at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>
> --
> 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
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
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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