[Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)

Sat Mar 1 19:41:46 CET 2014

Hi,

It installed correctly without mpi but it still doesn't work with mpi. Not sure if it has anything to do with whether octave was compiled with mpi (in both cases they were, the two Ubuntu systems are clones) The only difference is that in one system (the one where rcppoctave now works) I have removed the hdf5 packages with mpi enabled and replaced them with the version without mpi. So it is a hdf5 issue.

There is a thread on the shogun-toolbox forum which may be of interest (no solution, but the same issue apparently)

https://github.com/shogun-toolbox/shogun/issues/1856

Thanks

Date: Fri, 28 Feb 2014 14:21:21 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org

Hi,

I have just pushed a fix for this issue, at least when installing on Octave compiled without MPI.
Can you please try:

library(devtools)

install_github("RcppOctave", 'renozao', ref = 'develop')

Thanks.

Renaud

On 27 February 2014 22:45, kam kammon <kammon101 at hotmail.ca> wrote:

Hello, 

I tried installed rcppoctave  from git with and without  mpi. The failure logs are attached.
They were from git on Feb 23

Thanks

BernardDate: Wed, 12 Feb 2014 15:19:51 +0200

Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca

Putting rcppoctave-user at lists.r-forge.r-project.org in Cc of all your emails should do the trick (not changing the email Subject).

Renaud

On 12 February 2014 14:52, kam kammon <kammon101 at hotmail.ca> wrote:

Hi Renaud,

Thanks for the reply. I am currently unable to reproduce the log without mpi because if I remove the mpi packages it would remove a bunch of other things as well. But I can create a partial clone of my current system elsewhere and remove the mpi packages there. Since you are busy at the moment this can wait for a week or so.

I am kind of new to this and I am not sure how to reply to you on the mailing list on the same thread. There is no option to "reply" apparently and I don't want to create a new thread by sending  another email to rcppoctave-user at lists.r-forge.r-project.org. Please advice. 

Thanks

Bernard
Date: Sun, 9 Feb 2014 10:50:05 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za

To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org

Hi Bernard,

thank you for reporting this.
It looks like there are 2 different issues here:
  * with mpi: this issue is due to Octave trying to compile modules with MPI support. I have seen this before and am not yet sure why/how to fix it.

  * without mpi: this seems to be due to incompatibilities with 3.8, on which I have not tested RcppOctave

I cannot look into these errors now, but will do in the next couple of weeks.

Just to get a log of these errors for the latest dev version, can you please run the same installations using the version on github:

library(devtools)
install_github("RcppOctave", 'renozao', ref = 'develop')

Thank you.

Bests,
Renaud

On 8 February 2014 04:45, kam kammon <kammon101 at hotmail.ca> wrote:

Hi, I am trying to install Rcppoctave from R with install.packages('RcppOctave') without success.

My OS is Ubuntu 13.10. R version 3.0.2, Octave version 3.8.0 (Octave is compiled from source with prefix=/usr/local)

I have tried installing hdf5  with mpi (libhdf5-mpi-dev, libhdf5-openmpi-dev and libhdf5-openmpi-7 from repository ) and without mpi (libhdf5-dev and libhdf5-7 from repository) and in both cases RcppOctave would not install. 

When libgdf5 is installed with mpi the install log shows "/usr/include/H5public.h:63:20: fatal error: mpi.h: No such file or directory"  while without mpi it shows a different error. 

I am attaching the installation log for both instances for further investigations.

Not sure if this is relevant, but when hdf5 is installed with mpi Octave needs to be recompiled  with 

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

Otherwise some octave-forge packages don't install.

http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460

Thanks,

Bernard

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