[Rcppoctave-user] Error in installing RcppOctave

Wed Nov 12 09:28:39 CET 2014

Hi, Renaud,

The failed install where mpi not found was for octave 3.8.1 from Ubuntu's repo.  I think that is just because Debian doesn't compile octave with mpi. It works after I removed libhdf5-openmpi-7 and replaced it with libhdf5-7.The log is attached here.

Cran's version of RcppOctave fails on Octave 3.8.2 compiled with hdf5-openmpi-7, the log was attached in my first message of this thread. However the develop version works.

I have not compiled Octave 3.8.2 with hdf5-7 so I can't confirm either way.

Bernard

> Date: Wed, 12 Nov 2014 09:25:30 +0200
> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave
> From: renaud at mancala.cbio.uct.ac.za
> To: kammon101 at hotmail.ca
> CC: edd at debian.org; renaud at mancala.cbio.uct.ac.za; rcppoctave-user at lists.r-forge.r-project.org
> 
> Can you please provide us with the install log of the failed
> installation, the one with mpi.h not found?
> Can you confirm:
>   * Octave 3.8.1 from Ubuntu repo works.
>   * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails.
>   * Octave 3.8.2 locally compiled against libhdf5-7 works (?)
> 
> RcppOctave uses compilation flags given by mkoctfile, which in theory
> should fit each type of installation. I thought I had fixed this
> problem back then
> (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html).
> Maybe I am not retrieving them correctly, or maybe there is a conflict
> between installations. Do you have both versions of Octave (mpi and
> non-mpi) installed when testing?
> It would help to see if you can effectively identify differences in
> octave compilation flags between the two versions (have a look at the
> variables in mkoctfile -h).
> Thanks.
> 
> 
> Renaud
> 
> On 12 November 2014 00:49, kam kammon <kammon101 at hotmail.ca> wrote:
> > Just did an experiment on a small test Ubuntu 14.04 installation on an
> > external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If
> > libhdf5-7 was installed, RcppOctave installed successfully, if instead
> > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing
> > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error:
> > mpi.h: No such file or directory" Same result with both RccpOctave from cran
> > and github.
> >
> > Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi
> > support.
> >
> > I think RcppOctave is sensitive to how hdf5 is compiled in octave and the
> > cran version may have problems with hdf5 with mpi. Since Dirk built without
> > hdf5  he didn't experience any issue.
> >
> > Thanks Renaud again!
> >
> > Bernard
> >
> >
> >
> >> Date: Tue, 11 Nov 2014 10:04:57 -0600
> >> To: renaud at mancala.cbio.uct.ac.za
> >> CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org
> >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave
> >> From: edd at debian.org
> >
> >>
> >>
> >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote:
> >> | Great.
> >> | So I guess now is a good time for me to release that version to CRAN.
> >> | Dirk, which version had installed fine on your machine, CRAN or Github
> >> | (master/develop)?
> >>
> >> Almost surely just plain CRAN on several machines. Have not had issues in
> >> ages.
> >>
> >> But then I don't do unusual things like building with MPI, hdf5, or other
> >> local patches.
> >>
> >> Dirk
> >>
> >>
> >> | Thanks.
> >> |
> >> | Bests,
> >> | Renaud
> >> |
> >> | On 11 November 2014 10:45, kam kammon <kammon101 at hotmail.ca> wrote:
> >> | > Hi, Renaud,
> >> | >
> >> | > Thanks for the quick reply.
> >> | >
> >> | > I was installing RcppOctave in R with the command
> >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from
> >> cran's
> >> | > mirror.
> >> | >
> >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source
> >> myself)
> >> | >
> >> | > The developmental version does install!
> >> | >
> >> | >
> >> | >
> >> | >
> >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200
> >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave
> >> | >> From: renaud at mancala.cbio.uct.ac.za
> >> | >
> >> | >> To: kammon101 at hotmail.ca
> >> | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org
> >> | >>
> >> | >> Hi Bernard,
> >> | >>
> >> | >> The error happens at loading time when rendering the man pages (which
> >> | >> contain some calls to Octave functions).
> >> | >> Which version of RcppOctave are you installing and how? And which R
> >> | >> version are you running?
> >> | >>
> >> | >> I believe I fixed this error some time ago.
> >> | >> Can you please try the latest develop version:
> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop')
> >> | >> # and also if this still fails
> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick
> >> =
> >> | >> TRUE)
> >> | >>
> >> | >> Thanks.
> >> | >>
> >> | >> Bests,
> >> | >> Renaud
> >> | >>
> >> | >> On 11 November 2014 07:33, kam kammon <kammon101 at hotmail.ca> wrote:
> >> | >> > Hi, there are two additional things that may be relevant. First
> >> Octave
> >> | >> > 3.8.2
> >> | >> > was compiled from source and I have used a patch from
> >> | >> >
> >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html
> >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit.
> >> | >> >
> >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a
> >> | >> > problem
> >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but
> >> the
> >> | >> > problem has been fixed.
> >> | >> >
> >> | >> > Bernard
> >> | >> >
> >> | >> > ________________________________
> >> | >> > From: kammon101 at hotmail.ca
> >> | >> > To: edd at debian.org
> >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500
> >> | >> > CC: rcppoctave-user at lists.r-forge.r-project.org
> >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave
> >> | >> >
> >> | >> >
> >> | >> > I am not sure what info you will need then.
> >> | >> >
> >> | >> > What is the meaning of "error: object 'dlibs' not found"? That
> >> seems to
> >> | >> > be
> >> | >> > the issue.
> >> | >> >
> >> | >> > Bernard
> >> | >> >
> >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600
> >> | >> >> To: kammon101 at hotmail.ca
> >> | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org
> >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave
> >> | >> >> From: edd at debian.org
> >> | >> >>
> >> | >> >>
> >> | >> >> That's uninformative. As I said, works on my box ...
> >> | >> >>
> >> | >> >> Dirk
> >> | >> >>
> >> | >> >> --
> >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> >> | >> >
> >> | >> > _______________________________________________ Rcppoctave-user
> >> mailing
> >> | >> > list
> >> | >> > Rcppoctave-user at lists.r-forge.r-project.org
> >> | >> >
> >> | >> >
> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
> >> | >> >
> >> | >> > _______________________________________________
> >> | >> > Rcppoctave-user mailing list
> >> | >> > Rcppoctave-user at lists.r-forge.r-project.org
> >> | >> >
> >> | >> >
> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
> >> | >> >
> >> | >> >
> >> | >> >
> >> | _______________________________________________
> >> | Rcppoctave-user mailing list
> >> | Rcppoctave-user at lists.r-forge.r-project.org
> >> |
> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
> >>
> >> --
> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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