[Rcppoctave-user] Error in installing RcppOctave

[Renaud Gaujoux]

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
>> | >> >
>> | >> >
>> | >> >
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>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org