[Rcppoctave-user] Error in installing RcppOctave

[Renaud Gaujoux]

I will check if/how you can pass extra flags to the compilation. I may
need to change the configure script for this to work.
Otherwise, if you know of a way to detect if libhdf5 is the mpi
version, I can add relevant flags for this case.

On 13 November 2014 03:22, kam kammon <kammon101 at hotmail.ca> wrote:
> Hi, Renaud,
>
> I have compiled Octave 3.8.2 with hdf5-7 (no openmpi) to test RcppOctave.
> Again version from cran did not install (see attached log) but the
> development version did. Took a while to get back because the test partition
> went out of space.
>
> This is kind of strange since Dirk's installation worked.
>
> ________________________________
> From: kammon101 at hotmail.ca
> To: renaud at mancala.cbio.uct.ac.za
> Date: Wed, 12 Nov 2014 03:28:39 -0500
>
> CC: rcppoctave-user at lists.r-forge.r-project.org
> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave
>
> 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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