[Rcppoctave-user] Error in installing RcppOctave

[kam kammon]

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
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20141111/a8dc0e3c/attachment.html>