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<body class='hmmessage'><div dir='ltr'>Hi, Renaud,<br><br>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.<br><br>This is kind of strange since Dirk's installation worked.<br><br><div><hr id="stopSpelling">From: kammon101@hotmail.ca<br>To: renaud@mancala.cbio.uct.ac.za<br>Date: Wed, 12 Nov 2014 03:28:39 -0500<br>CC: rcppoctave-user@lists.r-forge.r-project.org<br>Subject: Re: [Rcppoctave-user] Error in installing RcppOctave<br><br>
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<div dir="ltr">Hi, Renaud,<br><br>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.<br><br>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.<br><br>I have not compiled Octave 3.8.2 with hdf5-7 so I can't confirm either way.<br><br>Bernard<br><br><br><br><br><div>> Date: Wed, 12 Nov 2014 09:25:30 +0200<br>> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave<br>> From: renaud@mancala.cbio.uct.ac.za<br>> To: kammon101@hotmail.ca<br>> CC: edd@debian.org; renaud@mancala.cbio.uct.ac.za; rcppoctave-user@lists.r-forge.r-project.org<br>> <br>> Can you please provide us with the install log of the failed<br>> installation, the one with mpi.h not found?<br>> Can you confirm:<br>> * Octave 3.8.1 from Ubuntu repo works.<br>> * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails.<br>> * Octave 3.8.2 locally compiled against libhdf5-7 works (?)<br>> <br>> RcppOctave uses compilation flags given by mkoctfile, which in theory<br>> should fit each type of installation. I thought I had fixed this<br>> problem back then<br>> (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html).<br>> Maybe I am not retrieving them correctly, or maybe there is a conflict<br>> between installations. Do you have both versions of Octave (mpi and<br>> non-mpi) installed when testing?<br>> It would help to see if you can effectively identify differences in<br>> octave compilation flags between the two versions (have a look at the<br>> variables in mkoctfile -h).<br>> Thanks.<br>> <br>> <br>> Renaud<br>> <br>> On 12 November 2014 00:49, kam kammon <kammon101@hotmail.ca> wrote:<br>> > Just did an experiment on a small test Ubuntu 14.04 installation on an<br>> > external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If<br>> > libhdf5-7 was installed, RcppOctave installed successfully, if instead<br>> > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing<br>> > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error:<br>> > mpi.h: No such file or directory" Same result with both RccpOctave from cran<br>> > and github.<br>> ><br>> > Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi<br>> > support.<br>> ><br>> > I think RcppOctave is sensitive to how hdf5 is compiled in octave and the<br>> > cran version may have problems with hdf5 with mpi. Since Dirk built without<br>> > hdf5 he didn't experience any issue.<br>> ><br>> > Thanks Renaud again!<br>> ><br>> > Bernard<br>> ><br>> ><br>> ><br>> >> Date: Tue, 11 Nov 2014 10:04:57 -0600<br>> >> To: renaud@mancala.cbio.uct.ac.za<br>> >> CC: kammon101@hotmail.ca; rcppoctave-user@lists.r-forge.r-project.org<br>> >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave<br>> >> From: edd@debian.org<br>> ><br>> >><br>> >><br>> >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote:<br>> >> | Great.<br>> >> | So I guess now is a good time for me to release that version to CRAN.<br>> >> | Dirk, which version had installed fine on your machine, CRAN or Github<br>> >> | (master/develop)?<br>> >><br>> >> Almost surely just plain CRAN on several machines. Have not had issues in<br>> >> ages.<br>> >><br>> >> But then I don't do unusual things like building with MPI, hdf5, or other<br>> >> local patches.<br>> >><br>> >> Dirk<br>> >><br>> >><br>> >> | Thanks.<br>> >> |<br>> >> | Bests,<br>> >> | Renaud<br>> >> |<br>> >> | On 11 November 2014 10:45, kam kammon <kammon101@hotmail.ca> wrote:<br>> >> | > Hi, Renaud,<br>> >> | ><br>> >> | > Thanks for the quick reply.<br>> >> | ><br>> >> | > I was installing RcppOctave in R with the command<br>> >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from<br>> >> cran's<br>> >> | > mirror.<br>> >> | ><br>> >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source<br>> >> myself)<br>> >> | ><br>> >> | > The developmental version does install!<br>> >> | ><br>> >> | ><br>> >> | ><br>> >> | ><br>> >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200<br>> >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave<br>> >> | >> From: renaud@mancala.cbio.uct.ac.za<br>> >> | ><br>> >> | >> To: kammon101@hotmail.ca<br>> >> | >> CC: edd@debian.org; rcppoctave-user@lists.r-forge.r-project.org<br>> >> | >><br>> >> | >> Hi Bernard,<br>> >> | >><br>> >> | >> The error happens at loading time when rendering the man pages (which<br>> >> | >> contain some calls to Octave functions).<br>> >> | >> Which version of RcppOctave are you installing and how? And which R<br>> >> | >> version are you running?<br>> >> | >><br>> >> | >> I believe I fixed this error some time ago.<br>> >> | >> Can you please try the latest develop version:<br>> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop')<br>> >> | >> # and also if this still fails<br>> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick<br>> >> =<br>> >> | >> TRUE)<br>> >> | >><br>> >> | >> Thanks.<br>> >> | >><br>> >> | >> Bests,<br>> >> | >> Renaud<br>> >> | >><br>> >> | >> On 11 November 2014 07:33, kam kammon <kammon101@hotmail.ca> wrote:<br>> >> | >> > Hi, there are two additional things that may be relevant. First<br>> >> Octave<br>> >> | >> > 3.8.2<br>> >> | >> > was compiled from source and I have used a patch from<br>> >> | >> ><br>> >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html<br>> >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit.<br>> >> | >> ><br>> >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a<br>> >> | >> > problem<br>> >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but<br>> >> the<br>> >> | >> > problem has been fixed.<br>> >> | >> ><br>> >> | >> > Bernard<br>> >> | >> ><br>> >> | >> > ________________________________<br>> >> | >> > From: kammon101@hotmail.ca<br>> >> | >> > To: edd@debian.org<br>> >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500<br>> >> | >> > CC: rcppoctave-user@lists.r-forge.r-project.org<br>> >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave<br>> >> | >> ><br>> >> | >> ><br>> >> | >> > I am not sure what info you will need then.<br>> >> | >> ><br>> >> | >> > What is the meaning of "error: object 'dlibs' not found"? That<br>> >> seems to<br>> >> | >> > be<br>> >> | >> > the issue.<br>> >> | >> ><br>> >> | >> > Bernard<br>> >> | >> ><br>> >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600<br>> >> | >> >> To: kammon101@hotmail.ca<br>> >> | >> >> CC: edd@debian.org; rcppoctave-user@lists.r-forge.r-project.org<br>> >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave<br>> >> | >> >> From: edd@debian.org<br>> >> | >> >><br>> >> | >> >><br>> >> | >> >> That's uninformative. As I said, works on my box ...<br>> >> | >> >><br>> >> | >> >> Dirk<br>> >> | >> >><br>> >> | >> >> --<br>> >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org<br>> >> | >> ><br>> >> | >> > _______________________________________________ Rcppoctave-user<br>> >> mailing<br>> >> | >> > list<br>> >> | >> > Rcppoctave-user@lists.r-forge.r-project.org<br>> >> | >> ><br>> >> | >> ><br>> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user<br>> >> | >> ><br>> >> | >> > _______________________________________________<br>> >> | >> > Rcppoctave-user mailing list<br>> >> | >> > Rcppoctave-user@lists.r-forge.r-project.org<br>> >> | >> ><br>> >> | >> ><br>> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user<br>> >> | >> ><br>> >> | >> ><br>> >> | >> ><br>> >> | _______________________________________________<br>> >> | Rcppoctave-user mailing list<br>> >> | Rcppoctave-user@lists.r-forge.r-project.org<br>> >> |<br>> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user<br>> >><br>> >> --<br>> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org<br></div> </div>
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