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<body class='hmmessage'><div dir='ltr'><br>Hello, <br><br>I tried installed rcppoctave from git with and without mpi. The failure logs are attached.<br>They were from git on Feb 23<br><br>Thanks<br><br>Bernard<div><hr id="stopSpelling">Date: Wed, 12 Feb 2014 15:19:51 +0200<br>Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)<br>From: renaud@mancala.cbio.uct.ac.za<br>To: kammon101@hotmail.ca<br><br><div dir="ltr"><div>Putting <a href="mailto:rcppoctave-user@lists.r-forge.r-project.org">rcppoctave-user@lists.r-forge.r-project.org</a> in Cc of all your emails should do the trick (not changing the email Subject).<br><br>
</div>Renaud<br></div><div class="ecxgmail_extra"><br><br><div class="ecxgmail_quote">On 12 February 2014 14:52, kam kammon <span dir="ltr"><<a href="mailto:kammon101@hotmail.ca" target="_blank">kammon101@hotmail.ca</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Hi Renaud,<br><br>Thanks for the reply. I am currently unable to reproduce the log without mpi because if I remove the mpi packages it would remove a bunch of other things as well. But I can create a partial clone of my current system elsewhere and remove the mpi packages there. Since you are busy at the moment this can wait for a week or so.<br>
<br>I am kind of new to this and I am not sure how to reply to you on the mailing list on the same thread. There is no option to "reply" apparently and I don't want to create a new thread by sending another email to <a href="mailto:rcppoctave-user@lists.r-forge.r-project.org" target="_blank">rcppoctave-user@lists.r-forge.r-project.org</a>. Please advice. <br>
<br>Thanks<br><br>Bernard<br><div><div class="ecxhm ecxHOEnZb"><hr>Date: Sun, 9 Feb 2014 10:50:05 +0200<br>Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)<br>From: <a href="mailto:renaud@mancala.cbio.uct.ac.za" target="_blank">renaud@mancala.cbio.uct.ac.za</a><br>
To: <a href="mailto:kammon101@hotmail.ca" target="_blank">kammon101@hotmail.ca</a><br>CC: <a href="mailto:rcppoctave-user@lists.r-forge.r-project.org" target="_blank">rcppoctave-user@lists.r-forge.r-project.org</a></div><div>
<div class="h5"><br><br><div dir="ltr"><div><div><div><div><div><div><div><div>Hi Bernard,<br><br></div>thank you for reporting this.<br></div>It looks like there are 2 different issues here:<br></div> * with mpi: this issue is due to Octave trying to compile modules with MPI support. I have seen this before and am not yet sure why/how to fix it.<br>
</div> * without mpi: this seems to be due to incompatibilities with 3.8, on which I have not tested RcppOctave<br><br></div><div>I cannot look into these errors now, but will do in the next couple of weeks.<br></div><div>
<br></div>Just to get a log of these errors for the latest dev version, can you please run the same installations using the version on github:<br><br></div><div>library(devtools)<br></div>install_github("RcppOctave", 'renozao', ref = 'develop')<br>
<br></div>Thank you.<br><br></div>Bests,<br>Renaud<br><div><div><div><br></div></div></div></div><div><br><br><div>On 8 February 2014 04:45, kam kammon <span dir="ltr"><<a href="mailto:kammon101@hotmail.ca" target="_blank">kammon101@hotmail.ca</a>></span> wrote:<br>
<blockquote style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Hi, I am trying to install Rcppoctave from R with install.packages('RcppOctave') without success.<br><br>My OS is Ubuntu 13.10. R version 3.0.2, Octave version 3.8.0 (Octave is compiled from source with prefix=/usr/local)<br>
<br>I have tried installing hdf5 with mpi (libhdf5-mpi-dev, libhdf5-openmpi-dev and libhdf5-openmpi-7 from repository ) and without mpi (libhdf5-dev and libhdf5-7 from repository) and in both cases RcppOctave would not install. <br>
<br>When libgdf5 is installed with mpi the install log shows "/usr/include/H5public.h:63:20: fatal error: mpi.h: No such file or directory" while without mpi it shows a different error. <br><br><br>I am attaching the installation log for both instances for further investigations.<br>
<br>Not sure if this is relevant, but when hdf5 is installed with mpi Octave needs to be recompiled with <br><br>export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"<br><br>Otherwise some octave-forge packages don't install.<br>
<br><a href="http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460" target="_blank">http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460</a><br>
<br>Thanks,<br><br>Bernard<br> </div></div>
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