From kammon101 at hotmail.ca  Sat Feb  8 03:45:43 2014
From: kammon101 at hotmail.ca (kam kammon)
Date: Fri, 7 Feb 2014 21:45:43 -0500
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
Message-ID: <BAY174-W319FEA470397542F3020F097960@phx.gbl>

Hi, I am trying to install Rcppoctave from R with install.packages('RcppOctave') without success.

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)

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. 

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. 


I am attaching the installation log for both instances for further investigations.

Not sure if this is relevant, but when hdf5 is installed with mpi Octave needs to be recompiled  with 

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

Otherwise some octave-forge packages don't install.

http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460

Thanks,

Bernard
 		 	   		  
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From renaud at mancala.cbio.uct.ac.za  Sun Feb  9 09:50:05 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sun, 9 Feb 2014 10:50:05 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
Message-ID: <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>

Hi Bernard,

thank you for reporting this.
It looks like there are 2 different issues here:
  * 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.
  * without mpi: this seems to be due to incompatibilities with 3.8, on
which I have not tested RcppOctave

I cannot look into these errors now, but will do in the next couple of
weeks.

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:

library(devtools)
install_github("RcppOctave", 'renozao', ref = 'develop')

Thank you.

Bests,
Renaud



On 8 February 2014 04:45, kam kammon <kammon101 at hotmail.ca> wrote:

> Hi, I am trying to install Rcppoctave from R with
> install.packages('RcppOctave') without success.
>
> 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)
>
> 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.
>
> 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.
>
>
> I am attaching the installation log for both instances for further
> investigations.
>
> Not sure if this is relevant, but when hdf5 is installed with mpi Octave
> needs to be recompiled  with
>
> export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"
>
> Otherwise some octave-forge packages don't install.
>
>
> http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460
>
> Thanks,
>
> Bernard
>
> _______________________________________________
> 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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From scofield at calvin.edu  Tue Feb 18 04:45:50 2014
From: scofield at calvin.edu (Thomas Scofield)
Date: Tue, 18 Feb 2014 03:45:50 +0000
Subject: [Rcppoctave-user] trouble installing on Mac with OS 10.8
Message-ID: <089BD36F-3661-4F0C-9C72-A315BD5CD249@calvin.edu>


I'm getting errors installing the RcppOctave package.  Here is info about my version of R:

> version
               _                           
platform       x86_64-apple-darwin10.8.0   
arch           x86_64                      
os             darwin10.8.0                
system         x86_64, darwin10.8.0        
status                                     
major          3                           
minor          0.2                         
year           2013                        
month          09                          
day            25                          
svn rev        63987                       
language       R                           
version.string R version 3.0.2 (2013-09-25)
nickname       Frisbee Sailing

And here the command I used to install, along with output.

> install_github('RcppOctave', 'renozao', ref = 'develop')
Installing github repo RcppOctave/develop from renozao
Downloading RcppOctave.zip from https://github.com/renozao/RcppOctave/archive/develop.zip
Installing package from /var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T//RtmpPWewHM/RcppOctave.zip
arguments 'minimized' and 'invisible' are for Windows only
Installing RcppOctave
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build  \
  '/private/var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T/RtmpPWewHM/devtools1d0228aedaa5/RcppOctave-develop'  \
  --no-manual --no-resave-data 

* checking for file '/private/var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T/RtmpPWewHM/devtools1d0228aedaa5/RcppOctave-develop/DESCRIPTION' ... OK
* preparing 'RcppOctave':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running 'cleanup'
* installing the package to process help pages
      -----------------------------------
* installing *source* package 'RcppOctave' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
checking whether R is a shared library... yes
checking type of Operating System... Darwin
checking whether OS is Mac OS (Darwin)... yes
Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
checking for octave-config... /usr/local/bin/octave-config
checking for mkoctfile... /usr/local/bin/mkoctfile
checking Octave Octave bin directory... /usr/local/Cellar/octave/3.6.4/bin
checking Octave include flags... -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include
checking Octave -L flags... -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4 -L/usr/local/Cellar/octave/3.6.4/lib
checking Octave libraries... -loctinterp -loctave -lcruft
checking Octave C compiler... cc
checking Octave Fortran compiler... /usr/local/opt/gfortran/bin/gfortran
checking Octave platform... x86_64-apple-darwin12.4.0
checking Octave API version... api-v48+
checking Octave version... 3.6.4
checking whether to infer output names for Octave function (>= 3.4.3)... yes
Using Octave LDFLAGS:  -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4 -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
Using Octave CPPFLAGS: -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include -DOCT_POST_3_4_0=1
checking RcppOctave Octave module directory... /private/var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T/RtmpzuVLSU/Rinst1d1a14179a2d/RcppOctave/modules
configure: creating ./config.status
config.status: creating R/config-vars.R
configure: creating ./config.status
config.status: creating R/config-vars.R
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating R/config-vars.R
config.status: creating src/Makevars
config.status: creating src/modules/Makefile
** libs
"/usr/local/bin/mkoctfile" -v utils.cc
c++ -c -fPIC -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include -I/usr/local/Cellar/pcre/8.33/include -I/opt/X11/include/freetype2 -I/opt/X11/include -I/opt/X11/include -D_REENTRANT utils.cc -o utils.o
c++ -bundle -bundle_loader /usr/local/Cellar/octave/3.6.4/bin/octave-3.6.4 -o utils.oct utils.o -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4 -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
"/usr/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
c++ -c -fPIC -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include -I/usr/local/Cellar/pcre/8.33/include -I/opt/X11/include/freetype2 -I/opt/X11/include -I/opt/X11/include -D_REENTRANT -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
c++ -bundle -bundle_loader /usr/local/Cellar/octave/3.6.4/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4 -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
# Copying Octave modules to directory '/private/var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T/RtmpzuVLSU/Rinst1d1a14179a2d/RcppOctave/modules'
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c conversion.cpp -o conversion.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/.. -I/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave -I/usr/local/Cellar/octave/3.6.4/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4 -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/var/folders/bt/8hf67kkn6zv6jcpy0nc4y9k00000gn/T/RtmpzuVLSU/Rinst1d1a14179a2d/RcppOctave/libs
** R
** demo
** exec
** inst
** preparing package for lazy loading
** help
R(7461) malloc: *** error for object 0x7fff78a7f570: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34:  7460 Done                    echo 'tools:::.install_packages()'
      7461 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
      -----------------------------------
ERROR: package installation failed
Error: Command failed (1)



From kammon101 at hotmail.ca  Thu Feb 27 21:45:49 2014
From: kammon101 at hotmail.ca (kam kammon)
Date: Thu, 27 Feb 2014 15:45:49 -0500
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
 Linux)
In-Reply-To: <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>,
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>,
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>,
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
Message-ID: <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>


Hello, 

I tried installed rcppoctave  from git with and without  mpi. The failure logs are attached.
They were from git on Feb 23

Thanks

BernardDate: Wed, 12 Feb 2014 15:19:51 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca

Putting rcppoctave-user at lists.r-forge.r-project.org in Cc of all your emails should do the trick (not changing the email Subject).


Renaud


On 12 February 2014 14:52, kam kammon <kammon101 at hotmail.ca> wrote:




Hi Renaud,

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.


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 rcppoctave-user at lists.r-forge.r-project.org. Please advice. 


Thanks

Bernard
Date: Sun, 9 Feb 2014 10:50:05 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za

To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org


Hi Bernard,

thank you for reporting this.
It looks like there are 2 different issues here:
  * 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.


  * without mpi: this seems to be due to incompatibilities with 3.8, on which I have not tested RcppOctave

I cannot look into these errors now, but will do in the next couple of weeks.



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:

library(devtools)
install_github("RcppOctave", 'renozao', ref = 'develop')



Thank you.

Bests,
Renaud



On 8 February 2014 04:45, kam kammon <kammon101 at hotmail.ca> wrote:





Hi, I am trying to install Rcppoctave from R with install.packages('RcppOctave') without success.

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)



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. 



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. 


I am attaching the installation log for both instances for further investigations.



Not sure if this is relevant, but when hdf5 is installed with mpi Octave needs to be recompiled  with 

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

Otherwise some octave-forge packages don't install.



http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460



Thanks,

Bernard
 		 	   		  



_______________________________________________

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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From renaud at mancala.cbio.uct.ac.za  Fri Feb 28 13:21:21 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 28 Feb 2014 14:21:21 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
Message-ID: <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>

Hi,

I have just pushed a fix for this issue, at least when installing on Octave
compiled without MPI.
Can you please try:

library(devtools)
install_github("RcppOctave", 'renozao', ref = 'develop')

Thanks.

Renaud



On 27 February 2014 22:45, kam kammon <kammon101 at hotmail.ca> wrote:

>
> Hello,
>
> I tried installed rcppoctave  from git with and without  mpi. The failure
> logs are attached.
> They were from git on Feb 23
>
> Thanks
>
> Bernard
> ------------------------------
> Date: Wed, 12 Feb 2014 15:19:51 +0200
>
> Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
> Linux)
> From: renaud at mancala.cbio.uct.ac.za
> To: kammon101 at hotmail.ca
>
> Putting rcppoctave-user at lists.r-forge.r-project.org in Cc of all your
> emails should do the trick (not changing the email Subject).
>
> Renaud
>
>
> On 12 February 2014 14:52, kam kammon <kammon101 at hotmail.ca> wrote:
>
> Hi Renaud,
>
> 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.
>
> 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
> rcppoctave-user at lists.r-forge.r-project.org. Please advice.
>
> Thanks
>
> Bernard
> ------------------------------
> Date: Sun, 9 Feb 2014 10:50:05 +0200
> Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
> Linux)
> From: renaud at mancala.cbio.uct.ac.za
> To: kammon101 at hotmail.ca
> CC: rcppoctave-user at lists.r-forge.r-project.org
>
>
> Hi Bernard,
>
> thank you for reporting this.
> It looks like there are 2 different issues here:
>   * 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.
>   * without mpi: this seems to be due to incompatibilities with 3.8, on
> which I have not tested RcppOctave
>
> I cannot look into these errors now, but will do in the next couple of
> weeks.
>
> 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:
>
> library(devtools)
> install_github("RcppOctave", 'renozao', ref = 'develop')
>
> Thank you.
>
> Bests,
> Renaud
>
>
>
> On 8 February 2014 04:45, kam kammon <kammon101 at hotmail.ca> wrote:
>
> Hi, I am trying to install Rcppoctave from R with
> install.packages('RcppOctave') without success.
>
> 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)
>
> 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.
>
> 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.
>
>
> I am attaching the installation log for both instances for further
> investigations.
>
> Not sure if this is relevant, but when hdf5 is installed with mpi Octave
> needs to be recompiled  with
>
> export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"
>
> Otherwise some octave-forge packages don't install.
>
>
> http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460
>
> Thanks,
>
> Bernard
>
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> Rcppoctave-user at lists.r-forge.r-project.org
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>
>
>
>
>
>
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