From renaud at mancala.cbio.uct.ac.za  Fri Apr  4 09:40:52 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 4 Apr 2014 09:40:52 +0200
Subject: [Rcppoctave-user] trouble installing on Mac with OS 10.8
In-Reply-To: <089BD36F-3661-4F0C-9C72-A315BD5CD249@calvin.edu>
References: <089BD36F-3661-4F0C-9C72-A315BD5CD249@calvin.edu>
Message-ID: <CAHavPHHXv7iGj_pVQ6j7LTQUP_P7V=Cc8z+3x1ve8mxauVZNtQ@mail.gmail.com>

Hi Thomas,

not sure if you already solved your issue.
We have seen such error before, and it seemed to come from mixing
compilers (Octave and R):

http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2013-October/000010.html

How did you install Octave? There are detailed instructions in the
vignette and the README file.
Are you able to try with the latest R version (3.1)?
Thank you.

Bests,
Renaud


On 18 February 2014 05:45, Thomas Scofield <scofield at calvin.edu> wrote:
>
> 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)
>
>
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