[Rcppoctave-user] trouble installing on Mac with OS 10.8
Thomas Scofield
scofield at calvin.edu
Tue Feb 18 04:45:50 CET 2014
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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