[Rcppoctave-user] Apple Blues

[Dominick Samperi]

Make sure to install Rcpp and RcppOctave from
source using the same tool chain (g++/gcc or
clang++/clang). Remove any old .o, .so, and .oct
files.
On Nov 4, 2013 6:16 PM, "Giuseppe" <neox86 at gmail.com> wrote:

> I tried with the .R/Makevars trick. The malloc error is gone, but now I
> get the following error:
>
> Error : /Users/osxuser/scratch/RcppOctave/man/o_addpath.Rd:41: .onLoad
> failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so':
>   dlopen(/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so, 6):
> Symbol not found:
> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>   Referenced from: /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
> ERROR: installing Rd objects failed for package ‘RcppOctave’
>
>
> Any pointer on what this may be due?
>
>
>
> On Mon, Nov 4, 2013 at 5:17 PM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> By default R package builds will use the C/C++ compiler that was used
>> to build R, but llvm-g++-4.2 does not work under Mavericks. Try
>> creating .R/Makevars containing
>> CXX=g++
>> CC=gcc
>> or
>> CXX=clang++
>> CC=clang
>>
>>
>>
>> On Mon, Nov 4, 2013 at 10:18 AM, Giuseppe <neox86 at gmail.com> wrote:
>>
>>> I have been reading the thread about woes with osx and RcppOctave.
>>>
>>> If I am correct, it seems that the issue is declared closed if
>>> "--no-test-load" is added to "R CMD INSTALL". Unfortunately, this does not
>>> work for me. This is what I get :
>>>
>>> [omitted]
>>>
>>> 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 /Users/osxuser/Library/R/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 /Users/osxuser/Library/R/RcppOctave/libs
>>>
>>>
>>> R(24620) malloc: *** error for object 0x7fff71042570: pointer being
>>> freed was not allocated
>>>  *** set a breakpoint in malloc_error_break to debug
>>> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24619
>>> Done                    echo 'tools:::.install_packages()'
>>>      24620 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
>>> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>>>
>>>
>>>
>>> However, i think the Makevars does not picks up the correct location of
>>> the R library. I saw in the list that a patch was sent. Can I have it too
>>> to test and see weather this is my case?
>>>
>>> ----
>>>
>>> This is my setup:
>>>
>>> [~/scratch]$ gfortran --version
>>> GNU Fortran (GCC) 4.8.2
>>>
>>> [~/scratch]$ octave --version
>>> GNU Octave, version 3.6.4
>>>
>>> [~/scratch]$ R --version
>>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>>
>>> Octave and gfortran are from homebrew. Osx version is Maverick. Xcode
>>> tools 5.0.1.
>>>
>>> [ ~/scratch]$ clang --version
>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>
>>> [ ~/scratch]$ g++ --version
>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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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