[Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS

Dominick Samperi djsamperi at gmail.com
Fri Nov 22 17:42:40 CET 2013 

I am not seeing this behavior. RcppOctave works the same from
the command line or from the R GUI, and in the GUI I get:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/Cellar/octave/3.6.4/bin:/usr/local/Cellar/octave/3.6.4/libexec/octave/3.6.4/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/api-v48+/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/3.6.4/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/bin"

On Fri, Nov 22, 2013 at 11:26 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
> That is what I did. Reinstall both Rcpp and RcppOctave from the source. Yes, I am using Mavericks.
>
> I think the problem I have right now is related to how the code is checking for the Octave related environment during library loading. I could be wrong but I think the /bin/sh script that is calling octave-config is not reading the user’s shell environment settings therefore not able finding the Octave binary.
>
> Check out this the Sys.getenv(‘PATH’) from the R GUI. It is quite obvious that the search is a standard one instead of a user customized one. MacPorts binaries are stored (by default) in /opt/local/bin.
>
>> Sys.getenv('PATH')
> [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
>
> Please advise.
>
> On Nov 22, 2013, at 5:18 PM, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> Make sure to reinstall both Rcpp and RcppOctave from source after
>> configuring ~/.R/Makevars. Have you upgraded to Mavericks?
>> If you installed Octave using Homebrew then clang/clang++ will
>> be used as needed. This may not be the case if MacPorts is
>> used to install.
>>
>> You could also try using gcc/g++ instead of clang/clang++ (not
>> llvm-gcc-4.2/llvm-g++-4.2), assuming that you are using
>> Mavericks.
>>
>>
>> On Fri, Nov 22, 2013 at 3:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> Hi all,
>>>
>>> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and
>>> I got a different symbol not found. This symbol and the previous one are
>>> indeed in RcppOctave.so but why is R not loading it? I have also tried
>>> setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
>>>
>>> Any suggestions would be very welcome. Thanks in advance again.
>>>
>>> Yitping
>>>
>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>  error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found:
>>> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>>>  Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>  Expected in: flat namespace
>>> in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>
>>>
>>>
>>>
>>> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>
>>> Hi Renaud,
>>>
>>> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was
>>> reported not found in the error message belongs to RcppOctave.so instead of
>>> to liboctave.
>>>
>>> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>>>                 U __Z22bind_internal_variableRKSsRK12octave_value
>>>
>>> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep
>>> __Z22bind_internal_variable
>>>
>>> I tried your suggestion anyway but similar error returned.
>>>
>>> Yitping
>>>
>>>
>>> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>> wrote:
>>>
>>> Ah, true, you would need to add type = 'source' to the install.packages
>>> command.
>>> Anyway this is not the actual problem.
>>>
>>> It looks like the octave library are either not found or not loaded
>>> correctly (maybe due to the compiler discrepancy).
>>> Can you try this (not sure this is correct on Mac)
>>>
>>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
>>> RcppOctave_0.13.3.tar.gz
>>>
>>> The idea is to put ensure the octave libraries are in the PATH.
>>>
>>> Renaud
>>>
>>>
>>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>
>>>> Hi Renaud,
>>>>
>>>> I tried your suggestion but R complains that the package is not available
>>>> as a binary. This is the same error that led me to compile it from the
>>>> command line in the first place. But trying it from the command line with
>>>> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
>>>> suggested installation options did not work either. The output of is below.
>>>>
>>>> Thanks again.
>>>>
>>>> Yitping
>>>>
>>>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>>>> * installing to library
>>>> ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’
>>>> * 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... /opt/local/bin/octave-config
>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>> checking Octave include flags...
>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>> checking Octave version... 3.6.4
>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>> yes
>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> -loctinterp -loctave -lcruft
>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1
>>>> checking RcppOctave Octave module directory...
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> config.status: creating src/modules/Makefile
>>>> ** libs
>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>> -loctave -lcruft -arch x86_64
>>>> "/opt/local/bin/mkoctfile" -v
>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -arch x86_64
>>>> # Copying Octave modules to directory
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/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/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -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/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -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/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>> -Wl,CoreFoundation
>>>> installing to
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>> ** R
>>>> ** demo
>>>> ** inst
>>>> ** preparing package for lazy loading
>>>> ** building package indices
>>>> ** installing vignettes
>>>> ** testing if installed package can be loaded
>>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>  error: unable to load shared object
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>
>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>  Referenced from:
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>  Expected in: flat namespace
>>>> in
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>> Error: loading failed
>>>> Execution halted
>>>> ERROR: loading failed
>>>> * removing
>>>> ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave’
>>>>
>>>>
>>>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux
>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>
>>>> Hi Dominick,
>>>>
>>>> Yitping is compiling (successfully) with macports, but there seem to be an
>>>> issue when actually calling the code.
>>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
>>>> that be the origin of the problem?
>>>>
>>>> Yitping, could you please try the following:
>>>>
>>>> install.packages('RcppOctave',
>>>> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
>>>> --no-help')
>>>> library(RcppOctave)
>>>> OctaveConfig()
>>>> getLoadedDLLs()
>>>> o_runif(1)
>>>>
>>>>
>>>> Thank you
>>>>
>>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>>> wrote:
>>>>>
>>>>> Thanks for the details Yitping, forwarding now to the list.
>>>>> Please remember to Cc the list in your replies, so that there is a record
>>>>> for future public reference.
>>>>>
>>>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>>
>>>>>> Hi Renaud,
>>>>>>
>>>>>> Thanks for your prompt reply. I tried the install_github() method you
>>>>>> suggested but to no success either. The error is similar to what I had
>>>>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>>>>> are the log and error messages in case it is helpful.
>>>>>>
>>>>>> I have also included the output of sessionInfo() and Sys.info(). My
>>>>>> Octave installation was done through MacPorts (octave-devel
>>>>>> @3.6.4_9+atlas+docs+gcc48).
>>>>>>
>>>>>> Thanks in advance.
>>>>>>
>>>>>> Yitping
>>>>>>
>>>>>>> library(devtools)
>>>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>>>> Downloading RcppOctave.zip from
>>>>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>>>>> Installing package from
>>>>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>>>> Installing RcppOctave
>>>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>>>>> \
>>>>>>
>>>>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>>>>> \
>>>>>>
>>>>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>>>>> \
>>>>>>  --with-keep.source --install-tests
>>>>>>
>>>>>> * 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... /opt/local/bin/octave-config
>>>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>>>> checking Octave include flags...
>>>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>>>>> -L/opt/local/lib
>>>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>>>> checking Octave version... 3.6.4
>>>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>>>> yes
>>>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>>>> -loctinterp -loctave -lcruft
>>>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1
>>>>>> checking RcppOctave Octave module directory...
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>>>> configure: creating ./config.status
>>>>>> config.status: creating src/Makevars
>>>>>> configure: creating ./config.status
>>>>>> config.status: creating src/Makevars
>>>>>> config.status: creating src/modules/Makefile
>>>>>> ** libs
>>>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>>>> -loctave -lcruft -arch x86_64
>>>>>> "/opt/local/bin/mkoctfile" -v
>>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>>> -arch x86_64
>>>>>> # Copying Octave modules to directory
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/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/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>>> -fPIC  -I/opt/local/include -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/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>>> -fPIC  -I/opt/local/include -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/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>>>> -Wl,CoreFoundation
>>>>>> installing to
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>>>> ** R
>>>>>> ** demo
>>>>>> ** inst
>>>>>> ** tests
>>>>>> ** preparing package for lazy loading
>>>>>> ** help
>>>>>> Error :
>>>>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>>>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>>>  error: unable to load shared object
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>>>
>>>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>  Referenced from:
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>>  Expected in: flat namespace
>>>>>> in
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>>>> * removing
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> R version 3.0.2 (2013-09-25)
>>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>
>>>>>>
>>>>>>  sysname
>>>>>>
>>>>>> "Darwin"
>>>>>>
>>>>>> release
>>>>>>
>>>>>> "13.0.0"
>>>>>>
>>>>>> version
>>>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>>>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>>>>
>>>>>> nodename
>>>>>>
>>>>>> "dooku.local"
>>>>>>
>>>>>> machine
>>>>>>
>>>>>> "x86_64"
>>>>>>
>>>>>> login
>>>>>>
>>>>>> "yitping"
>>>>>>
>>>>>> user
>>>>>>
>>>>>> "yitping"
>>>>>>
>>>>>> effective_user
>>>>>>
>>>>>> “yitping"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>>>
>>>>>> Hi Yitping,
>>>>>>
>>>>>> thank you for your interest in the RcppOctave package, which will
>>>>>> hopefully provide what you need... once you get it working :D
>>>>>> It will be great to get your feedback on how things work from a
>>>>>> Mac-Octave user point of view.
>>>>>>
>>>>>> The package should compile fine with the settings described in the
>>>>>> README file.
>>>>>> Can you please send more details on your R (output of sessionInfo() and
>>>>>> Sys.info) and Octave installation.
>>>>>> Did you fetch the latest version of the source package from github?
>>>>>>
>>>>>> In R, try:
>>>>>>
>>>>>> library(devtools)
>>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>>>
>>>>>>
>>>>>> Renaud
>>>>>>
>>>>>>
>>>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>>>
>>>>>>> Hi RcppOctave users,
>>>>>>>
>>>>>>> I have just found out about this R packages and I am very excited about
>>>>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>>>>> package will be perfect for me.
>>>>>>>
>>>>>>> I also understand that the package still has some installation issues
>>>>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>>>>> for the sake of trying and this is what I got.
>>>>>>>
>>>>>>> - I have Octave 3.6.4 installed.
>>>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>>>> - But I cannot proceed (to generating the documentation part) because
>>>>>>> the library cannot be loaded. This is the error message I got.
>>>>>>>
>>>>>>> Error in dyn.load("RcppOctave.so") :
>>>>>>>  unable to load shared object
>>>>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>>>  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>>  Referenced from:
>>>>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>>  Expected in: flat namespace
>>>>>>> in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>>
>>>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Yitping
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> 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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