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

Yitping Kok yitping at mpe.mpg.de
Fri Nov 22 17:26:27 CET 2013 

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
>> 
>> 
>> 
>> _______________________________________________
>> 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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