[Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
Renaud Gaujoux
renaud at mancala.cbio.uct.ac.za
Thu Nov 21 10:49:21 CET 2013
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
>> <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
>>>
>>>
>>>
>>>
>>
>>
>
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