[Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
Renaud Gaujoux
renaud at mancala.cbio.uct.ac.za
Thu Nov 21 10:36:39 CET 2013
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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