[Rcpp-devel] Trouble linking with Rcpp

Dirk Eddelbuettel edd at debian.org
Tue Jul 8 16:11:39 CEST 2014 

On 8 July 2014 at 15:58, Jonathon Love wrote:
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| thanks for your speedy response dirk!
| 
| > | I have an R install which I can link my application against, and
| > that | all works fine, but whenever I try and use a new R
| > installation, | linking against Rcpp always fails. (I guess I
| > fluked it the first time)
| > 
| > Please define "try and use a new R installation".
| 
| i prepare a special directory containing R (and all the packages)
| which gets bundled with my application. ( http://jasp-stats.org if you
| were wondering)
| 
| i have a bundle which i've been using for the last 12 months or so,
| which i apparently fluked getting it into a configuration that will
| link (remarkably, i fluked both osx and windows versions early on, and
| haven't been able to repeat the trick on either platform since)
| 
| > See above. Your hunch is good.  If you build everything with the
| > same compiler it should work.
| 
| i can confirm that i'm using the same compiler :/, below are the
| installing of RInside and the compilation of my program which links
| against RInside and Rcpp.
| 
| > | I thought that perhaps it had to do with link flags, but on my |
| > machine, Rcpp::RcppLdFlags() always returns an empty string.
| > 
| > See the release notes for 0.11.0. This changed, and is easier now.
| > We no longer use an external library, so this helper function no
| > longer provides link instructions for one.
| 
| i'm not sure this is relevant, but Rcpp:::RcppLdFlags() returns an
| empty string when i use 0.10.6 (i would like to use 0.11.x series, but

Nope. 

I surmise that you have your versions mixed up, and possibly different
releases of Rcpp in different places in your .libPaths().  

Which could explain the errors too.

| i get compile errors and haven't been able to produce a minimal
| example which reproduces it.)
| 
| is there something you would recommend trying next?

This works reliably for a lot of people.  Start again, make sure you check
every step.  Virtual machines (eg Docker) are get if you really want to make
sure you have clean and pristine environments.

I'm at work and can't dig too deeply into this, and I also don't have access
to OS X for testing -- but other list members do and they may help you here.

Dirk
 
| with thanks
| 
| 
| here is the output:
| 
| 
| compilers
| 
| clang++ --version
| Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
| 
| and
| 
| /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
| - --version
| Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
| 
| compiling my application:
| 
| /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
| - -headerpad_max_install_names
| -
| -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk
| - -mmacosx-version-min=10.6 -o ../JASPEngine main.o engine.o
| rcppbridge.o   -L.. -lJASP-Common
| -
| -L/Users/jonathon/Documents/build-JASP-Desktop_Qt_5_3_clang_64bit-Debug/JASP-Engine/../../Frameworks/R.framework/Versions/3.0/Resources/library/RInside/lib
| - -lRInside
| -
| -L/Users/jonathon/Documents/build-JASP-Desktop_Qt_5_3_clang_64bit-Debug/JASP-Engine/../../Frameworks/R.framework/Versions/3.0/Resources/lib
| - -lR
| -
| -L/Users/jonathon/Documents/build-JASP-Desktop_Qt_5_3_clang_64bit-Debug/JASP-Engine/../../Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib
| - -lRcpp
| Undefined symbols for architecture x86_64:
|   "demangle(std::string const&)", referenced from:
|       std::string
| Rcpp::get_return_type_dispatch<Rcpp::DataFrame>(Rcpp::traits::integral_constant<bool,
| false>) in rcppbridge.o
|   "Rcpp::Environment::operator[](std::string const&)", referenced from:
|       Rcpp::InternalFunction::set(SEXPREC*) in rcppbridge.o
|   "RInside::parseEvalQNT(std::string const&)", referenced from:
|       RcppBridge::RcppBridge() in rcppbridge.o
|   "RInside::parseEval(std::string const&, SEXPREC*&)", referenced from:
|       RcppBridge::init(std::string const&, Json::Value const&) in
| rcppbridge.o
|       RcppBridge::run(std::string const&, Json::Value const&,
| boost::function<int (Json::Value)>) in rcppbridge.o
|   "RInside::operator[](std::string const&)", referenced from:
|       RcppBridge::RcppBridge() in rcppbridge.o
|       RcppBridge::init(std::string const&, Json::Value const&) in
| rcppbridge.o
|       RcppBridge::run(std::string const&, Json::Value const&,
| boost::function<int (Json::Value)>) in rcppbridge.o
| 
| .....
| 
| installing RInside:
| 
| * installing *source* package ‘RInside’ ...
| ** package ‘RInside’ successfully unpacked and MD5 sums checked
| ** libs
| about to run R CMD SHLIB -o RInside.so MemBuf.cpp RInside.cpp
| /Library/Frameworks/R.framework/Resources/bin/Rscript
| tools/RInsideAutoloads.r > RInsideAutoloads.h
| /Library/Frameworks/R.framework/Resources/bin/Rscript
| tools/RInsideEnvVars.r   > RInsideEnvVars.h
| clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
| - -I. -I../inst/include/ -I/usr/local/include
| -
| -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
|   -fPIC  -mtune=core2 -g -O2  -c MemBuf.cpp -o MemBuf.o
| clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
| - -I. -I../inst/include/ -I/usr/local/include
| -
| -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
|   -fPIC  -mtune=core2 -g -O2  -c RInside.cpp -o RInside.o
| clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
| dynamic_lookup -single_module -multiply_defined suppress
| - -L/usr/local/lib -L/usr/local/lib -o RInside.so MemBuf.o RInside.o
| /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
| - -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
| - -Wl,CoreFoundation
| clang++ -o libRInside.dylib MemBuf.o RInside.o -dynamiclib
| - -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
| - -single_module -multiply_defined suppress
| `/Library/Frameworks/R.framework/Resources/bin/Rscript -e
| "Rcpp:::LdFlags()"`  -F/Library/Frameworks/R.framework/.. -framework R
| - -Wl,-framework -Wl,CoreFoundation
| ar qc libRInside.a MemBuf.o RInside.o
| cp libRInside.dylib ../inst/lib
| cp libRInside.a ../inst/lib
| rm libRInside.dylib libRInside.a
| installing to
| /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RInside/libs
| ** R
| ** inst
| ** preparing package for lazy loading
| ** help
| *** installing help indices
| ** building package indices
| ** testing if installed package can be loaded
| sh: /usr/bin/gnutar: No such file or directory
| gzip: can't stat:
| /Users/jonathon/Documents/Frameworks/R.framework/Versions/3.0/Resources/RInside_0.2.10_R_x86_64-apple-darwin10.8.0.tar
| (/Users/jonathon/Documents/Frameworks/R.framework/Versions/3.0/Resources/RInside_0.2.10_R_x86_64-apple-darwin10.8.0.tar):
| No such file or directory
| Warning in file.rename(file.path(startdir, filename),
| file.path(startdir,  :
|   cannot rename file
| '/Users/jonathon/Documents/Frameworks/R.framework/Versions/3.0/Resources/RInside_0.2.10_R_x86_64-apple-darwin10.8.0.tar.gz'
| to
| '/Users/jonathon/Documents/Frameworks/R.framework/Versions/3.0/Resources/RInside_0.2.10.tgz',
| reason 'No such file or directory'
| packaged installation of ‘RInside’ as ‘RInside_0.2.10.tgz’
| * DONE (RInside)
| 
| 
| 
| > 
| > Dirk
| > 
| > | If anyone could help me understand what's going on, I would
| > appreciate | that. | | with thanks | | Jonathon | | | | | Undefined
| > symbols for architecture x86_64: |   "demangle(std::string
| > const&)", referenced from: |       std::string |
| > Rcpp::get_return_type_dispatch<Rcpp::DataFrame>(Rcpp::traits::integral_constant<bool,
| >
| > 
| | false>) in rcppbridge.o
| > |   "Rcpp::Environment::operator[](std::string const&)", referenced
| > from: |       Rcpp::InternalFunction::set(SEXPREC*) in
| > rcppbridge.o |   "Rcpp::Environment::get(std::string const&)
| > const", referenced from: |
| > Rcpp::Environment::Binding::operator |
| > Rcpp::Function<Rcpp::Function>() const in rcppbridge.o |
| > "Rcpp::Environment::assign(std::string const&, SEXPREC*) const", |
| > referenced from: |       bool
| > Rcpp::Environment::assign<std::string>(std::string const&, |
| > std::string const&) const in rcppbridge.o |       bool
| > Rcpp::Environment::assign<Rcpp::Vector<19> >(std::string | const&,
| > Rcpp::Vector<19> const&) const in rcppbridge.o |       bool |
| > Rcpp::Environment::assign<Rcpp::InternalFunction>(std::string
| > const&, | Rcpp::InternalFunction const&) const in rcppbridge.o |
| > "Rcpp::RObject::attr(std::string const&) const", referenced from: |
| > RcppBridge::readDataSet(std::map<std::string, | Column::ColumnType,
| > std::less<std::string>, | std::allocator<std::pair<std::string
| > const, Column::ColumnType> > > | const&) in rcppbridge.o |
| > RcppBridge::makeFactor(Rcpp::Vector<13>&, Labels const&, bool) | in
| > rcppbridge.o |       RcppBridge::makeFactor(Rcpp::Vector<13>&, |
| > std::vector<std::string, std::allocator<std::string> > const&,
| > bool) | in rcppbridge.o |
| > RcppBridge::readDataSetHeader(std::map<std::string, |
| > Column::ColumnType, std::less<std::string>, |
| > std::allocator<std::pair<std::string const, Column::ColumnType> >
| > > | const&) in rcppbridge.o |
| > Rcpp::Vector<16>::push_back__impl(SEXPREC* const&, |
| > Rcpp::traits::integral_constant<bool, true>) in rcppbridge.o | ld:
| > symbol(s) not found for architecture x86_64 | | | | - -- | | How
| > happy is he born and taught, | That serveth not another's will; |
| > Whose armour is his honest thought, | And simple truth his utmost
| > skill | | This man is freed from servile bands | Of hope to rise,
| > or fear to fall: | Lord of himself, though not of lands, | And,
| > having nothing, yet hath all. | |   -- Sir Henry Wotton | | | | | |
| > -----BEGIN PGP SIGNATURE----- | Version: GnuPG/MacGPG2 v2.0.20
| > (Darwin) | Comment: GPGTools - https://gpgtools.org | Comment:
| > Using GnuPG with Thunderbird - http://www.enigmail.net/ | |
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| > JWf2mub/jtyAdG9/2fja | =qWw7 | -----END PGP SIGNATURE----- |
| > _______________________________________________ | Rcpp-devel
| > mailing list | Rcpp-devel at lists.r-forge.r-project.org |
| > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
| >
| > 
| - -- 
| 
| How happy is he born and taught,
| That serveth not another's will;
| Whose armour is his honest thought,
| And simple truth his utmost skill
| 
| This man is freed from servile bands
| Of hope to rise, or fear to fall:
| Lord of himself, though not of lands,
| And, having nothing, yet hath all.
| 
|   -- Sir Henry Wotton
| 
| 
| 
| 
| 
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| Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
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-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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