[Rcpp-devel] Trouble linking with Rcpp
Jonathon Love
jon at thon.cc
Tue Jul 8 15:58:04 CEST 2014
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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
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?
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 | | | | | |
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>
- --
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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