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@mike-lawrence
Created November 4, 2013 18:07
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Log from attempt to install minqa and RcppEigen
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** libs
gfortran -arch x86_64 -fPIC -g -O2 -c altmov.f -o altmov.o
gfortran -arch x86_64 -fPIC -g -O2 -c bigden.f -o bigden.o
gfortran -arch x86_64 -fPIC -g -O2 -c biglag.f -o biglag.o
gfortran -arch x86_64 -fPIC -g -O2 -c bobyqa.f -o bobyqa.o
gfortran -arch x86_64 -fPIC -g -O2 -c bobyqb.f -o bobyqb.o
gfortran -arch x86_64 -fPIC -g -O2 -c lagmax.f -o lagmax.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c minqa.cpp -o minqa.o
gfortran -arch x86_64 -fPIC -g -O2 -c newuoa.f -o newuoa.o
gfortran -arch x86_64 -fPIC -g -O2 -c newuob.f -o newuob.o
gfortran -arch x86_64 -fPIC -g -O2 -c prelim.f -o prelim.o
gfortran -arch x86_64 -fPIC -g -O2 -c rescue.f -o rescue.o
gfortran -arch x86_64 -fPIC -g -O2 -c trsapp.f -o trsapp.o
gfortran -arch x86_64 -fPIC -g -O2 -c trsbox.f -o trsbox.o
gfortran -arch x86_64 -fPIC -g -O2 -c trstep.f -o trstep.o
gfortran -arch x86_64 -fPIC -g -O2 -c uobyqa.f -o uobyqa.o
gfortran -arch x86_64 -fPIC -g -O2 -c uobyqb.f -o uobyqb.o
gfortran -arch x86_64 -fPIC -g -O2 -c update.f -o update.o
gfortran -arch x86_64 -fPIC -g -O2 -c updatebobyqa.f -o updatebobyqa.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 minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa/libs/minqa.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa/libs/minqa.so, 6): Symbol not found: __ZN4Rcpp8FunctionC1ERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa/libs/minqa.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa/libs/minqa.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/minqa’
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I../inst/include -fPIC -mtune=core2 -g -O2 -c RcppEigen.cpp -o RcppEigen.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I../inst/include -fPIC -mtune=core2 -g -O2 -c fastLm.cpp -o fastLm.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 RcppEigen.so RcppEigen.o fastLm.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen/libs/RcppEigen.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen/libs/RcppEigen.so, 6): Symbol not found: __ZNSoD0Ev
Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen/libs/RcppEigen.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen/libs/RcppEigen.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppEigen’
@dmbates
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dmbates commented Nov 4, 2013

Demangling the names of the symbols that are not present produces

bates@thin40:/tmp$ c++filt _ZN4Rcpp8FunctionC1ERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
Rcpp::Function::Function(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)
bates@thin40:/tmp$ c++filt _ZNSoD0Ev
std::basic_ostream<char, std::char_traits<char> >::~basic_ostream()

on a Linux system (I don't have access to an OS X system).

I guess I would start by trying to install Rcpp from sources. The order seems to be backwards in that the new version of RcppEigen should be installed before the minqa version. I would try the order Rcpp, RcppEigen then minqa.

@mike-lawrence
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Installing in the order you suggested works! :O)

@dkvasnicka
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Installing Rcpp from sources also helped when I was trying to install rmr2 (R & Hadoop lib) and was getting the very same "Symbol not found" message.
So thanks for this little info! Saved my day!

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