Created
November 4, 2013 18:07
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Log from attempt to install minqa and RcppEigen
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* 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’ |
Installing in the order you suggested works! :O)
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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Demangling the names of the symbols that are not present produces
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.