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Building RcppArmadillo with and without Armadillo (homebrew) installed
Installing package into ‘/Users/lpuerto/Library/R/3.x/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.9.600.4.0.tar.gz'
Content type 'application/x-gzip' length 1360028 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
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 /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ accepts -g... yes
checking how to run the C++ preprocessor... /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... found and suitable
checking LAPACK_LIBS... system LAPACK found
checking for OpenMP... missing
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c RcppArmadillo.cpp -o RcppArmadillo.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c RcppExports.cpp -o RcppExports.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c fastLm.cpp -o fastLm.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.6.1/lib/R/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/usr/local/opt/openblas/lib -lopenblas -L/usr/local/lib/gcc/9 -lgfortran -lquadmath -lm -L/usr/local/Cellar/r/3.6.1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 from temporary location
Error: package or namespace load failed for ‘RcppArmadillo’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so':
dlopen(/Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so, 6): Symbol not found: _wrapper2_ddot_
Referenced from: /Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so
Expected in: flat namespace
in /Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs/RcppArmadillo.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/lpuerto/Library/R/3.x/library/RcppArmadillo’
* restoring previous ‘/Users/lpuerto/Library/R/3.x/library/RcppArmadillo’
Warning in install.packages :
installation of package ‘RcppArmadillo’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/4m/8dbgslcd3mb62brwc7nzskn40000gn/T/Rtmp5vwz48/downloaded_packages’
Installing package into ‘/Users/lpuerto/Library/R/3.x/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.9.600.4.0.tar.gz'
Content type 'application/x-gzip' length 1360028 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
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 /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ accepts -g... yes
checking how to run the C++ preprocessor... /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... found and suitable
checking LAPACK_LIBS... system LAPACK found
checking for OpenMP... missing
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c RcppArmadillo.cpp -o RcppArmadillo.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c RcppExports.cpp -o RcppExports.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -I"/usr/local/Cellar/r/3.6.1/lib/R/include" -DNDEBUG -I"/Users/lpuerto/Library/R/3.x/library/Rcpp/include" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/usr/local/include -I/usr/local/opt/llvm/include -I/usr/local/opt/openssl/include -I/usr/local/opt/gettext/include -I/usr/local/opt/tcl-tk/include -I../inst/include -fPIC -g -O3 -Wall -pedantic -mtune=native -pipe -c fastLm.cpp -o fastLm.o
/usr/local/bin/ccache /usr/local/opt/llvm/bin/clang++ -std=c++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.6.1/lib/R/lib -L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/usr/local/opt/openblas/lib -lopenblas -L/usr/local/lib/gcc/9 -lgfortran -lquadmath -lm -L/usr/local/Cellar/r/3.6.1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /Users/lpuerto/Library/R/3.x/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
The downloaded source packages are in
‘/private/var/folders/4m/8dbgslcd3mb62brwc7nzskn40000gn/T/Rtmp5vwz48/downloaded_packages’
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