* installing *source* package ‘PSGD’ ... ** package ‘PSGD’ 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 clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking climits usability... yes checking climits presence... yes checking for climits... yes Type unsigned long long is supported uint16_t and unit8_t are available in stdint.h uint16_t and unit8_t are available in inttypes.h Found builtin CTZ method (for unsigned long) Found builtin CTZ method (for unsigned long long) checking for ffsl... yes checking for ffsll... yes Found builtin popcount method (for unsigned long) Found builtin popcount method (for unsigned long long) checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP... unsupported configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/autoconfig.h ** libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Logistic_Model.cpp -o Logistic_Model.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Main_CV_PSGD.cpp -o Main_CV_PSGD.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Main_PSGD.cpp -o Main_PSGD.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PSGD.cpp -o PSGD.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PS_Model.cpp -o PS_Model.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Step_Model.cpp -o Step_Model.o In file included from PSGD.cpp:17: In file included from ./PSGD.hpp:19: In file included from ./PS_Model.hpp:19: In file included from ./Logistic_Model.hpp:19: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from PS_Model.cpp:16: In file included from ./PS_Model.hpp:19: In file included from ./Logistic_Model.hpp:19: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from Main_CV_PSGD.cpp:16: In file included from ./PSGD.hpp:19: In file included from ./PS_Model.hpp:19: In file included from ./Logistic_Model.hpp:19: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from Step_Model.cpp:16: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from Main_PSGD.cpp:16: In file included from ./PSGD.hpp:19: In file included from ./PS_Model.hpp:19: In file included from ./Logistic_Model.hpp:19: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from Logistic_Model.cpp:17: In file included from ./Logistic_Model.hpp:19: ./config.h:23:12: warning: 'ARMA_DONT_USE_OPENMP' macro redefined [-Wmacro-redefined] # define ARMA_DONT_USE_OPENMP ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h:31:9: note: previous definition is here #define ARMA_DONT_USE_OPENMP 1 ^ In file included from Logistic_Model.cpp:17: ./Logistic_Model.hpp:41:15: warning: private field 'beta_size' is not used [-Wunused-private-field] arma::uword beta_size; // Number of coefficients ^ 1 warning generated. 1 warning generated. 2 warnings generated. 1 warning generated. 1 warning generated. 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o PSGD.so Logistic_Model.o Main_CV_PSGD.o Main_PSGD.o PSGD.o PS_Model.o RcppExports.o Step_Model.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/PSGD.Rcheck/00LOCK-PSGD/00new/PSGD/libs ** generating debug symbols (dSYM) ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (PSGD)