* installing *source* package ‘GSE’ ... ** package ‘GSE’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ 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 cov-em.cpp -o cov-em.o In file included from cov-em.cpp:1: In file included from ./cov-em.h:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ 3 warnings generated. 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 emve.cpp -o emve.o In file included from emve.cpp:4: In file included from ./emve.h:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ emve.cpp:153:16: warning: variable 'max_cand_scale' set but not used [-Wunused-but-set-variable] double max_cand_scale; ^ emve.cpp:154:16: warning: variable 'min_cand_scale' set but not used [-Wunused-but-set-variable] double min_cand_scale; ^ 5 warnings generated. 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 gse-rocke.cpp -o gse-rocke.o In file included from gse-rocke.cpp:1: In file included from ./gse-rocke.h:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ gse-rocke.cpp:46:6: warning: unused variable 'print_step' [-Wunused-variable] int print_step = as(Print_step); ^ gse-rocke.cpp:131:6: warning: unused variable 'ximp_update' [-Wunused-variable] int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, gamma_tune_group, wgts_mem, wgtsp_mem, ximp_mem); ^ gse-rocke.cpp:162:6: warning: variable 'error_code' set but not used [-Wunused-but-set-variable] int error_code = *error_code_mem; // 0 = no error, 1 = non-positive scale, 2 = non-positive definite est scatter ^ gse-rocke.cpp:295:6: warning: unused variable 'n' [-Wunused-variable] int n = x.n_rows; ^ gse-rocke.cpp:416:12: warning: unused variable 'weight2' [-Wunused-variable] double weight2 = weight1 * (md / ppi); ^ 8 warnings generated. 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 gse.cpp -o gse.o In file included from gse.cpp:1: In file included from ./gse.h:4: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:338:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:343:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") ^ /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:346:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ gse.cpp:41:9: warning: unused variable 'print_step' [-Wunused-variable] int print_step = as(Print_step); ^ gse.cpp:102:9: warning: unused variable 'ximp_update' [-Wunused-variable] int ximp_update = update(x, Omega, Sigma0, false, mu0, stilde0, miss_group_unique, miss_group_counts, tuning_const_group, wgts_mem, wgtsp_mem, ximp_mem); ^ gse.cpp:132:9: warning: variable 'error_code' set but not used [-Wunused-but-set-variable] int error_code = *error_code_mem; // 0 = no error, 1 = non-positive scale, 2 = non-positive definite est scatter ^ gse.cpp:337:24: warning: unused variable 'weight2' [-Wunused-variable] double weight2 = weight1 * (md / ppi); ^ 7 warnings generated. clang -arch x86_64 -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 init.c -o init.o 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 GSE.so cov-em.o emve.o gse-rocke.o gse.o init.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/GSE.Rcheck/00LOCK-GSE/00new/GSE/libs ** generating debug symbols (dSYM) ** R ** data ** 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 (GSE)