* installing *source* package ‘Morpho’ ... ** package ‘Morpho’ 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CVAdists.cpp -o CVAdists.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CubeStuff.cpp -o CubeStuff.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ang_calc.cpp -o ang_calc.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c armaGinvCpp.cpp -o armaGinvCpp.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c asymPerm.cpp -o asymPerm.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c barycenter.cpp -o barycenter.o In file included from ang_calc.cpp:1: In file included from ./doozers.h:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:326:11: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:331:13: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:334:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c covPCA.cpp -o covPCA.o In file included from covPCA.cpp:1: In file included from ./covPCA.h:5: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:326:11: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:331:13: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:334:11: 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createL.cpp -o createL.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doozers.cpp -o doozers.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c edgePlane.cpp -o edgePlane.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c face_zero.cpp -o face_zero.o In file included from edgePlane.cpp:1: In file included from ./doozers.h:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:326:11: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:331:13: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:334:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastSubsetMeans.cpp -o fastSubsetMeans.o createL.cpp:14:9: warning: variable 'omp' set but not used [-Wunused-but-set-variable] int omp = 1; ^ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c meshres.cpp -o meshres.o 1 warning 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c permudistArma.cpp -o permudistArma.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c points2mesh.cpp -o points2mesh.o fastSubsetMeans.cpp:10:9: warning: unused variable 'threads' [-Wunused-variable] int threads = as<int>(threads_); ^ 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tpsfx.cpp -o tpsfx.o 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tweakU.cpp -o tweakU.o 1 warning 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c updateNormals.cpp -o updateNormals.o In file included from updateNormals.cpp:1: In file included from ./updateNormals.h:4: In file included from ./doozers.h:7: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo:26: /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:326:11: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:331:13: 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/4.4/RcppArmadillo/include/armadillo_bits/config.hpp:334:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ permudistArma.cpp:9:10: warning: unused variable 'usemedian' [-Wunused-variable] bool usemedian = Rcpp::as<bool>(usemedian_); ^ tpsfx.cpp:24:9: warning: unused variable 'threads' [-Wunused-variable] int threads = as<int>(threads_); ^ 1 warning generated. 1 warning generated. 3 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Morpho.so CVAdists.o CubeStuff.o ang_calc.o armaGinvCpp.o asymPerm.o barycenter.o covPCA.o createL.o doozers.o edgePlane.o face_zero.o fastSubsetMeans.o init.o meshres.o permudistArma.o points2mesh.o tpsfx.o tweakU.o updateNormals.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/4.4/Morpho.Rcheck/00LOCK-Morpho/00new/Morpho/libs ** generating debug symbols (dSYM) ** R ** data ** inst ** 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 (Morpho)