* installing *source* package ‘Morpho’ ...
** package ‘Morpho’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CVAdists.cpp -o CVAdists.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CubeStuff.cpp -o CubeStuff.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ang_calc.cpp -o ang_calc.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-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo:26:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c armaGinvCpp.cpp -o armaGinvCpp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c asymPerm.cpp -o asymPerm.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c barycenter.cpp -o barycenter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/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-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo:26:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createL.cpp -o createL.o
createL.cpp:14:9: warning: variable 'omp' set but not used [-Wunused-but-set-variable]
int omp = 1;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doozers.cpp -o doozers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c edgePlane.cpp -o edgePlane.o
In file included from edgePlane.cpp:1:
In file included from ./doozers.h:7:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo:26:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c face_zero.cpp -o face_zero.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastSubsetMeans.cpp -o fastSubsetMeans.o
fastSubsetMeans.cpp:10:9: warning: unused variable 'threads' [-Wunused-variable]
int threads = as<int>(threads_);
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c meshres.cpp -o meshres.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c permudistArma.cpp -o permudistArma.o
permudistArma.cpp:9:10: warning: unused variable 'usemedian' [-Wunused-variable]
bool usemedian = Rcpp::as<bool>(usemedian_);
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c points2mesh.cpp -o points2mesh.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tpsfx.cpp -o tpsfx.o
tpsfx.cpp:24:9: warning: unused variable 'threads' [-Wunused-variable]
int threads = as<int>(threads_);
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tweakU.cpp -o tweakU.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I/opt/R/arm64/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-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo:26:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: 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-arm64/Rlib/4.3/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
#pragma message ("INFO: see the documentation for details")
^
3 warnings generated.
clang++ -arch arm64 -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/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/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)