* installing *source* package ‘Morpho’ ...
** this is package ‘Morpho’ version ‘2.13’
** package ‘Morpho’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c ang_calc.cpp -o ang_calc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c covPCA.cpp -o covPCA.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c createL.cpp -o createL.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c edgePlane.cpp -o edgePlane.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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]
14 | int omp = 1;
| ^
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c inscribeEllipse.cpp -o inscribeEllipse.o
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c meshres.cpp -o meshres.o
fastSubsetMeans.cpp:10:9: warning: unused variable 'threads' [-Wunused-variable]
10 | int threads = as<int>(threads_);
| ^~~~~~~
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c permudistArma.cpp -o permudistArma.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -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/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c tpsfx.cpp -o tpsfx.o
inscribeEllipse.cpp:98:13: warning: unused variable 's3' [-Wunused-variable]
98 | float s3 = step;
| ^~
inscribeEllipse.cpp:82:11: warning: unused variable 'minrr' [-Wunused-variable]
82 | float minrr = 6;
| ^~~~~
inscribeEllipse.cpp:87:11: warning: unused variable 'bestx' [-Wunused-variable]
87 | float bestx = init_point[0];
| ^~~~~
inscribeEllipse.cpp:89:11: warning: unused variable 'besty' [-Wunused-variable]
89 | float besty = init_point[1];
| ^~~~~
inscribeEllipse.cpp:92:11: warning: variable 'bestiter' set but not used [-Wunused-but-set-variable]
92 | float bestiter = 0;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c tweakU.cpp -o tweakU.o
permudistArma.cpp:9:10: warning: unused variable 'usemedian' [-Wunused-variable]
9 | bool usemedian = Rcpp::as<bool>(usemedian_);
| ^~~~~~~~~
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_USE_CURRENT -fPIC -falign-functions=64 -Wall -g -O2 -c updateNormals.cpp -o updateNormals.o
tpsfx.cpp:24:9: warning: unused variable 'threads' [-Wunused-variable]
24 | int threads = as<int>(threads_);
| ^~~~~~~
5 warnings generated.
1 warning generated.
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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 inscribeEllipse.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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/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)