Install log for 'Morpho'

* installing *source* package ‘Morpho’ ...
** this is package ‘Morpho’ version ‘2.12’
** 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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c barycenter.cpp -o barycenter.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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c covPCA.cpp -o covPCA.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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c face_zero.cpp -o face_zero.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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c permudistArma.cpp -o permudistArma.o
fastSubsetMeans.cpp:10:9: warning: unused variable 'threads' [-Wunused-variable]
    int threads = as<int>(threads_);
        ^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c points2mesh.cpp -o points2mesh.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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c tpsfx.cpp -o tpsfx.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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c updateNormals.cpp -o updateNormals.o
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.
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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/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)