Install log for 'hsphase'

* installing *source* package ‘hsphase’ ...
** this is package ‘hsphase’ version ‘3.0.0’
** package ‘hsphase’ 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++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FastDist.cpp -o FastDist.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FillGap.cpp -o FillGap.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FixBothStrand.cpp -o FixBothStrand.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MAF.cpp -o MAF.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Ohd.cpp -o Ohd.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SwitchAdd.cpp -o SwitchAdd.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SwitchDetector.cpp -o SwitchDetector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TypeConversion.cpp -o TypeConversion.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c block.cpp -o block.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c block4Phase.cpp -o block4Phase.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c co.cpp -o co.o
SwitchAdd.cpp:29:9: warning: unused variable 'minLength' [-Wunused-variable]
    int minLength = as<int>(minlength);
        ^
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c diag.cpp -o diag.o
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/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fixRotation.cpp -o fixRotation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hsp.cpp -o hsp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ibdcluster.cpp -o ibdcluster.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c memory.cpp -o memory.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c mhMat.cpp -o mhMat.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c oh.cpp -o oh.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ohg.cpp -o ohg.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ohp.cpp -o ohp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c swDetect.cpp -o swDetect.o
mhMat.cpp:63:24: warning: unused variable 'iElemnt' [-Wunused-variable]
        vector<int>::iterator iElemnt;
                              ^
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 hsphase.so FastDist.o FillGap.o FixBothStrand.o MAF.o Ohd.o SwitchAdd.o SwitchDetector.o TypeConversion.o block.o block4Phase.o co.o diag.o fixRotation.o hsp.o ibdcluster.o main.o memory.o mhMat.o oh.o ohg.o ohp.o swDetect.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
ld: warning: could not create compact unwind for ___emutls_get_address: does not use standard frame
ld: warning: could not create compact unwind for _allocate_tramp_ctrl: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_created: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_deleted: does not use standard frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.5/hsphase.Rcheck/00LOCK-hsphase/00new/hsphase/libs
** generating debug symbols (dSYM)
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (hsphase)