* installing *source* package ‘magi’ ... ** package ‘magi’ 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 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c MagiMain.cpp -o MagiMain.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c MagiSolver.cpp -o MagiSolver.o In file included from MagiSolver.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppFullloglikelihood.cpp -o RcppFullloglikelihood.o In file included from RcppFullloglikelihood.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppTestingUtilities.cpp -o RcppTestingUtilities.o In file included from RcppTestingUtilities.cpp:10: In file included from ./RcppWrapper.h:9: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppTranslation.cpp -o RcppTranslation.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppWrapper.cpp -o RcppWrapper.o In file included from RcppWrapper.cpp:2: In file included from ./RcppWrapper.h:9: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppXthetasigma.cpp -o RcppXthetasigma.o In file included from RcppXthetasigma.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c Rcppgpsmoothing.cpp -o Rcppgpsmoothing.o Rcppgpsmoothing.cpp:1:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c RcppsolveMagi.cpp -o RcppsolveMagi.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c Sampler.cpp -o Sampler.o In file included from Sampler.cpp:1: ./Sampler.h:19:10: warning: private field 'positiveSystem' is not used [-Wunused-private-field] bool positiveSystem; ^ 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c band.cpp -o band.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c classDefinition.cpp -o classDefinition.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c dynamicalSystemModels.cpp -o dynamicalSystemModels.o dynamicalSystemModels.cpp:377:15: warning: unused variable 'dS' [-Wunused-variable] const vec & dS = x.col(1); ^ dynamicalSystemModels.cpp:398:15: warning: unused variable 'dS' [-Wunused-variable] const vec & dS = x.col(1); ^ dynamicalSystemModels.cpp:400:15: warning: unused variable 'RS' [-Wunused-variable] const vec & RS = x.col(3); ^ dynamicalSystemModels.cpp:429:15: warning: unused variable 'dS' [-Wunused-variable] const vec & dS = x.col(1); ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c fullloglikelihood.cpp -o fullloglikelihood.o In file included from fullloglikelihood.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c gpcov.cpp -o gpcov.o In file included from gpcov.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c hmc.cpp -o hmc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c testingUtilities.cpp -o testingUtilities.o In file included from testingUtilities.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c tgtdistr.cpp -o tgtdistr.o tgtdistr.cpp:2:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 1 ^ tgtdistr.cpp:514:48: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] fOdeModelShifted.fOdeDx = [&muAllDimension, &dotmuAllDimension, &fOdeModel] ~~~^~~~~~~~~~~~~~~~~ tgtdistr.cpp:519:52: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] fOdeModelShifted.fOdeDtheta = [&muAllDimension, &dotmuAllDimension, &fOdeModel] ~~~^~~~~~~~~~~~~~~~~ 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/roptim/include' -I/opt/R/arm64/include -DNDEBUG -I'../inst/include' -fPIC -falign-functions=64 -Wall -g -O2 -c xthetasigma.cpp -o xthetasigma.o In file included from xthetasigma.cpp:3: ./tgtdistr.h:4:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :2:9: note: previous definition is here #define NDEBUG 1 ^ xthetasigma.cpp:46:50: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] fOdeModelShifted.fOdeDx = [&muAllDimension, &dotmuAllDimension, &fOdeModel] ~~~^~~~~~~~~~~~~~~~~ xthetasigma.cpp:51:54: warning: lambda capture 'dotmuAllDimension' is not used [-Wunused-lambda-capture] fOdeModelShifted.fOdeDtheta = [&muAllDimension, &dotmuAllDimension, &fOdeModel] ~~~^~~~~~~~~~~~~~~~~ 3 warnings 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 magi.so MagiMain.o MagiSolver.o RcppExports.o RcppFullloglikelihood.o RcppTestingUtilities.o RcppTranslation.o RcppWrapper.o RcppXthetasigma.o Rcppgpsmoothing.o RcppsolveMagi.o Sampler.o band.o classDefinition.o dynamicalSystemModels.o fullloglikelihood.o gpcov.o hmc.o testingUtilities.o tgtdistr.o xthetasigma.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/4.4/magi.Rcheck/00LOCK-magi/00new/magi/libs ** generating debug symbols (dSYM) ** R ** data ** 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 (magi)