* installing *source* package ‘magi’ ...
** package ‘magi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’
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'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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/4.3/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.3/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
^
<command line>: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 -single_module -multiply_defined suppress -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
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/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)