* installing *source* package ‘medfate’ ...
** package ‘medfate’ 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 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aspwb.cpp -o aspwb.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c biophysicsutils.cpp -o biophysicsutils.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c carbon.cpp -o carbon.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c communication_structures.cpp -o communication_structures.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c firebehaviour.cpp -o firebehaviour.o
carbon.cpp:7:14: warning: unused variable 'carbonMolarMass' [-Wunused-const-variable]
const double carbonMolarMass = 12.0107; //g*mol-1
^
carbon.cpp:12:14: warning: unused variable 'leafCperDry' [-Wunused-const-variable]
const double leafCperDry = 0.3; //g C · g dry-1
^
carbon.cpp:13:14: warning: unused variable 'rootCperDry' [-Wunused-const-variable]
const double rootCperDry = 0.4959; //g C · g dry-1
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fireseverity.cpp -o fireseverity.o
3 warnings 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c forestutils.cpp -o forestutils.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fuelmoisture.cpp -o fuelmoisture.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fuelstructure.cpp -o fuelstructure.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c growth.cpp -o growth.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hydraulics.cpp -o hydraulics.o
hydraulics.cpp:12:14: warning: unused variable 'maxPsi' [-Wunused-const-variable]
double const maxPsi = -0.000001;
^
hydraulics.cpp:13:14: warning: unused variable 'cmhead2MPa' [-Wunused-const-variable]
double const cmhead2MPa = 0.00009804139; //Constant to transform cm head to MPa
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hydrology.cpp -o hydrology.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c incbeta.cpp -o incbeta.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c incgamma.cpp -o incgamma.o
2 warnings 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inner_sperry.cpp -o inner_sperry.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c inner_sureau.cpp -o inner_sureau.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lightextinction_advanced.cpp -o lightextinction_advanced.o
incgamma.cpp:9:14: warning: unused variable 'machtol' [-Wunused-const-variable]
const double machtol = 1.0E-15;
^
inner_sperry.cpp:10:14: warning: unused variable 'eps_xylem' [-Wunused-const-variable]
const double eps_xylem = 1e3; // xylem elastic modulus (1 GPa = 1000 MPa)
^
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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lightextinction_basic.cpp -o lightextinction_basic.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c modelInput.cpp -o modelInput.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c numerical_solving.cpp -o numerical_solving.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c paramutils.cpp -o paramutils.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phenology.cpp -o phenology.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c photosynthesis.cpp -o photosynthesis.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c root.cpp -o root.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c soil.cpp -o soil.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c soil_thermodynamics.cpp -o soil_thermodynamics.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spwb.cpp -o spwb.o
soil.cpp:15:14: warning: unused variable 'cmTOMPa' [-Wunused-const-variable]
const double cmTOMPa = 0.00009804139432;
^
soil.cpp:20:14: warning: unused variable 'mTOMPa' [-Wunused-const-variable]
const double mTOMPa = 0.009804139432; //1/9.804139*0.000001;
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tissuemoisture.cpp -o tissuemoisture.o
spwb.cpp:538:106: warning: variable 'LAIcellmax' set but not used [-Wunused-but-set-variable]
double s = 0.0, LAIcell = 0.0, LAIcelldead = 0.0, LAIcelllive = 0.0, LAIcellexpanded = 0.0, Cm = 0.0, LAIcellmax = 0.0;
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transpiration_advanced.cpp -o transpiration_advanced.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transpiration_basic.cpp -o transpiration_basic.o
transpiration_basic.cpp:189:10: warning: variable 's' set but not used [-Wunused-but-set-variable]
double s = 0.0, LAIcell = 0.0, canopyHeight = 0.0, LAIcelllive = 0.0, LAIcellexpanded = 0.0,LAIcelldead = 0.0;
^
2 warnings 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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c windKatul.cpp -o windKatul.o
transpiration_advanced.cpp:25:14: warning: unused variable 'SIGMA_Wm2' [-Wunused-const-variable]
const double SIGMA_Wm2 = 5.67*1e-8;
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c windextinction.cpp -o windextinction.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/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/meteoland/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c woodformation.cpp -o woodformation.o
1 warning generated.
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 medfate.so RcppExports.o aspwb.o biophysicsutils.o carbon.o communication_structures.o firebehaviour.o fireseverity.o forestutils.o fuelmoisture.o fuelstructure.o growth.o hydraulics.o hydrology.o incbeta.o incgamma.o inner_sperry.o inner_sureau.o lightextinction_advanced.o lightextinction_basic.o modelInput.o numerical_solving.o paramutils.o phenology.o photosynthesis.o root.o soil.o soil_thermodynamics.o spwb.o tissuemoisture.o transpiration_advanced.o transpiration_basic.o windKatul.o windextinction.o woodformation.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/medfate.Rcheck/00LOCK-medfate/00new/medfate/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** 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 (medfate)