* installing *source* package ‘medfate’ ...
** package ‘medfate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c biophysicsutils.cpp -o biophysicsutils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c carbon.cpp -o carbon.o
carbon.cpp:6:14: warning: unused variable 'carbonMolarMass' [-Wunused-const-variable]
const double carbonMolarMass = 12.0107; //g*mol-1
             ^
carbon.cpp:11:14: warning: unused variable 'leafCperDry' [-Wunused-const-variable]
const double leafCperDry = 0.3; //g C · g dry-1
             ^
carbon.cpp:12:14: warning: unused variable 'rootCperDry' [-Wunused-const-variable]
const double rootCperDry = 0.4959; //g C · g dry-1
             ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c firebehaviour.cpp -o firebehaviour.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fireseverity.cpp -o fireseverity.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c forestutils.cpp -o forestutils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fuelmoisture.cpp -o fuelmoisture.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fuelstructure.cpp -o fuelstructure.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c growth.cpp -o growth.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -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
             ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c hydrology.cpp -o hydrology.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c incgamma.cpp -o incgamma.o
incgamma.cpp:9:14: warning: unused variable 'machtol' [-Wunused-const-variable]
const double machtol = 1.0E-15;
             ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c inner_cochard.cpp -o inner_cochard.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c inner_sperry.cpp -o inner_sperry.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c lightextinction.cpp -o lightextinction.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c modelInput.cpp -o modelInput.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c paramutils.cpp -o paramutils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c phenology.cpp -o phenology.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c photosynthesis.cpp -o photosynthesis.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c root.cpp -o root.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c soil.cpp -o soil.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c spwb.cpp -o spwb.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tissuemoisture.cpp -o tissuemoisture.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c transpiration_advanced.cpp -o transpiration_advanced.o
transpiration_advanced.cpp:20:14: warning: unused variable 'SIGMA_Wm2' [-Wunused-const-variable]
const double SIGMA_Wm2 = 5.67*1e-8;
             ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c transpiration_basic.cpp -o transpiration_basic.o
transpiration_basic.cpp:245:12: warning: unused variable 'E_cut' [-Wunused-variable]
    double E_cut = E_gmin*LAIphe[c]*(24.0*3600.0*0.018);
           ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c windKatul.cpp -o windKatul.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c windextinction.cpp -o windextinction.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/Rcpp/include' -I'/Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.2/meteoland/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c woodformation.cpp -o woodformation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o medfate.so RcppExports.o biophysicsutils.o carbon.o firebehaviour.o fireseverity.o forestutils.o fuelmoisture.o fuelstructure.o growth.o hydraulics.o hydrology.o incgamma.o inner_cochard.o inner_sperry.o lightextinction.o modelInput.o paramutils.o phenology.o photosynthesis.o root.o soil.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/high-sierra-x86_64/results/4.2/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)