* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘medfate’ ...
** package ‘medfate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.5 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpc7Wgl0/R.INSTALL7fd746a20c5c6/medfate/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c aspwb.cpp -o aspwb.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c biophysicsutils.cpp -o biophysicsutils.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c carbon.cpp -o carbon.o
carbon.cpp:7:14: warning: unused variable 'carbonMolarMass' [-Wunused-const-variable]
7 | const double carbonMolarMass = 12.0107; //g*mol-1
| ^~~~~~~~~~~~~~~
carbon.cpp:12:14: warning: unused variable 'leafCperDry' [-Wunused-const-variable]
12 | const double leafCperDry = 0.3; //g C · g dry-1
| ^~~~~~~~~~~
carbon.cpp:13:14: warning: unused variable 'rootCperDry' [-Wunused-const-variable]
13 | const double rootCperDry = 0.4959; //g C · g dry-1
| ^~~~~~~~~~~
3 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c communication_structures.cpp -o communication_structures.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c firebehaviour.cpp -o firebehaviour.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c fireseverity.cpp -o fireseverity.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c forestutils.cpp -o forestutils.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c fuelmoisture.cpp -o fuelmoisture.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c fuelstructure.cpp -o fuelstructure.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c growth.cpp -o growth.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c hydraulics.cpp -o hydraulics.o
hydraulics.cpp:12:14: warning: unused variable 'maxPsi' [-Wunused-const-variable]
12 | double const maxPsi = -0.000001;
| ^~~~~~
hydraulics.cpp:13:14: warning: unused variable 'cmhead2MPa' [-Wunused-const-variable]
13 | double const cmhead2MPa = 0.00009804139; //Constant to transform cm head to MPa
| ^~~~~~~~~~
2 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c hydrology.cpp -o hydrology.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c incbeta.cpp -o incbeta.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c incgamma.cpp -o incgamma.o
incgamma.cpp:9:14: warning: unused variable 'machtol' [-Wunused-const-variable]
9 | const double machtol = 1.0E-15;
| ^~~~~~~
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c inner_sperry.cpp -o inner_sperry.o
inner_sperry.cpp:10:14: warning: unused variable 'eps_xylem' [-Wunused-const-variable]
10 | const double eps_xylem = 1e3; // xylem elastic modulus (1 GPa = 1000 MPa)
| ^~~~~~~~~
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c inner_sureau.cpp -o inner_sureau.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c lightextinction_advanced.cpp -o lightextinction_advanced.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c lightextinction_basic.cpp -o lightextinction_basic.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c modelInput.cpp -o modelInput.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c numerical_solving.cpp -o numerical_solving.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c paramutils.cpp -o paramutils.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c phenology.cpp -o phenology.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c photosynthesis.cpp -o photosynthesis.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c root.cpp -o root.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c soil.cpp -o soil.o
soil.cpp:15:14: warning: unused variable 'cmTOMPa' [-Wunused-const-variable]
15 | const double cmTOMPa = 0.00009804139432;
| ^~~~~~~
soil.cpp:20:14: warning: unused variable 'mTOMPa' [-Wunused-const-variable]
20 | const double mTOMPa = 0.009804139432; //1/9.804139*0.000001;
| ^~~~~~
2 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c soil_thermodynamics.cpp -o soil_thermodynamics.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c spwb.cpp -o spwb.o
spwb.cpp:538:106: warning: variable 'LAIcellmax' set but not used [-Wunused-but-set-variable]
538 | double s = 0.0, LAIcell = 0.0, LAIcelldead = 0.0, LAIcelllive = 0.0, LAIcellexpanded = 0.0, Cm = 0.0, LAIcellmax = 0.0;
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c tissuemoisture.cpp -o tissuemoisture.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c transpiration_advanced.cpp -o transpiration_advanced.o
transpiration_advanced.cpp:25:14: warning: unused variable 'SIGMA_Wm2' [-Wunused-const-variable]
25 | const double SIGMA_Wm2 = 5.67*1e-8;
| ^~~~~~~~~
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c transpiration_basic.cpp -o transpiration_basic.o
transpiration_basic.cpp:189:10: warning: variable 's' set but not used [-Wunused-but-set-variable]
189 | double s = 0.0, LAIcell = 0.0, canopyHeight = 0.0, LAIcelllive = 0.0, LAIcellexpanded = 0.0,LAIcelldead = 0.0;
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c windKatul.cpp -o windKatul.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c windextinction.cpp -o windextinction.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/meteoland/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c woodformation.cpp -o woodformation.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpc7Wgl0/R.INSTALL7fd746a20c5c6/medfate/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpc7Wgl0/R.INSTALL7fd746a20c5c6/medfate/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpc7Wgl0/R.INSTALL7fd746a20c5c6/medfate/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-medfate/00new/medfate/libs
** 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)