* 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 18.1.0 (rc4-1)’
make[1]: Entering directory '/tmp/RtmpKXqC5o/R.INSTALL32d0a57e62ed83/medfate/src'
clang++-18 -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 -c RcppExports.cpp -o RcppExports.o
clang++-18 -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 -c biophysicsutils.cpp -o biophysicsutils.o
clang++-18 -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 -c carbon.cpp -o carbon.o
carbon.cpp:6:14: warning: unused variable 'carbonMolarMass' [-Wunused-const-variable]
6 | const double carbonMolarMass = 12.0107; //g*mol-1
| ^~~~~~~~~~~~~~~
carbon.cpp:11:14: warning: unused variable 'leafCperDry' [-Wunused-const-variable]
11 | const double leafCperDry = 0.3; //g C · g dry-1
| ^~~~~~~~~~~
carbon.cpp:12:14: warning: unused variable 'rootCperDry' [-Wunused-const-variable]
12 | const double rootCperDry = 0.4959; //g C · g dry-1
| ^~~~~~~~~~~
3 warnings generated.
clang++-18 -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 -c firebehaviour.cpp -o firebehaviour.o
clang++-18 -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 -c fireseverity.cpp -o fireseverity.o
clang++-18 -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 -c forestutils.cpp -o forestutils.o
clang++-18 -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 -c fuelmoisture.cpp -o fuelmoisture.o
clang++-18 -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 -c fuelstructure.cpp -o fuelstructure.o
clang++-18 -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 -c growth.cpp -o growth.o
clang++-18 -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 -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++-18 -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 -c hydrology.cpp -o hydrology.o
clang++-18 -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 -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++-18 -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 -c inner_cochard.cpp -o inner_cochard.o
clang++-18 -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 -c inner_sperry.cpp -o inner_sperry.o
clang++-18 -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 -c lightextinction.cpp -o lightextinction.o
clang++-18 -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 -c modelInput.cpp -o modelInput.o
clang++-18 -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 -c paramutils.cpp -o paramutils.o
clang++-18 -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 -c phenology.cpp -o phenology.o
clang++-18 -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 -c photosynthesis.cpp -o photosynthesis.o
clang++-18 -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 -c root.cpp -o root.o
clang++-18 -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 -c soil.cpp -o soil.o
clang++-18 -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 -c spwb.cpp -o spwb.o
spwb.cpp:384:106: warning: variable 'LAIcellmax' set but not used [-Wunused-but-set-variable]
384 | 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++-18 -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 -c tissuemoisture.cpp -o tissuemoisture.o
clang++-18 -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 -c transpiration_advanced.cpp -o transpiration_advanced.o
transpiration_advanced.cpp:20:14: warning: unused variable 'SIGMA_Wm2' [-Wunused-const-variable]
20 | const double SIGMA_Wm2 = 5.67*1e-8;
| ^~~~~~~~~
1 warning generated.
clang++-18 -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 -c transpiration_basic.cpp -o transpiration_basic.o
transpiration_basic.cpp:245:12: warning: unused variable 'E_cut' [-Wunused-variable]
245 | double E_cut = E_gmin*LAIphe[c]*(24.0*3600.0*0.018);
| ^~~~~
transpiration_basic.cpp:161:10: warning: variable 's' set but not used [-Wunused-but-set-variable]
161 | double s = 0.0, LAIcell = 0.0, canopyHeight = 0.0, LAIcelllive = 0.0, LAIcellexpanded = 0.0,LAIcelldead = 0.0;
| ^
2 warnings generated.
clang++-18 -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 -c windKatul.cpp -o windKatul.o
clang++-18 -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 -c windextinction.cpp -o windextinction.o
clang++-18 -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 -c woodformation.cpp -o woodformation.o
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpKXqC5o/R.INSTALL32d0a57e62ed83/medfate/src'
make[1]: Entering directory '/tmp/RtmpKXqC5o/R.INSTALL32d0a57e62ed83/medfate/src'
make[1]: Leaving directory '/tmp/RtmpKXqC5o/R.INSTALL32d0a57e62ed83/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)