* installing *source* package ‘BioCro’ ... ** this is package ‘BioCro’ version ‘3.2.0’ ** package ‘BioCro’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BioCro/src' g++ -std=gnu++11 -MT R_dynamical_system.o -MMD -MP -MF .deps/R_dynamical_system.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_dynamical_system.o R_dynamical_system.cpp mv -f .deps/R_dynamical_system.Td .deps/R_dynamical_system.d && touch R_dynamical_system.o g++ -std=gnu++11 -MT R_framework_version.o -MMD -MP -MF .deps/R_framework_version.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_framework_version.o R_framework_version.cpp mv -f .deps/R_framework_version.Td .deps/R_framework_version.d && touch R_framework_version.o g++ -std=gnu++11 -MT R_get_all_ode_solvers.o -MMD -MP -MF .deps/R_get_all_ode_solvers.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_get_all_ode_solvers.o R_get_all_ode_solvers.cpp mv -f .deps/R_get_all_ode_solvers.Td .deps/R_get_all_ode_solvers.d && touch R_get_all_ode_solvers.o g++ -std=gnu++11 -MT R_module_library.o -MMD -MP -MF .deps/R_module_library.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_module_library.o R_module_library.cpp mv -f .deps/R_module_library.Td .deps/R_module_library.d && touch R_module_library.o g++ -std=gnu++11 -MT R_modules.o -MMD -MP -MF .deps/R_modules.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_modules.o R_modules.cpp mv -f .deps/R_modules.Td .deps/R_modules.d && touch R_modules.o g++ -std=gnu++11 -MT R_run_biocro.o -MMD -MP -MF .deps/R_run_biocro.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_run_biocro.o R_run_biocro.cpp g++ -std=gnu++11 -MT R_system_derivatives.o -MMD -MP -MF .deps/R_system_derivatives.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o R_system_derivatives.o R_system_derivatives.cpp mv -f .deps/R_run_biocro.Td .deps/R_run_biocro.d && touch R_run_biocro.o g++ -std=gnu++11 -MT init.o -MMD -MP -MF .deps/init.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o init.o init.cpp mv -f .deps/init.Td .deps/init.d && touch init.o g++ -std=gnu++11 -MT module_library/AuxBioCro.o -MMD -MP -MF .deps/module_library/AuxBioCro.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/AuxBioCro.o module_library/AuxBioCro.cpp mv -f .deps/module_library/AuxBioCro.Td .deps/module_library/AuxBioCro.d && touch module_library/AuxBioCro.o g++ -std=gnu++11 -MT module_library/CanAC.o -MMD -MP -MF .deps/module_library/CanAC.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/CanAC.o module_library/CanAC.cpp mv -f .deps/R_system_derivatives.Td .deps/R_system_derivatives.d && touch R_system_derivatives.o mv -f .deps/module_library/CanAC.Td .deps/module_library/CanAC.d && touch module_library/CanAC.o g++ -std=gnu++11 -MT module_library/FvCB_assim.o -MMD -MP -MF .deps/module_library/FvCB_assim.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/FvCB_assim.o module_library/FvCB_assim.cpp mv -f .deps/module_library/FvCB_assim.Td .deps/module_library/FvCB_assim.d && touch module_library/FvCB_assim.o g++ -std=gnu++11 -MT module_library/ball_berry_gs.o -MMD -MP -MF .deps/module_library/ball_berry_gs.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/ball_berry_gs.o module_library/ball_berry_gs.cpp mv -f .deps/module_library/ball_berry_gs.Td .deps/module_library/ball_berry_gs.d && touch module_library/ball_berry_gs.o g++ -std=gnu++11 -MT module_library/boundary_layer_conductance.o -MMD -MP -MF .deps/module_library/boundary_layer_conductance.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/boundary_layer_conductance.o module_library/boundary_layer_conductance.cpp mv -f .deps/module_library/boundary_layer_conductance.Td .deps/module_library/boundary_layer_conductance.d && touch module_library/boundary_layer_conductance.o g++ -std=gnu++11 -MT module_library/c3CanAC.o -MMD -MP -MF .deps/module_library/c3CanAC.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c3CanAC.o module_library/c3CanAC.cpp mv -f .deps/module_library/c3CanAC.Td .deps/module_library/c3CanAC.d && touch module_library/c3CanAC.o g++ -std=gnu++11 -MT module_library/c3_canopy.o -MMD -MP -MF .deps/module_library/c3_canopy.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c3_canopy.o module_library/c3_canopy.cpp mv -f .deps/module_library/c3_canopy.Td .deps/module_library/c3_canopy.d && touch module_library/c3_canopy.o g++ -std=gnu++11 -MT module_library/c3_leaf_photosynthesis.o -MMD -MP -MF .deps/module_library/c3_leaf_photosynthesis.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c3_leaf_photosynthesis.o module_library/c3_leaf_photosynthesis.cpp mv -f .deps/module_library/c3_leaf_photosynthesis.Td .deps/module_library/c3_leaf_photosynthesis.d && touch module_library/c3_leaf_photosynthesis.o g++ -std=gnu++11 -MT module_library/c3_temperature_response.o -MMD -MP -MF .deps/module_library/c3_temperature_response.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c3_temperature_response.o module_library/c3_temperature_response.cpp mv -f .deps/module_library/c3_temperature_response.Td .deps/module_library/c3_temperature_response.d && touch module_library/c3_temperature_response.o g++ -std=gnu++11 -MT module_library/c3photo.o -MMD -MP -MF .deps/module_library/c3photo.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c3photo.o module_library/c3photo.cpp mv -f .deps/module_library/c3photo.Td .deps/module_library/c3photo.d && touch module_library/c3photo.o g++ -std=gnu++11 -MT module_library/c4_leaf_photosynthesis.o -MMD -MP -MF .deps/module_library/c4_leaf_photosynthesis.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c4_leaf_photosynthesis.o module_library/c4_leaf_photosynthesis.cpp mv -f .deps/module_library/c4_leaf_photosynthesis.Td .deps/module_library/c4_leaf_photosynthesis.d && touch module_library/c4_leaf_photosynthesis.o g++ -std=gnu++11 -MT module_library/c4photo.o -MMD -MP -MF .deps/module_library/c4photo.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/c4photo.o module_library/c4photo.cpp mv -f .deps/module_library/c4photo.Td .deps/module_library/c4photo.d && touch module_library/c4photo.o g++ -std=gnu++11 -MT module_library/collatz_photo.o -MMD -MP -MF .deps/module_library/collatz_photo.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/collatz_photo.o module_library/collatz_photo.cpp mv -f .deps/module_library/collatz_photo.Td .deps/module_library/collatz_photo.d && touch module_library/collatz_photo.o g++ -std=gnu++11 -MT module_library/eC4photo.o -MMD -MP -MF .deps/module_library/eC4photo.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/eC4photo.o module_library/eC4photo.cpp mv -f .deps/module_library/eC4photo.Td .deps/module_library/eC4photo.d && touch module_library/eC4photo.o g++ -std=gnu++11 -MT module_library/leaf_energy_balance.o -MMD -MP -MF .deps/module_library/leaf_energy_balance.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/leaf_energy_balance.o module_library/leaf_energy_balance.cpp g++ -std=gnu++11 -MT module_library/lightME.o -MMD -MP -MF .deps/module_library/lightME.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/lightME.o module_library/lightME.cpp mv -f .deps/module_library/lightME.Td .deps/module_library/lightME.d && touch module_library/lightME.o g++ -std=gnu++11 -MT module_library/module_library.o -MMD -MP -MF .deps/module_library/module_library.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/module_library.o module_library/module_library.cpp mv -f .deps/module_library/leaf_energy_balance.Td .deps/module_library/leaf_energy_balance.d && touch module_library/leaf_energy_balance.o g++ -std=gnu++11 -MT module_library/multilayer_c3_canopy.o -MMD -MP -MF .deps/module_library/multilayer_c3_canopy.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/multilayer_c3_canopy.o module_library/multilayer_c3_canopy.cpp mv -f .deps/module_library/multilayer_c3_canopy.Td .deps/module_library/multilayer_c3_canopy.d && touch module_library/multilayer_c3_canopy.o g++ -std=gnu++11 -MT module_library/multilayer_c4_canopy.o -MMD -MP -MF .deps/module_library/multilayer_c4_canopy.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/multilayer_c4_canopy.o module_library/multilayer_c4_canopy.cpp mv -f .deps/module_library/multilayer_c4_canopy.Td .deps/module_library/multilayer_c4_canopy.d && touch module_library/multilayer_c4_canopy.o g++ -std=gnu++11 -MT module_library/multilayer_canopy_properties.o -MMD -MP -MF .deps/module_library/multilayer_canopy_properties.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/multilayer_canopy_properties.o module_library/multilayer_canopy_properties.cpp mv -f .deps/module_library/multilayer_canopy_properties.Td .deps/module_library/multilayer_canopy_properties.d && touch module_library/multilayer_canopy_properties.o mv -f .deps/module_library/module_library.Td .deps/module_library/module_library.d && touch module_library/module_library.o g++ -std=gnu++11 -MT module_library/multilayer_rue_canopy.o -MMD -MP -MF .deps/module_library/multilayer_rue_canopy.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/multilayer_rue_canopy.o module_library/multilayer_rue_canopy.cpp mv -f .deps/module_library/multilayer_rue_canopy.Td .deps/module_library/multilayer_rue_canopy.d && touch module_library/multilayer_rue_canopy.o g++ -std=gnu++11 -MT module_library/penman_monteith_leaf_temperature.o -MMD -MP -MF .deps/module_library/penman_monteith_leaf_temperature.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/penman_monteith_leaf_temperature.o module_library/penman_monteith_leaf_temperature.cpp mv -f .deps/module_library/penman_monteith_leaf_temperature.Td .deps/module_library/penman_monteith_leaf_temperature.d && touch module_library/penman_monteith_leaf_temperature.o g++ -std=gnu++11 -MT module_library/rasmussen_specific_heat.o -MMD -MP -MF .deps/module_library/rasmussen_specific_heat.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/rasmussen_specific_heat.o module_library/rasmussen_specific_heat.cpp mv -f .deps/module_library/rasmussen_specific_heat.Td .deps/module_library/rasmussen_specific_heat.d && touch module_library/rasmussen_specific_heat.o g++ -std=gnu++11 -MT module_library/rue_leaf_photosynthesis.o -MMD -MP -MF .deps/module_library/rue_leaf_photosynthesis.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/rue_leaf_photosynthesis.o module_library/rue_leaf_photosynthesis.cpp g++ -std=gnu++11 -MT module_library/sunML.o -MMD -MP -MF .deps/module_library/sunML.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o module_library/sunML.o module_library/sunML.cpp mv -f .deps/module_library/rue_leaf_photosynthesis.Td .deps/module_library/rue_leaf_photosynthesis.d && touch module_library/rue_leaf_photosynthesis.o g++ -std=gnu++11 -MT framework/R_helper_functions.o -MMD -MP -MF .deps/framework/R_helper_functions.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/R_helper_functions.o framework/R_helper_functions.cpp g++ -std=gnu++11 -MT framework/dynamical_system.o -MMD -MP -MF .deps/framework/dynamical_system.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/dynamical_system.o framework/dynamical_system.cpp mv -f .deps/module_library/sunML.Td .deps/module_library/sunML.d && touch module_library/sunML.o mv -f .deps/framework/R_helper_functions.Td .deps/framework/R_helper_functions.d && touch framework/R_helper_functions.o g++ -std=gnu++11 -MT framework/dynamical_system_helper_functions.o -MMD -MP -MF .deps/framework/dynamical_system_helper_functions.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/dynamical_system_helper_functions.o framework/dynamical_system_helper_functions.cpp mv -f .deps/framework/dynamical_system_helper_functions.Td .deps/framework/dynamical_system_helper_functions.d && touch framework/dynamical_system_helper_functions.o g++ -std=gnu++11 -MT framework/module_helper_functions.o -MMD -MP -MF .deps/framework/module_helper_functions.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/module_helper_functions.o framework/module_helper_functions.cpp mv -f .deps/framework/dynamical_system.Td .deps/framework/dynamical_system.d && touch framework/dynamical_system.o g++ -std=gnu++11 -MT framework/modules.o -MMD -MP -MF .deps/framework/modules.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/modules.o framework/modules.cpp mv -f .deps/framework/modules.Td .deps/framework/modules.d && touch framework/modules.o mv -f .deps/framework/module_helper_functions.Td .deps/framework/module_helper_functions.d && touch framework/module_helper_functions.o g++ -std=gnu++11 -MT framework/ode_solver.o -MMD -MP -MF .deps/framework/ode_solver.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/ode_solver.o framework/ode_solver.cpp g++ -std=gnu++11 -MT framework/quadratic_root.o -MMD -MP -MF .deps/framework/quadratic_root.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/quadratic_root.o framework/quadratic_root.cpp mv -f .deps/framework/ode_solver.Td .deps/framework/ode_solver.d && touch framework/ode_solver.o mv -f .deps/framework/quadratic_root.Td .deps/framework/quadratic_root.d && touch framework/quadratic_root.o g++ -std=gnu++11 -MT framework/state_map.o -MMD -MP -MF .deps/framework/state_map.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/state_map.o framework/state_map.cpp g++ -std=gnu++11 -MT framework/validate_dynamical_system.o -MMD -MP -MF .deps/framework/validate_dynamical_system.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/validate_dynamical_system.o framework/validate_dynamical_system.cpp mv -f .deps/framework/state_map.Td .deps/framework/state_map.d && touch framework/state_map.o mv -f .deps/framework/validate_dynamical_system.Td .deps/framework/validate_dynamical_system.d && touch framework/validate_dynamical_system.o g++ -std=gnu++11 -MT framework/ode_solver_library/boost_ode_solvers.o -MMD -MP -MF .deps/framework/ode_solver_library/boost_ode_solvers.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/ode_solver_library/boost_ode_solvers.o framework/ode_solver_library/boost_ode_solvers.cpp mv -f .deps/framework/ode_solver_library/boost_ode_solvers.Td .deps/framework/ode_solver_library/boost_ode_solvers.d && touch framework/ode_solver_library/boost_ode_solvers.o g++ -std=gnu++11 -MT framework/ode_solver_library/ode_solver_factory.o -MMD -MP -MF .deps/framework/ode_solver_library/ode_solver_factory.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/ode_solver_library/ode_solver_factory.o framework/ode_solver_library/ode_solver_factory.cpp g++ -std=gnu++11 -MT framework/utils/module_dependency_utilities.o -MMD -MP -MF .deps/framework/utils/module_dependency_utilities.Td -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../src/inc -DR_NO_REMAP -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c -o framework/utils/module_dependency_utilities.o framework/utils/module_dependency_utilities.cpp mv -f .deps/framework/utils/module_dependency_utilities.Td .deps/framework/utils/module_dependency_utilities.d && touch framework/utils/module_dependency_utilities.o mv -f .deps/framework/ode_solver_library/ode_solver_factory.Td .deps/framework/ode_solver_library/ode_solver_factory.d && touch framework/ode_solver_library/ode_solver_factory.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o BioCro.so R_dynamical_system.o R_framework_version.o R_get_all_ode_solvers.o R_module_library.o R_modules.o R_run_biocro.o R_system_derivatives.o init.o module_library/AuxBioCro.o module_library/CanAC.o module_library/FvCB_assim.o module_library/ball_berry_gs.o module_library/boundary_layer_conductance.o module_library/c3CanAC.o module_library/c3_canopy.o module_library/c3_leaf_photosynthesis.o module_library/c3_temperature_response.o module_library/c3photo.o module_library/c4_leaf_photosynthesis.o module_library/c4photo.o module_library/collatz_photo.o module_library/eC4photo.o module_library/leaf_energy_balance.o module_library/lightME.o module_library/module_library.o module_library/multilayer_c3_canopy.o module_library/multilayer_c4_canopy.o module_library/multilayer_canopy_properties.o module_library/multilayer_rue_canopy.o module_library/penman_monteith_leaf_temperature.o module_library/rasmussen_specific_heat.o module_library/rue_leaf_photosynthesis.o module_library/sunML.o framework/R_helper_functions.o framework/dynamical_system.o framework/dynamical_system_helper_functions.o framework/module_helper_functions.o framework/modules.o framework/ode_solver.o framework/quadratic_root.o framework/state_map.o framework/validate_dynamical_system.o framework/ode_solver_library/boost_ode_solvers.o framework/ode_solver_library/ode_solver_factory.o framework/utils/module_dependency_utilities.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BioCro/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BioCro/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BioCro/src' installing to /data/gannet/ripley/R/packages/tests-devel/BioCro.Rcheck/00LOCK-BioCro/00new/BioCro/libs ** R ** data *** moving datasets to lazyload DB ** 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 (BioCro)