* installing *source* package ‘rsofun’ ... ** package ‘rsofun’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 13.2.0’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/rsofun/src' gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c params_core.mod.f90 -o params_core.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c params_siml_biomee.mod.f90 -o params_siml_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c grid_siterun.mod.f90 -o grid_siterun.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c forcing_siterun_biomee.mod.f90 -o forcing_siterun_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c params_soil_biomee.mod.f90 -o params_soil_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c interface_biosphere_biomee.mod.f90 -o interface_biosphere_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c classdefs.mod.f90 -o classdefs.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c datatypes.mod.f90 -o datatypes.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c soil_biomee.mod.f90 -o soil_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c sofunutils.mod.f90 -o sofunutils.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c photosynth_pmodel.mod.f90 -o photosynth_pmodel.mod.o photosynth_pmodel.mod.f90:806:61: 806 | function calc_soilmstress( wcont, thetastar, betao, isgrass ) result( outstress ) | 1 Warning: Unused dummy argument 'isgrass' at (1) [-Wunused-dummy-argument] photosynth_pmodel.mod.f90:115:15: 115 | real :: gpp ! gross primary productivity (g CO2 m-2 d-1) | 1 Warning: Unused variable 'gpp' declared at (1) [-Wunused-variable] photosynth_pmodel.mod.f90:137:50: 137 | real :: omega, omega_star, vcmax_unitiabs_star, tcref, jmax_over_vcmax, jmax_prime | 1 Warning: Unused variable 'vcmax_unitiabs_star' declared at (1) [-Wunused-variable] photosynth_pmodel.mod.f90:108:14: 108 | real :: xi = 0 ! relative cost parameter, Eq. 9 in Stocker et al., 2019 | 1 Warning: Unused variable 'xi' declared at (1) [-Wunused-variable] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c gpp_biomee.mod.f90 -o gpp_biomee.mod.o gpp_biomee.mod.f90:582:18: 582 | integer :: pft | 1 Warning: Unused variable 'pft' declared at (1) [-Wunused-variable] gpp_biomee.mod.f90:79:42: 79 | real :: crownarea_layer(nlayers_max) ! additional GPP for lower layer cohorts due to gaps | 1 Warning: Unused variable 'crownarea_layer' declared at (1) [-Wunused-variable] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c vegetation_biomee.mod.f90 -o vegetation_biomee.mod.o vegetation_biomee.mod.f90:2144:16: 2144 | real :: r | 1 Warning: Unused variable 'r' declared at (1) [-Wunused-variable] vegetation_biomee.mod.f90:46:21: 46 | integer :: iyears | 1 Warning: Unused variable 'iyears' declared at (1) [-Wunused-variable] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c biosphere_biomee.mod.f90 -o biosphere_biomee.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c params_siml_pmodel.mod.f90 -o params_siml_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c forcing_siterun_pmodel.mod.f90 -o forcing_siterun_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c interface_biosphere_pmodel.mod.f90 -o interface_biosphere_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c plant_pmodel.mod.f90 -o plant_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c tile_pmodel.mod.f90 -o tile_pmodel.mod.o tile_pmodel.mod.f90:601:17: 601 | integer :: lu, pft | 1 Warning: Unused variable 'lu' declared at (1) [-Wunused-variable] tile_pmodel.mod.f90:601:22: 601 | integer :: lu, pft | 1 Warning: Unused variable 'pft' declared at (1) [-Wunused-variable] tile_pmodel.mod.f90:588:30: 588 | subroutine diag_annual( tile, tile_fluxes ) | 1 Warning: Unused dummy argument 'tile' at (1) [-Wunused-dummy-argument] tile_pmodel.mod.f90:588:43: 588 | subroutine diag_annual( tile, tile_fluxes ) | 1 Warning: Unused dummy argument 'tile_fluxes' at (1) [-Wunused-dummy-argument] tile_pmodel.mod.f90:536:22: 536 | integer :: lu, pft | 1 Warning: Unused variable 'pft' declared at (1) [-Wunused-variable] tile_pmodel.mod.f90:508:18: 508 | integer :: pft | 1 Warning: Unused variable 'pft' declared at (1) [-Wunused-variable] tile_pmodel.mod.f90:500:37: 500 | subroutine init_annual( tile_fluxes ) | 1 Warning: Unused dummy argument 'tile_fluxes' at (1) [-Wunused-dummy-argument] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c waterbal_splash.mod.f90 -o waterbal_splash.mod.o waterbal_splash.mod.f90:41:15: 41 | real :: delta ! declination angle | 1 Warning: Unused PRIVATE module variable 'delta' declared at (1) [-Wunused-value] waterbal_splash.mod.f90:531:8: 531 | use md_interface_pmodel, only: myinterface | 1 Warning: Unused module variable 'myinterface' which has been explicitly imported at (1) [-Wunused-variable] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c gpp_pmodel.mod.f90 -o gpp_pmodel.mod.o gpp_pmodel.mod.f90:48:33: 48 | real, dimension(npft) :: dassim ! daily leaf-level assimilation rate (per unit leaf area) [gC/m2/d] | 1 Warning: Unused PRIVATE module variable 'dassim' declared at (1) [-Wunused-value] gpp_pmodel.mod.f90:493:18: 493 | integer :: pft | 1 Warning: Unused variable 'pft' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:92:15: 92 | real :: a_c, a_j, a_returned, fact_jmaxlim | 1 Warning: Unused variable 'a_c' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:92:20: 92 | real :: a_c, a_j, a_returned, fact_jmaxlim | 1 Warning: Unused variable 'a_j' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:92:32: 92 | real :: a_c, a_j, a_returned, fact_jmaxlim | 1 Warning: Unused variable 'a_returned' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:92:46: 92 | real :: a_c, a_j, a_returned, fact_jmaxlim | 1 Warning: Unused variable 'fact_jmaxlim' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:78:22: 78 | real :: iabs | 1 Warning: Unused variable 'iabs' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:89:29: 89 | real, save :: tmin_memory ! for low temperature stress | 1 Warning: Unused variable 'tmin_memory' declared at (1) [-Wunused-variable] gpp_pmodel.mod.f90:52:59: 52 | subroutine gpp( tile, tile_fluxes, co2, climate, vegcover, grid, init, in_ppfd) | 1 Warning: Unused dummy argument 'vegcover' at (1) [-Wunused-dummy-argument] gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c vegdynamics_pmodel.mod.f90 -o vegdynamics_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c soiltemp_sitch.mod.f90 -o soiltemp_sitch.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c biosphere_pmodel.mod.f90 -o biosphere_pmodel.mod.o gfortran-13 -fpic -g -O2 -mtune=native -Wall -pedantic -flto=10 -c sofun_r.f90 -o sofun_r.o sofun_r.f90:478:44: 478 | type(outtype_biosphere) :: out_biosphere ! holds all the output used for calculating the cost or maximum likelihood function | 1 Warning: Array 'out_biosphere' at (1) is larger than limit set by '-fmax-stack-var-size=', moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the '-fmax-stack-var-size=' limit (or use '-frecursive', which implies unlimited '-fmax-stack-var-size') - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] sofun_r.f90:282:28: 282 | output_daily_cohorts_cID, & | 1 Warning: Dummy argument 'output_daily_cohorts_cid' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:285:32: 285 | output_daily_cohorts_density, & | 1 Warning: Dummy argument 'output_daily_cohorts_density' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:280:28: 280 | output_daily_cohorts_doy, & | 1 Warning: Dummy argument 'output_daily_cohorts_doy' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:286:32: 286 | output_daily_cohorts_f_layer, & | 1 Warning: Dummy argument 'output_daily_cohorts_f_layer' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:288:28: 288 | output_daily_cohorts_gpp, & | 1 Warning: Dummy argument 'output_daily_cohorts_gpp' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:281:29: 281 | output_daily_cohorts_hour, & | 1 Warning: Dummy argument 'output_daily_cohorts_hour' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:299:29: 299 | output_daily_cohorts_HW_C, & | 1 Warning: Dummy argument 'output_daily_cohorts_hw_c' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:305:29: 305 | output_daily_cohorts_HW_N, & | 1 Warning: Dummy argument 'output_daily_cohorts_hw_n' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:287:28: 287 | output_daily_cohorts_LAI, & | 1 Warning: Dummy argument 'output_daily_cohorts_lai' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:284:30: 284 | output_daily_cohorts_layer, & | 1 Warning: Dummy argument 'output_daily_cohorts_layer' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:296:30: 296 | output_daily_cohorts_leafC, & | 1 Warning: Dummy argument 'output_daily_cohorts_leafc' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:302:30: 302 | output_daily_cohorts_leafN, & | 1 Warning: Dummy argument 'output_daily_cohorts_leafn' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:291:32: 291 | output_daily_cohorts_NPPleaf, & | 1 Warning: Dummy argument 'output_daily_cohorts_nppleaf' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:292:32: 292 | output_daily_cohorts_NPProot, & | 1 Warning: Dummy argument 'output_daily_cohorts_npproot' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:293:32: 293 | output_daily_cohorts_NPPwood, & | 1 Warning: Dummy argument 'output_daily_cohorts_nppwood' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:294:28: 294 | output_daily_cohorts_NSC, & | 1 Warning: Dummy argument 'output_daily_cohorts_nsc' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:300:28: 300 | output_daily_cohorts_NSN, & | 1 Warning: Dummy argument 'output_daily_cohorts_nsn' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:283:28: 283 | output_daily_cohorts_PFT, & | 1 Warning: Dummy argument 'output_daily_cohorts_pft' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:289:29: 289 | output_daily_cohorts_resp, & | 1 Warning: Dummy argument 'output_daily_cohorts_resp' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:297:30: 297 | output_daily_cohorts_rootC, & | 1 Warning: Dummy argument 'output_daily_cohorts_rootc' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:303:30: 303 | output_daily_cohorts_rootN, & | 1 Warning: Dummy argument 'output_daily_cohorts_rootn' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:295:30: 295 | output_daily_cohorts_seedC, & | 1 Warning: Dummy argument 'output_daily_cohorts_seedc' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:301:30: 301 | output_daily_cohorts_seedN, & | 1 Warning: Dummy argument 'output_daily_cohorts_seedn' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:298:29: 298 | output_daily_cohorts_SW_C, & | 1 Warning: Dummy argument 'output_daily_cohorts_sw_c' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:304:29: 304 | output_daily_cohorts_SW_N, & | 1 Warning: Dummy argument 'output_daily_cohorts_sw_n' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:290:31: 290 | output_daily_cohorts_transp, & | 1 Warning: Dummy argument 'output_daily_cohorts_transp' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:279:29: 279 | output_daily_cohorts_year, & | 1 Warning: Dummy argument 'output_daily_cohorts_year' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:278:21: 278 | output_daily_tile, & | 1 Warning: Dummy argument 'output_daily_tile' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:277:22: 277 | output_hourly_tile, & | 1 Warning: Dummy argument 'output_hourly_tile' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument] sofun_r.f90:780:42: 780 | subroutine populate_outarray_hourly_tile( hourly_tile, out_hourly_tile ) !, idx_daily_start, idx_daily_end | ^ Warning: 'populate_outarray_hourly_tile' defined but not used [-Wunused-function] sofun_r.f90:812:41: 812 | subroutine populate_outarray_daily_tile( daily_tile, out_daily_tile ) !, idx_daily_start, idx_daily_end | ^ Warning: 'populate_outarray_daily_tile' defined but not used [-Wunused-function] gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c wrappersc.c -o wrappersc.o gcc-13 -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -fpic -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rsofun.so biosphere_biomee.mod.o biosphere_pmodel.mod.o classdefs.mod.o datatypes.mod.o forcing_siterun_biomee.mod.o forcing_siterun_pmodel.mod.o gpp_biomee.mod.o gpp_pmodel.mod.o grid_siterun.mod.o interface_biosphere_biomee.mod.o interface_biosphere_pmodel.mod.o params_core.mod.o params_siml_biomee.mod.o params_siml_pmodel.mod.o params_soil_biomee.mod.o photosynth_pmodel.mod.o plant_pmodel.mod.o sofun_r.o sofunutils.mod.o soil_biomee.mod.o soiltemp_sitch.mod.o tile_pmodel.mod.o vegdynamics_pmodel.mod.o vegetation_biomee.mod.o waterbal_splash.mod.o wrappersc.o -lgfortran -lm -lquadmath wrappersc.c:12:6: warning: type of 'pmodel_f_' does not match original declaration [-Wlto-type-mismatch] 12 | void F77_NAME(pmodel_f)( | ^ sofun_r.f90:14:21: note: 'pmodel_f' was previously declared here 14 | subroutine pmodel_f( & | ^ sofun_r.f90:14:21: note: code may be misoptimized unless '-fno-strict-aliasing' is used wrappersc.c:113:6: warning: type of 'biomee_f_' does not match original declaration [-Wlto-type-mismatch] 113 | void F77_NAME(biomee_f)( | ^ sofun_r.f90:230:21: note: 'biomee_f' was previously declared here 230 | subroutine biomee_f( & | ^ sofun_r.f90:230:21: note: code may be misoptimized unless '-fno-strict-aliasing' is used make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/rsofun/src' installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/rsofun-lib/00LOCK-rsofun/00new/rsofun/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 (rsofun) Time 5:14.51, 33.59 + 3.36