* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘xbioclim’ ...
** this is package ‘xbioclim’ version ‘1.0.3’
** package ‘xbioclim’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gdal-config... /usr/bin/gdal-config
checking GDAL version >= 2.0.1... yes (3.13.3)
checking whether GDAL links correctly... checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++-16 -std=gnu++20 accepts -g... yes
checking for g++-16 -std=gnu++20 option to enable C++11 features... -std=gnu++11
yes
checking for nvcc... not-found
configure: Building without CUDA support (GPU acceleration disabled)
configure: creating ./config.status
config.status: creating src/Makevars
** libs
specified C++17
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjpRA1i/R.INSTALL3c6fcd6f8feca/xbioclim/src'
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c bioclim.cpp -o bioclim.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c bioclim_cuda.cpp -o bioclim_cuda.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c bioclim_model.cpp -o bioclim_model.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c bioclim_xt.cpp -o bioclim_xt.o
bioclim_xt.cpp: In function ‘Rcpp::NumericMatrix bioclim_xt(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int)’:
bioclim_xt.cpp:170:25: warning: variable ‘t_sumsq’ set but not used [-Wunused-but-set-variable=]
170 | double t_sum = 0.0, t_sumsq = 0.0;
| ^~~~~~~
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c BioclimEngine.cpp -o BioclimEngine.o
BioclimEngine.cpp: In member function ‘std::string xbioclim::BioclimEngine::compute_pipelined()’:
BioclimEngine.cpp:992:10: warning: unused variable ‘use_gpu’ [-Wunused-variable]
992 | bool use_gpu = false;
| ^~~~~~~
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c cuda_utils.cpp -o cuda_utils.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c era5_monthly.cpp -o era5_monthly.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c gdal_io.cpp -o gdal_io.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c gdal_io_rcpp.cpp -o gdal_io_rcpp.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c gdal_mask.cpp -o gdal_mask.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c gdal_mask_rcpp.cpp -o gdal_mask_rcpp.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_bioclim_mod.cpp -o rcpp_bioclim_mod.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/gdal -DHAVE_GDAL -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -pthread -O2 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o xbioclim.so bioclim.o bioclim_cuda.o bioclim_model.o bioclim_xt.o BioclimEngine.o cuda_utils.o era5_monthly.o gdal_io.o gdal_io_rcpp.o gdal_mask.o gdal_mask_rcpp.o rcpp_bioclim_mod.o RcppExports.o -L/usr/lib/x86_64-linux-gnu -lgdal -fopenmp -pthread -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjpRA1i/R.INSTALL3c6fcd6f8feca/xbioclim/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjpRA1i/R.INSTALL3c6fcd6f8feca/xbioclim/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjpRA1i/R.INSTALL3c6fcd6f8feca/xbioclim/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-xbioclim/00new/xbioclim/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘xbioclim’
finding HTML links ... done
BioclimData-class html
BioclimData html
BioclimModel-class html
BioclimModel-methods html
BioclimModel html
ClimateBlock html
apply_mask_cpp html
bio01_cpp html
bio02_cpp html
bio03_cpp html
bio04_cpp html
bio05_cpp html
bio06_cpp html
bio07_cpp html
bio08_cpp html
bio09_cpp html
bio10_cpp html
bio11_cpp html
bio12_cpp html
bio13_cpp html
bio14_cpp html
bio15_cpp html
bio16_cpp html
bio17_cpp html
bio18_cpp html
bio19_cpp html
bioclim-raster html
bioclim-variables html
bioclim_block html
bioclim_cpp html
bioclim_engine html
bioclim_errors html
bioclim_model_compute html
bioclim_model_is_null html
bioclim_model_new html
bioclim_raster html
bioclim_rolling html
bioclim_rolling_cpp html
bioclim_warnings html
bioclim_window html
bioclim_window_cpp html
bioclim_xt html
check_messages html
clear_messages html
create_mask html
cuda_device_count html
cuda_device_info html
cuda_info html
days_in_month html
dot-compute_bioclim_block html
dot-resolve_climate_input html
dot-resolve_engine_mask html
engine_compute html
engine_create html
engine_open html
engine_set_device html
engine_set_dtype html
engine_set_mask html
engine_set_output html
engine_set_pipeline html
engine_set_threads html
engine_set_tile_size html
engine_set_variables html
era5-monthly html
era5_bioclim html
era5_bioclim_years html
era5_t2m_to_monthly_cpp html
era5_to_monthly_cpp html
era5_tp_to_monthly_cpp html
gdal_can_open html
gdal_info html
has_cuda html
has_error html
has_gdal html
has_warning html
primitives html
push_error html
push_warning html
quarter_argmax html
quarter_argmin html
quarter_values html
quarterly_fixed html
quarterly_rolling html
quarterly_variables html
quarterly_variables_cpp html
rasterize_mask_cpp html
rolling_quarter_mean html
rolling_quarter_sum html
sd_pop html
validate_monthly html
validate_spatraster html
xbioclim-messages html
xbioclim-package html
** 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 (xbioclim)