* 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/local/clang/bin/gdal-config
checking GDAL version >= 2.0.1... yes (3.12.4)
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 /usr/local/clang23/bin/clang++ -std=gnu++20 accepts -g... yes
checking for /usr/local/clang23/bin/clang++ -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: ‘clang version 23.1.2’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/xbioclim/src'
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c bioclim.cpp -o bioclim.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c bioclim_cuda.cpp -o bioclim_cuda.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c bioclim_model.cpp -o bioclim_model.o
bioclim.cpp:61:22: warning: unused function 'sd_pop_ptr' [-Wunused-function]
61 | static inline double sd_pop_ptr(const double* x) {
| ^~~~~~~~~~
bioclim.cpp:77:22: warning: unused function 'quarter_mean_ptr' [-Wunused-function]
77 | static inline double quarter_mean_ptr(const double* x, int start) {
| ^~~~~~~~~~~~~~~~
bioclim.cpp:82:19: warning: unused function 'quarter_argmax_ptr' [-Wunused-function]
82 | static inline int quarter_argmax_ptr(const double* x) {
| ^~~~~~~~~~~~~~~~~~
bioclim.cpp:93:19: warning: unused function 'quarter_argmin_ptr' [-Wunused-function]
93 | static inline int quarter_argmin_ptr(const double* x) {
| ^~~~~~~~~~~~~~~~~~
bioclim.cpp:465:12: warning: unused function 'count_valid_r' [-Wunused-function]
465 | inline int count_valid_r(const double* x, int n) {
| ^~~~~~~~~~~~~
bioclim.cpp:733:19: warning: unused function 'n_valid_sel' [-Wunused-function]
733 | static inline int n_valid_sel(const NumericVector& x, const IntegerVector& months) {
| ^~~~~~~~~~~
6 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c bioclim_xt.cpp -o bioclim_xt.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c BioclimEngine.cpp -o BioclimEngine.o
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;
| ^
bioclim_xt.cpp:72:22: warning: unused function 'quarter_mean_xt' [-Wunused-function]
72 | static inline double quarter_mean_xt(const double* x, int start) {
| ^~~~~~~~~~~~~~~
2 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c cuda_utils.cpp -o cuda_utils.o
BioclimEngine.cpp:992:10: warning: unused variable 'use_gpu' [-Wunused-variable]
992 | bool use_gpu = false;
| ^~~~~~~
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c era5_monthly.cpp -o era5_monthly.o
1 warning generated.
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c gdal_io.cpp -o gdal_io.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c gdal_io_rcpp.cpp -o gdal_io_rcpp.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c gdal_mask.cpp -o gdal_mask.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c gdal_mask_rcpp.cpp -o gdal_mask_rcpp.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c rcpp_bioclim_mod.cpp -o rcpp_bioclim_mod.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/local/clang/include -DHAVE_GDAL -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -fopenmp -pthread -O2 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -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/local/clang/lib64 -lgdal -fopenmp -pthread
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/xbioclim/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/xbioclim/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/xbioclim/src'
installing to /data/localhost/ripley/R/packages/tests-clang/xbioclim.Rcheck/00LOCK-xbioclim/00new/xbioclim/libs
** R
** 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 (xbioclim)