* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘stLMM’ ...
** this is package ‘stLMM’ version ‘0.0.2’
** package ‘stLMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C compiler: ‘gcc-15 (Debian 15.3.0-1) 15.3.0’
using C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJmK8KB/R.INSTALL6498511fd6c79/stLMM/src'
gcc-15 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Matrix_stubs.c -o Matrix_stubs.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c corModels.cpp -o corModels.o
gcc-15 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nn.cpp -o nn.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_common.cpp -o stLMM_common.o
stLMM_common.cpp: In function ‘double logDetFactor(cholmod_factor*)’:
stLMM_common.cpp:308:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
308 | for(i = 0; i < L->nsuper; i++){
| ~~^~~~~~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_covariance.cpp -o stLMM_covariance.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_precision.cpp -o stLMM_precision.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_predict.cpp -o stLMM_predict.o
stLMM_predict.cpp: In function ‘SEXPREC* stLMM_predict_nngp_joint_false(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
stLMM_predict.cpp:168:10: warning: unused variable ‘one’ [-Wunused-variable]
168 | double one, h, u, mean, rBr, var;
| ^~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_recover.cpp -o stLMM_recover.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_sampler.cpp -o stLMM_sampler.o
stLMM_sampler.cpp: In function ‘void update_mean_without_alpha(SamplerState*, const double*, double*)’:
stLMM_sampler.cpp:78:7: warning: unused variable ‘i’ [-Wunused-variable]
78 | int i, inc;
| ^
stLMM_sampler.cpp: In function ‘double log_cov_params_target_collapsed(SamplerState*, const double*)’:
stLMM_sampler.cpp:295:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
295 | else if(s->residualModel == 2)
| ^
stLMM_sampler.cpp: In function ‘int log_cov_params_target_collapsed_try(SamplerState*, const double*, double*)’:
stLMM_sampler.cpp:343:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
343 | else if(s->residualModel == 2)
| ^
stLMM_sampler.cpp: In function ‘int cov_params_block_mh_collapsed_step(SamplerState*, CovProposalBlock*, const double*)’:
stLMM_sampler.cpp:748:10: warning: unused variable ‘j’ [-Wunused-variable]
748 | int i, j;
| ^
stLMM_sampler.cpp: In function ‘SEXPREC* list_B_by_term(SamplerState*)’:
stLMM_sampler.cpp:1135:13: warning: unused variable ‘m_i’ [-Wunused-variable]
1135 | int t, j, m_i, total_nnbr;
| ^~~
stLMM_sampler.cpp: In function ‘SEXPREC* build_term_description_object(SamplerState*, SEXP, int)’:
stLMM_sampler.cpp:2197:32: warning: variable ‘fixed_r’ set but not used [-Wunused-but-set-variable]
2197 | SEXP meta_r, td_r, global_r, fixed_r, random_r, re_terms_r, process_terms_r;
| ^~~~~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c stLMM_state.cpp -o stLMM_state.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BayesLogit/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Matrix/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o stLMM.so Matrix_stubs.o corModels.o init.o nn.o stLMM_common.o stLMM_covariance.o stLMM_precision.o stLMM_predict.o stLMM_recover.o stLMM_sampler.o stLMM_state.o utils.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJmK8KB/R.INSTALL6498511fd6c79/stLMM/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJmK8KB/R.INSTALL6498511fd6c79/stLMM/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJmK8KB/R.INSTALL6498511fd6c79/stLMM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-stLMM/00new/stLMM/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘stLMM’
finding HTML links ... done
as_mcmc html
as_samples html
car_graph html
fitted.stLMM html
get_cor_models html
log_lik html
predict.stLMM_recovery html
recover html
resid html
stLMM-methods html
stLMM-priors html
stLMM-terms html
stLMM html
stunitco html
*** copying figures
** 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 (stLMM)