* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘GpGp’ ...
** package ‘GpGp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppJ7xRH/R.INSTALL23754865a06b74/GpGp/src'
g++-14 -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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c matrix_mult.cpp -o matrix_mult.o
g++-14 -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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c vecchia_loglik_grad_info.cpp -o vecchia_loglik_grad_info.o
In file included from covmatrix_funs.h:9,
from onepass.h:8,
from vecchia_loglik_grad_info.cpp:8:
covmatrix_funs_01.h: In function ‘arma::cube d_exponential_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_01.h:108:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
108 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_01.h: In function ‘arma::cube d_matern_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_01.h:240:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
240 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_01.h: In function ‘arma::cube d_matern15_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_01.h:341:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
341 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
In file included from covmatrix_funs.h:10:
covmatrix_funs_02.h: In function ‘arma::cube d_matern_anisotropic2D(arma::vec, arma::mat)’:
covmatrix_funs_02.h:150:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
150 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h: In function ‘arma::cube d_matern_anisotropic3D(arma::vec, arma::mat)’:
covmatrix_funs_02.h:304:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
304 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h: In function ‘arma::cube d_matern_anisotropic3D_alt(arma::vec, arma::mat)’:
covmatrix_funs_02.h:498:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
498 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h: In function ‘arma::cube d_exponential_anisotropic2D(arma::vec, arma::mat)’:
covmatrix_funs_02.h:624:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
624 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h: In function ‘arma::cube d_exponential_anisotropic3D(arma::vec, arma::mat)’:
covmatrix_funs_02.h:768:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
768 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h:727:12: warning: unused variable ‘nugget’ [-Wunused-variable]
727 | double nugget = covparms( 0 )*covparms( 7 );
| ^~~~~~
covmatrix_funs_02.h: In function ‘arma::cube d_exponential_anisotropic3D_alt(arma::vec, arma::mat)’:
covmatrix_funs_02.h:945:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
945 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
In file included from covmatrix_funs.h:11:
covmatrix_funs_03.h: In function ‘arma::mat matern_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_03.h:41:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
41 | if( covparms.n_elem - 3 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_03.h: In function ‘arma::cube d_matern_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_03.h:90:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
90 | if( covparms.n_elem - 3 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_03.h:144:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
144 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_03.h:95:12: warning: unused variable ‘nugget’ [-Wunused-variable]
95 | double nugget = covparms( 0 )*covparms( dim + 2 );
| ^~~~~~
covmatrix_funs_03.h: In function ‘arma::mat exponential_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_03.h:179:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
179 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_03.h: In function ‘arma::cube d_exponential_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_03.h:224:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
224 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_03.h:267:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
267 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_03.h:229:12: warning: unused variable ‘nugget’ [-Wunused-variable]
229 | double nugget = covparms( 0 )*covparms( dim + 1 );
| ^~~~~~
covmatrix_funs_03.h: In function ‘arma::cube d_matern_spacetime(arma::vec, arma::mat)’:
covmatrix_funs_03.h:395:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
395 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_03.h:337:12: warning: unused variable ‘nugget’ [-Wunused-variable]
337 | double nugget = covparms( 0 )*covparms( 4 );
| ^~~~~~
covmatrix_funs_03.h: In function ‘arma::cube d_exponential_spacetime(arma::vec, arma::mat)’:
covmatrix_funs_03.h:507:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
507 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
In file included from covmatrix_funs.h:16:
covmatrix_funs_08.h: In function ‘arma::cube d_matern_nonstat_var(arma::vec, arma::mat)’:
covmatrix_funs_08.h:156:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
156 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_08.h: In function ‘arma::cube d_exponential_nonstat_var(arma::vec, arma::mat)’:
covmatrix_funs_08.h:295:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
295 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
In file included from covmatrix_funs.h:17:
covmatrix_funs_09.h: In function ‘arma::mat matern15_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_09.h:39:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
39 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_09.h: In function ‘arma::cube d_matern15_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_09.h:84:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
84 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_09.h:127:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
127 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_09.h:89:12: warning: unused variable ‘nugget’ [-Wunused-variable]
89 | double nugget = covparms( 0 )*covparms( dim + 1 );
| ^~~~~~
In file included from covmatrix_funs.h:18:
covmatrix_funs_10.h: In function ‘arma::cube d_matern25_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_10.h:102:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
102 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_10.h: In function ‘arma::mat matern25_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_10.h:137:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
137 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_10.h: In function ‘arma::cube d_matern25_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_10.h:182:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
182 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_10.h:226:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
226 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_10.h:187:12: warning: unused variable ‘nugget’ [-Wunused-variable]
187 | double nugget = covparms( 0 )*covparms( dim + 1 );
| ^~~~~~
In file included from covmatrix_funs.h:19:
covmatrix_funs_11.h: In function ‘arma::cube d_matern35_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_11.h:116:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
116 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_11.h: In function ‘arma::mat matern35_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_11.h:151:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
151 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_11.h: In function ‘arma::cube d_matern35_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_11.h:201:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
201 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_11.h:251:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
251 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_11.h:206:12: warning: unused variable ‘nugget’ [-Wunused-variable]
206 | double nugget = covparms( 0 )*covparms( dim + 1 );
| ^~~~~~
In file included from covmatrix_funs.h:20:
covmatrix_funs_12.h: In function ‘arma::cube d_matern45_isotropic(arma::vec, arma::mat)’:
covmatrix_funs_12.h:118:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
118 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_12.h: In function ‘arma::mat matern45_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_12.h:153:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
153 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_12.h: In function ‘arma::cube d_matern45_scaledim(arma::vec, arma::mat)’:
covmatrix_funs_12.h:204:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
204 | if( covparms.n_elem - 2 != dim ){
| ~~~~~~~~~~~~~~~~~~~~^~~~~~
covmatrix_funs_12.h:255:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
255 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_12.h:209:12: warning: unused variable ‘nugget’ [-Wunused-variable]
209 | double nugget = covparms( 0 )*covparms( dim + 1 );
| ^~~~~~
In file included from covmatrix_funs.h:21:
covmatrix_funs_13.h: In function ‘arma::cube d_matern_categorical(arma::vec, arma::mat)’:
covmatrix_funs_13.h:177:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
177 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_13.h:126:12: warning: unused variable ‘nugget’ [-Wunused-variable]
126 | double nugget = covparms( 0 )*covparms( 4 );
| ^~~~~~
covmatrix_funs_13.h:127:16: warning: unused variable ‘categ’ [-Wunused-variable]
127 | double categ = covparms(0)*covparms(3);
| ^~~~~
covmatrix_funs_13.h: In function ‘arma::cube d_matern_spacetime_categorical(arma::vec, arma::mat)’:
covmatrix_funs_13.h:373:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
373 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_13.h: In function ‘arma::cube d_matern_spacetime_categorical_local(arma::vec, arma::mat)’:
covmatrix_funs_13.h:661:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
661 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_13.h:542:12: warning: unused variable ‘nugget’ [-Wunused-variable]
542 | double nugget = covparms(0)*covparms(8);
| ^~~~~~
onepass.h: In function ‘arma::mat mychol(arma::mat)’:
onepass.h:93:10: warning: variable ‘pd’ set but not used [-Wunused-but-set-variable]
93 | bool pd = true;
| ^~
onepass.h: In function ‘void synthesize_grouped(Rcpp::NumericVector, Rcpp::StringVector, Rcpp::NumericMatrix, Rcpp::List, Rcpp::NumericVector&, Rcpp::NumericMatrix, Rcpp::NumericVector*, Rcpp::NumericVector*, Rcpp::NumericVector*, Rcpp::NumericMatrix*, Rcpp::NumericMatrix*, bool, bool)’:
onepass.h:700:9: warning: unused variable ‘dim’ [-Wunused-variable]
700 | int dim = locs.ncol();
| ^~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o GpGp.so RcppExports.o matrix_mult.o vecchia_loglik_grad_info.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppJ7xRH/R.INSTALL23754865a06b74/GpGp/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppJ7xRH/R.INSTALL23754865a06b74/GpGp/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppJ7xRH/R.INSTALL23754865a06b74/GpGp/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-GpGp/00new/GpGp/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 ‘GpGp’
finding HTML links ... done
GpGp html
L_mult html
L_t_mult html
Linv_mult html
Linv_t_mult html
argo2016 html
cond_sim html
condition_number html
expit html
exponential_anisotropic2D html
exponential_anisotropic3D html
exponential_anisotropic3D_alt html
exponential_isotropic html
exponential_nonstat_var html
exponential_scaledim html
exponential_spacetime html
exponential_sphere html
exponential_sphere_warp html
exponential_spheretime html
exponential_spheretime_warp html
fast_Gp_sim html
fast_Gp_sim_Linv html
find_ordered_nn html
find_ordered_nn_brute html
fisher_scoring html
fit_model html
get_linkfun html
get_penalty html
get_start_parms html
group_obs html
jason3 html
matern15_isotropic html
matern15_scaledim html
matern25_isotropic html
matern25_scaledim html
matern35_isotropic html
matern35_scaledim html
matern45_isotropic html
matern45_scaledim html
matern_anisotropic2D html
matern_anisotropic3D html
matern_anisotropic3D_alt html
matern_categorical html
matern_isotropic html
matern_nonstat_var html
matern_scaledim html
matern_spacetime html
matern_spacetime_categorical html
matern_spacetime_categorical_local html
matern_sphere html
matern_sphere_warp html
matern_spheretime html
matern_spheretime_warp html
order_coordinate html
order_dist_to_point html
order_maxmin html
order_middleout html
pen_hi html
pen_lo html
pen_loglo html
predictions html
sph_grad_xyz html
summary.GpGp_fit html
test_likelihood_object html
vecchia_Linv html
vecchia_grouped_meanzero_loglik html
vecchia_grouped_profbeta_loglik html
vecchia_grouped_profbeta_loglik_grad_info
html
vecchia_meanzero_loglik html
vecchia_profbeta_loglik html
vecchia_profbeta_loglik_grad_info 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 (GpGp)