* installing *source* package ‘GpGp’ ...
** package ‘GpGp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GpGp/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c matrix_mult.cpp -o matrix_mult.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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: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_02.h: In function 'arma::cube d_matern_anisotropic3D(arma::vec, arma::mat)':
covmatrix_funs_02.h:298:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
298 | 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:492:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
492 | 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:618:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
618 | 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:762:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
762 | for(int j=0; j<covparms.n_elem; j++){
| ~^~~~~~~~~~~~~~~~
covmatrix_funs_02.h:721:12: warning: unused variable 'nugget' [-Wunused-variable]
721 | 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:939:27: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
939 | 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++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o GpGp.so RcppExports.o matrix_mult.o vecchia_loglik_grad_info.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GpGp/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/GpGp/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/GpGp/src'
installing to /data/gannet/ripley/R/packages/tests-devel/GpGp.Rcheck/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
** 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)