* installing *source* package ‘SpatPCA’ ...
** this is package ‘SpatPCA’ version ‘1.3.5’
** package ‘SpatPCA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SpatPCA/src'
g++ -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/RcppParallel/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++ -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/RcppParallel/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 RcppSpatPCA.cpp -o RcppSpatPCA.o
RcppSpatPCA.cpp: In member function ‘virtual void thinPlateSpline::operator()(std::size_t, std::size_t)’:
RcppSpatPCA.cpp:25:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   25 |         if(j > i) {
      |            ~~^~~
RcppSpatPCA.cpp: In member function ‘virtual void spatpcaCVPhi3::operator()(std::size_t, std::size_t)’:
RcppSpatPCA.cpp:501:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  501 |       for(int gj = 0; gj < gamma.n_elem; gj++) {
      |                       ~~~^~~~~~~~~~~~~~
RcppSpatPCA.cpp: In function ‘Rcpp::List spatpcaCV(Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::NumericVector)’:
RcppSpatPCA.cpp:600:21: warning: ‘elem_type arma::Base<elem_type, derived>::min(arma::uword&) const [with elem_type = double; derived = arma::Op<arma::Mat<double>, arma::op_sum>; arma::uword = unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations]
  600 |     (sum(cv, 0)).min(index1);
      |     ~~~~~~~~~~~~~~~~^~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:675,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
                 from RcppSpatPCA.cpp:5:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Base_meat.hpp:195:1: note: declared here
  195 | Base<elem_type,derived>::min(uword& index_of_min_val) const
      | ^~~~~~~~~~~~~~~~~~~~~~~
RcppSpatPCA.cpp:661:22: warning: ‘elem_type arma::Base<elem_type, derived>::min(arma::uword&) const [with elem_type = double; derived = arma::Op<arma::Mat<double>, arma::op_sum>; arma::uword = unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations]
  661 |     (sum(cv2, 0)).min(index2);
      |     ~~~~~~~~~~~~~~~~~^~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Base_meat.hpp:195:1: note: declared here
  195 | Base<elem_type,derived>::min(uword& index_of_min_val) const
      | ^~~~~~~~~~~~~~~~~~~~~~~
RcppSpatPCA.cpp:688:22: warning: ‘elem_type arma::Base<elem_type, derived>::min(arma::uword&) const [with elem_type = double; derived = arma::Op<arma::Mat<double>, arma::op_sum>; arma::uword = unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations]
  688 |     (sum(cv3, 0)).min(index3);
      |     ~~~~~~~~~~~~~~~~~^~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Base_meat.hpp:195:1: note: declared here
  195 | Base<elem_type,derived>::min(uword& index_of_min_val) const
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o SpatPCA.so RcppExports.o RcppSpatPCA.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SpatPCA/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SpatPCA/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SpatPCA/src'
installing to /data/gannet/ripley/R/packages/tests-devel/SpatPCA.Rcheck/00LOCK-SpatPCA/00new/SpatPCA/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (SpatPCA)