* installing *source* package ‘resemble’ ...
** this is package ‘resemble’ version ‘2.2.4’
** package ‘resemble’ 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/resemble/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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../inst/include -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 diss_helpers.cpp -o diss_helpers.o
diss_helpers.cpp: In function ‘Rcpp::NumericVector which_min(Rcpp::NumericMatrix)’:
diss_helpers.cpp:233:10: warning: ‘eT arma::Mat<eT>::min(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations]
  233 |     x.min(index); // don't assign result to a value since we are interested only in the index
      |     ~~~~~^~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:201,
                 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 diss_helpers.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:544:56: note: declared here
  544 |   [[deprecated("use .index_min() instead")]] inline eT min(uword& index_of_min_val) const;
      |                                                        ^~~
diss_helpers.cpp: In function ‘Rcpp::NumericVector which_min_vector(Rcpp::NumericVector)’:
diss_helpers.cpp:280:10: warning: ‘eT arma::Mat<eT>::min(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations]
  280 |     x.min(index); // don't assign result to a value since we are interested only in the index
      |     ~~~~~^~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:692:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7829:1: note: declared here
 7829 | Mat<eT>::min(uword& index_of_min_val) const
      | ^~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include -I. -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 regression_methods.cpp -o regression_methods.o
regression_methods.cpp: In function ‘arma::mat get_weights(arma::mat, arma::mat, Rcpp::String, int, int)’:
regression_methods.cpp:163:47: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Mat<double>, arma::eGlue<arma::subview_col<double>, arma::subview_col<double>, arma::eglue_minus>, arma::glue_cor>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  163 |         w(i, 0) += arma::conv_to<double>::from(arma::cor(Y, X.col(i) - X.col(j)));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:496,
                 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 regression_methods.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
regression_methods.cpp:164:47: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = double; T1 = arma::Glue<arma::Mat<double>, arma::eGlue<arma::subview_col<double>, arma::subview_col<double>, arma::eglue_minus>, arma::glue_cor>; out_eT = double; typename arma::arma_not_cx<in_eT>::result = double]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  164 |         w(j, 0) -= arma::conv_to<double>::from(arma::cor(Y, X.col(i) - X.col(j)));
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
   72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
      | ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o resemble.so RcppExports.o diss_helpers.o regression_methods.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/resemble/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/resemble/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/resemble/src'
installing to /data/gannet/ripley/R/packages/tests-devel/resemble.Rcheck/00LOCK-resemble/00new/resemble/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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 (resemble)