* installing *source* package ‘pmartR’ ...
** this is package ‘pmartR’ version ‘2.5.0’
** package ‘pmartR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/pmartR/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c calculate_cv.cpp -o calculate_cv.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c count_missing_cpp.cpp -o count_missing_cpp.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c imd_anova.cpp -o imd_anova.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c kw_rcpp.cpp -o kw_rcpp.o
imd_anova.cpp:450:43: warning: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  450 |       sigma2_red = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_red);
      |                                           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' has been explicitly marked deprecated here
   33 |   [[deprecated("replace conv_to<...>::from(X) with as_scalar(X)")]] inline static out_eT from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk = nullptr);
      |     ^
imd_anova.cpp:464:44: warning: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  464 |       sigma2_full = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_full);
      |                                            ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' has been explicitly marked deprecated here
   33 |   [[deprecated("replace conv_to<...>::from(X) with as_scalar(X)")]] inline static out_eT from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk = nullptr);
      |     ^
imd_anova.cpp:478:43: warning: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  478 |       sigma2_red = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_red);
      |                                           ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' has been explicitly marked deprecated here
   33 |   [[deprecated("replace conv_to<...>::from(X) with as_scalar(X)")]] inline static out_eT from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk = nullptr);
      |     ^
imd_anova.cpp:491:46: warning: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
  491 |         sigma2_full = arma::conv_to<double>::from(residual_vec.t()*residual_vec/df_full);
      |                                              ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eOp<arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>, arma::eop_scalar_div_post>>' has been explicitly marked deprecated here
   33 |   [[deprecated("replace conv_to<...>::from(X) with as_scalar(X)")]] inline static out_eT from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk = nullptr);
      |     ^
imd_anova.cpp:670:17: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  670 |       if (arma::is_finite(t_tests(i,k)) && dof > 0) {
      |                 ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
  164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
      |   ^
5 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c nonmissing_per_grp.cpp -o nonmissing_per_grp.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o pmartR.so RcppExports.o calculate_cv.o count_missing_cpp.o imd_anova.o kw_rcpp.o nonmissing_per_grp.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/pmartR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/pmartR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/pmartR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/pmartR.Rcheck/00LOCK-pmartR/00new/pmartR/libs
** R
** 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 (pmartR)