* installing *source* package ‘hmcdm’ ...
** this is package ‘hmcdm’ version ‘2.1.1’
** package ‘hmcdm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.1’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmcdm/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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c basic_functions.cpp -o basic_functions.o
basic_functions.cpp:178:47: warning: 'from<double, arma::eGlue<arma::Glue<arma::Row<double>, arma::Col<double>, arma::glue_times>, arma::Glue<arma::Row<double>, arma::Op<arma::Row<double>, arma::op_htrans>, arma::glue_times>, arma::eglue_minus>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
178 | double compare = arma::conv_to<double>::from(qj*alpha_c - qj*qj.t());
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eGlue<arma::Glue<arma::Row<double>, arma::Col<double>, arma::glue_times>, arma::Glue<arma::Row<double>, arma::Op<arma::Row<double>, arma::op_htrans>, arma::glue_times>, arma::eglue_minus>>' 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);
| ^
/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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c extract_functions.cpp -o extract_functions.o
1 warning 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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c mcmc_functions.cpp -o mcmc_functions.o
mcmc_functions.cpp:1459:45: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1459 | c_aik_1 = (arma::conv_to< double >::from( alpha_i_1.t()*bijectionvector(K) ));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1462:45: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1462 | c_aik_0 = (arma::conv_to< double >::from( alpha_i_0.t()*bijectionvector(K) ));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1549:53: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1549 | double Sumalphak = (arma::conv_to< double >::from(ak.t() * ak));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1550:49: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1550 | double SumXjk = (arma::conv_to< double >::from(Xjk.t() * Xjk));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1551:55: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1551 | double SumXjkalphak = (arma::conv_to< double >::from(Xjk.t() * ak));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1768:45: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1768 | c_aik_1 = (arma::conv_to< double >::from( alpha_i_1.t()*bijectionvector(K) ));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
mcmc_functions.cpp:1771:45: warning: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
1771 | c_aik_0 = (arma::conv_to< double >::from( alpha_i_0.t()*bijectionvector(K) ));
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::Glue<arma::Op<arma::Col<double>, arma::op_htrans>, arma::Col<double>, arma::glue_times>>' 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);
| ^
/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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c resp_functions.cpp -o resp_functions.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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rt_functions.cpp -o rt_functions.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/progress/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c trans_functions.cpp -o trans_functions.o
7 warnings generated.
/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 hmcdm.so RcppExports.o basic_functions.o extract_functions.o mcmc_functions.o resp_functions.o rt_functions.o trans_functions.o -fopenmp -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/hmcdm/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hmcdm/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hmcdm/src'
installing to /data/gannet/ripley/R/packages/tests-clang/hmcdm.Rcheck/00LOCK-hmcdm/00new/hmcdm/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (hmcdm)