* installing *source* package ‘hdpGLM’ ...
** this is package ‘hdpGLM’ version ‘1.0.4’
** package ‘hdpGLM’ 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/hdpGLM/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' -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' -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 src_dpGLM.cpp -o src_dpGLM.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' -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 src_gibbs_gaussian.cpp -o src_gibbs_gaussian.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' -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 src_hdpGLM.cpp -o src_hdpGLM.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' -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 src_hmc.cpp -o src_hmc.o
src_hdpGLM.cpp:102:45: warning: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtGlue<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::glue_rel_and>, arma::op_find_simple>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
102 | int idx_k_active_in_j = conv_to<int>::from( find(theta.col(0) == Zjstar(i) && theta.col(1) == j) );
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtGlue<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::glue_rel_and>, arma::op_find_simple>>' 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);
| ^
src_gibbs_gaussian.cpp:93:7: warning: unused variable 'Dw' [-Wunused-variable]
93 | int Dw = W.n_cols - 1;
| ^~
/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' -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 src_hmc_binomial.cpp -o src_hmc_binomial.o
1 warning generated.
1 warning generated.
src_hmc_binomial.cpp:40:7: warning: unused variable 'n' [-Wunused-variable]
40 | int n = Xk.n_rows;
| ^
src_hmc_binomial.cpp:64:7: warning: unused variable 'ncols' [-Wunused-variable]
64 | int ncols = Sigma_beta.n_cols;
| ^~~~~
2 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' -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 src_hmc_multinomial.cpp -o src_hmc_multinomial.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' -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 src_pi_z_update.cpp -o src_pi_z_update.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' -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 src_utils.cpp -o src_utils.o
src_pi_z_update.cpp:53:40: warning: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::op_find_simple>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
53 | int idx_k = conv_to<int>::from( find(theta.col(0)==k+1) );
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::op_find_simple>>' 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);
| ^
src_pi_z_update.cpp:141:37: warning: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtGlue<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::glue_rel_and>, arma::op_find_simple>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
141 | int idx_jk = conv_to<int>::from( find(theta.col(0)==k && theta.col(1)==j) );
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<unsigned int, arma::mtOp<unsigned int, arma::mtGlue<unsigned int, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::mtOp<unsigned int, arma::subview_col<double>, arma::op_rel_eq>, arma::glue_rel_and>, arma::op_find_simple>>' 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);
| ^
src_pi_z_update.cpp:155:36: warning: 'from<double, arma::eOp<arma::Col<double>, arma::eop_scalar_times>>' is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
155 | phii(k-1) = conv_to<double>::from(pi(k-1, j-1) * pyi);
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:33:5: note: 'from<double, arma::eOp<arma::Col<double>, arma::eop_scalar_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);
| ^
src_pi_z_update.cpp:130:22: warning: unused variable 'J' [-Wunused-variable]
130 | int J = conv_to<colvec>::from( unique(theta.col(1)) ).n_rows;
| ^
4 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 hdpGLM.so RcppExports.o src_dpGLM.o src_gibbs_gaussian.o src_hdpGLM.o src_hmc.o src_hmc_binomial.o src_hmc_multinomial.o src_pi_z_update.o src_utils.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/hdpGLM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hdpGLM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hdpGLM/src'
installing to /data/gannet/ripley/R/packages/tests-clang/hdpGLM.Rcheck/00LOCK-hdpGLM/00new/hdpGLM/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (hdpGLM)