* installing *source* package ‘matrixCorr’ ...
** this is package ‘matrixCorr’ version ‘0.5.1’
** package ‘matrixCorr’ 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/matrixCorr/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/cpp11/include' -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 -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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c biweight_mid_corr.cpp -o biweight_mid_corr.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c bland_altman.cpp -o bland_altman.o
In file included from biweight_mid_corr.cpp:14:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
In file included from bland_altman.cpp:9:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c bland_altman_repeated.cpp -o bland_altman_repeated.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ccc_repeated.cpp -o ccc_repeated.o
In file included from bland_altman_repeated.cpp:13:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ccc_repeated_helper.cpp -o ccc_repeated_helper.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ccc_repeated_mixed_model.cpp -o ccc_repeated_mixed_model.o
In file included from ccc_repeated_mixed_model.cpp:17:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
ccc_repeated_mixed_model.cpp:950:15: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
950 | auto kp = unit_kappas(times_obs);
| ^
ccc_repeated_mixed_model.cpp:947:13: note: previous statement is here
947 | for (size_t k = 0; k < tim_i.size(); ++k)
| ^
ccc_repeated_mixed_model.cpp:962:13: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
962 | auto kp = unit_kappas(times_obs);
| ^
ccc_repeated_mixed_model.cpp:959:11: note: previous statement is here
959 | for (size_t k = 0; k < tim_i.size(); ++k)
| ^
ccc_repeated_mixed_model.cpp:1265:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1265 | if ((int)idx.size() <= 1) continue;
| ^
ccc_repeated_mixed_model.cpp:1263:9: note: previous statement is here
1263 | for (int k = 0; k < n_i; ++k)
| ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c concordance_corr.cpp -o concordance_corr.o
4 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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c distance_correlation.cpp -o distance_correlation.o
In file included from concordance_corr.cpp:4:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
concordance_corr.cpp:23:13: warning: unused variable 'n' [-Wunused-variable]
23 | const int n = X.n_rows;
| ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c kendall_corr.cpp -o kendall_corr.o
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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c partial_correlation.cpp -o partial_correlation.o
In file included from kendall_corr.cpp:8:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c pearson.cpp -o pearson.o
1 warning generated.
In file included from partial_correlation.cpp:8:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c schafer_strimmer_shrinkage_correlation.cpp -o schafer_strimmer_shrinkage_correlation.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c spearman.cpp -o spearman.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c tetrachoric.cpp -o tetrachoric.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/cpp11/include' -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 -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c validate_corr_input.cpp -o validate_corr_input.o
In file included from spearman.cpp:4:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
In file included from tetrachoric.cpp:10:
./matrixCorr_detail.h:1179:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
1179 | int s = 0;
| ^
./matrixCorr_detail.h:1175:5: note: previous statement is here
1175 | for (int k = 0; k < (int)tim_ord.size(); ++k)
| ^
tetrachoric.cpp:70:5: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
70 | if (tot <= 0) stop("Empty table");
| ^
tetrachoric.cpp:64:3: note: previous statement is here
64 | for (int i=0;i<R;++i)
| ^
tetrachoric.cpp:180:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
180 | std::vector<double> alpha, beta;
| ^
tetrachoric.cpp:177:5: note: previous statement is here
177 | for (int j=0;j<C;++j)
| ^
1 warning generated.
tetrachoric.cpp:32:22: warning: unused function 'tetra_loglik' [-Wunused-function]
32 | static inline double tetra_loglik(double rho, double a, double b, double c, double d){
| ^~~~~~~~~~~~
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 matrixCorr.so RcppExports.o biweight_mid_corr.o bland_altman.o bland_altman_repeated.o ccc_repeated.o ccc_repeated_helper.o ccc_repeated_mixed_model.o concordance_corr.o distance_correlation.o kendall_corr.o partial_correlation.o pearson.o schafer_strimmer_shrinkage_correlation.o spearman.o tetrachoric.o validate_corr_input.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/matrixCorr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/matrixCorr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/matrixCorr/src'
installing to /data/gannet/ripley/R/packages/tests-clang/matrixCorr.Rcheck/00LOCK-matrixCorr/00new/matrixCorr/libs
** R
** 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 (matrixCorr)