* installing *source* package ‘matrixCorr’ ...
** this is package ‘matrixCorr’ version ‘0.12.2’
** package ‘matrixCorr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for required atomic ops support...
warning: could not compile atomic probe; falling back to default detection
clang on Linux detected; forcing atomic runtime
using atomic flags: -latomic
** libs
specified C++17
using C++ compiler: ‘clang version 22.1.7 (https://github.com/llvm/llvm-project a255c1ed36a1d06f79bd2633ba9f8d900153007c)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/matrixCorr/src'
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ccc_glmm_poisson.cpp -o ccc_glmm_poisson.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c chatterjee_xi.cpp -o chatterjee_xi.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c cia.cpp -o cia.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c cia_repeated.cpp -o cia_repeated.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c cohen_kappa.cpp -o cohen_kappa.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c gwet_ac.cpp -o gwet_ac.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c hsic.cpp -o hsic.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c icc.cpp -o icc.o
icc.cpp:193:13: warning: unused function 'icc_pair_complete_core' [-Wunused-function]
193 | inline bool icc_pair_complete_core(const double* x,
| ^~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c krippendorff_alpha.cpp -o krippendorff_alpha.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c multirater_kappa.cpp -o multirater_kappa.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c pearson.cpp -o pearson.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c prob_agree.cpp -o prob_agree.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c rmcorr.cpp -o rmcorr.o
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c robust_correlations.cpp -o robust_correlations.o
rmcorr.cpp:422:10: warning: variable 'syy' set but not used [-Wunused-but-set-variable]
422 | double syy = 0.0;
| ^
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c spearman.cpp -o spearman.o
1 warning generated.
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c tetrachoric.cpp -o tetrachoric.o
robust_correlations.cpp:31:15: warning: unused function 'median_sorted_std' [-Wunused-function]
31 | inline double median_sorted_std(const std::vector<double>& xs) {
| ^~~~~~~~~~~~~~~~~
robust_correlations.cpp:70:15: warning: unused function 'idealf_iqr' [-Wunused-function]
70 | inline double idealf_iqr(const arma::vec& x) {
| ^~~~~~~~~~
robust_correlations.cpp:86:15: warning: unused function 'idealf_iqr_sorted_std' [-Wunused-function]
86 | inline double idealf_iqr_sorted_std(const std::vector<double>& y) {
| ^~~~~~~~~~~~~~~~~~~~~
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -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
spearman.cpp:58:15: warning: unused function 'spearman_pair_core' [-Wunused-function]
58 | inline double spearman_pair_core(const arma::vec& x, const arma::vec& y) {
| ^~~~~~~~~~~~~~~~~~
3 warnings generated.
1 warning generated.
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c weighted_kappa.cpp -o weighted_kappa.o
clang++-22 -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o matrixCorr.so RcppExports.o biweight_mid_corr.o bland_altman.o bland_altman_repeated.o ccc_glmm_poisson.o ccc_repeated.o ccc_repeated_helper.o ccc_repeated_mixed_model.o chatterjee_xi.o cia.o cia_repeated.o cohen_kappa.o concordance_corr.o distance_correlation.o gwet_ac.o hsic.o icc.o kendall_corr.o krippendorff_alpha.o multirater_kappa.o partial_correlation.o pearson.o prob_agree.o rmcorr.o robust_correlations.o schafer_strimmer_shrinkage_correlation.o spearman.o tetrachoric.o validate_corr_input.o weighted_kappa.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm -fopenmp -latomic
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
** 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 (matrixCorr)