* installing *source* package ‘matrixCorr’ ... ** this is package ‘matrixCorr’ version ‘0.10.0’ ** 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: ‘Debian clang version 21.1.8 (3+b1)’ using C++17 clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c biweight_mid_corr.cpp -o biweight_mid_corr.o In file included from biweight_mid_corr.cpp:12: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c bland_altman.cpp -o bland_altman.o In file included from bland_altman.cpp:9: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c bland_altman_repeated.cpp -o bland_altman_repeated.o In file included from bland_altman_repeated.cpp:13: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c ccc_repeated.cpp -o ccc_repeated.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c ccc_repeated_helper.cpp -o ccc_repeated_helper.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c ccc_repeated_mixed_model.cpp -o ccc_repeated_mixed_model.o In file included from ccc_repeated_mixed_model.cpp:20: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c concordance_corr.cpp -o concordance_corr.o In file included from concordance_corr.cpp:4: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c distance_correlation.cpp -o distance_correlation.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c kendall_corr.cpp -o kendall_corr.o In file included from kendall_corr.cpp:11: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ kendall_corr.cpp:110:10: warning: variable 'f_right' set but not used [-Wunused-but-set-variable] 110 | double f_right = f_hi; | ^ 2 warnings generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c partial_correlation.cpp -o partial_correlation.o In file included from partial_correlation.cpp:8: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c pearson.cpp -o pearson.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c rmcorr.cpp -o rmcorr.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c robust_correlations.cpp -o robust_correlations.o In file included from robust_correlations.cpp:13: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ robust_correlations.cpp:35:15: warning: unused function 'median_sorted_std' [-Wunused-function] 35 | inline double median_sorted_std(const std::vector& xs) { | ^~~~~~~~~~~~~~~~~ robust_correlations.cpp:74:15: warning: unused function 'idealf_iqr' [-Wunused-function] 74 | inline double idealf_iqr(const arma::vec& x) { | ^~~~~~~~~~ robust_correlations.cpp:90:15: warning: unused function 'idealf_iqr_sorted_std' [-Wunused-function] 90 | inline double idealf_iqr_sorted_std(const std::vector& y) { | ^~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c schafer_strimmer_shrinkage_correlation.cpp -o schafer_strimmer_shrinkage_correlation.o clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c spearman.cpp -o spearman.o In file included from spearman.cpp:6: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ spearman.cpp:63:10: warning: variable 'f_right' set but not used [-Wunused-but-set-variable] 63 | double f_right = f_hi; | ^ spearman.cpp:47:15: warning: unused function 'spearman_pair_core' [-Wunused-function] 47 | inline double spearman_pair_core(const arma::vec& x, const arma::vec& y) { | ^~~~~~~~~~~~~~~~~~ 3 warnings generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c tetrachoric.cpp -o tetrachoric.o In file included from tetrachoric.cpp:12: ./matrixCorr_detail.h:917:17: warning: variable 'k' set but not used [-Wunused-but-set-variable] 917 | arma::uword k = 0; | ^ 1 warning generated. clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.7/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_USE_CURRENT -fpic -g -O3 -Wall -pedantic -c validate_corr_input.cpp -o validate_corr_input.o clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-21/lib -Wl,-O1 -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 rmcorr.o robust_correlations.o schafer_strimmer_shrinkage_correlation.o spearman.o tetrachoric.o validate_corr_input.o -llapack -L/home/hornik/tmp/R-d-clang-21/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -latomic -L/home/hornik/tmp/R-d-clang-21/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/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 ** 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)