Install log for 'matrixCorr'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* 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
  not required
** libs
specified C++17
using C++ compiler: ‘g++-16 (Debian 16.1.0-1) 16.1.0’
using C++17
make[1]: Entering directory '/tmp/RtmpYFn6WG/R.INSTALL15750b57cfed67/matrixCorr/src'
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c biweight_mid_corr.cpp -o biweight_mid_corr.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bland_altman.cpp -o bland_altman.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bland_altman_repeated.cpp -o bland_altman_repeated.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ccc_glmm_poisson.cpp -o ccc_glmm_poisson.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ccc_repeated.cpp -o ccc_repeated.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ccc_repeated_helper.cpp -o ccc_repeated_helper.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ccc_repeated_mixed_model.cpp -o ccc_repeated_mixed_model.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c chatterjee_xi.cpp -o chatterjee_xi.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cia.cpp -o cia.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cia_repeated.cpp -o cia_repeated.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cohen_kappa.cpp -o cohen_kappa.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c concordance_corr.cpp -o concordance_corr.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c distance_correlation.cpp -o distance_correlation.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c gwet_ac.cpp -o gwet_ac.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hsic.cpp -o hsic.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c icc.cpp -o icc.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c kendall_corr.cpp -o kendall_corr.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c krippendorff_alpha.cpp -o krippendorff_alpha.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c multirater_kappa.cpp -o multirater_kappa.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c partial_correlation.cpp -o partial_correlation.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pearson.cpp -o pearson.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c prob_agree.cpp -o prob_agree.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rmcorr.cpp -o rmcorr.o
rmcorr.cpp: In function ‘{anonymous}::RmStats {anonymous}::compute_rmcorr_weighted_stats(const double*, const double*, const SubjectIndex&, bool, double)’:
rmcorr.cpp:422:10: warning: variable ‘syy’ set but not used [-Wunused-but-set-variable=]
  422 |   double syy = 0.0;
      |          ^~~
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c robust_correlations.cpp -o robust_correlations.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c schafer_strimmer_shrinkage_correlation.cpp -o schafer_strimmer_shrinkage_correlation.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c spearman.cpp -o spearman.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c tetrachoric.cpp -o tetrachoric.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c validate_corr_input.cpp -o validate_corr_input.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -include matrixCorr_r_api_compat.h -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -DARMA_USE_CURRENT -fpic  -g -O2 -Wall -pedantic -mtune=native   -c weighted_kappa.cpp -o weighted_kappa.o
g++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpYFn6WG/R.INSTALL15750b57cfed67/matrixCorr/src'
make[1]: Entering directory '/tmp/RtmpYFn6WG/R.INSTALL15750b57cfed67/matrixCorr/src'
make[1]: Leaving directory '/tmp/RtmpYFn6WG/R.INSTALL15750b57cfed67/matrixCorr/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)