* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* 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: ‘Debian clang version 19.1.7 (7)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT1kRZh/R.INSTALL7f9b34ffd5e96/matrixCorr/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c RcppExports.cpp -o RcppExports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c biweight_mid_corr.cpp -o biweight_mid_corr.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)
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c bland_altman.cpp -o bland_altman.o
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.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c bland_altman_repeated.cpp -o bland_altman_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.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c ccc_repeated.cpp -o ccc_repeated.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c ccc_repeated_helper.cpp -o ccc_repeated_helper.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -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)
| ^
4 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c concordance_corr.cpp -o concordance_corr.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;
| ^
2 warnings generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c distance_correlation.cpp -o distance_correlation.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c kendall_corr.cpp -o kendall_corr.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)
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c partial_correlation.cpp -o partial_correlation.o
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.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pearson.cpp -o pearson.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c schafer_strimmer_shrinkage_correlation.cpp -o schafer_strimmer_shrinkage_correlation.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c spearman.cpp -o spearman.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)
| ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c tetrachoric.cpp -o tetrachoric.o
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)
| ^
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.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/cpp11/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c validate_corr_input.cpp -o validate_corr_input.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/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 schafer_strimmer_shrinkage_correlation.o spearman.o tetrachoric.o validate_corr_input.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -fopenmp -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT1kRZh/R.INSTALL7f9b34ffd5e96/matrixCorr/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT1kRZh/R.INSTALL7f9b34ffd5e96/matrixCorr/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT1kRZh/R.INSTALL7f9b34ffd5e96/matrixCorr/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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
Error: package or namespace load failed for ‘matrixCorr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-matrixCorr/00new/matrixCorr/libs/matrixCorr.so':
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-matrixCorr/00new/matrixCorr/libs/matrixCorr.so: undefined symbol: __atomic_compare_exchange
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/matrixCorr’