* 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: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/matrixCorr/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c biweight_mid_corr.cpp -o biweight_mid_corr.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bland_altman.cpp -o bland_altman.o
In file included from biweight_mid_corr.cpp:14:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
In file included from bland_altman.cpp:9:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bland_altman_repeated.cpp -o bland_altman_repeated.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ccc_repeated.cpp -o ccc_repeated.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ccc_repeated_helper.cpp -o ccc_repeated_helper.o
In file included from bland_altman_repeated.cpp:13:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -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: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
ccc_repeated_mixed_model.cpp: In function ‘Rcpp::List ccc_vc_cpp(Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, int, double, double, int, Rcpp::Nullable<Rcpp::Matrix<14> >, Rcpp::Nullable<Rcpp::Matrix<14> >, Rcpp::Nullable<Rcpp::Matrix<14> >, bool, double, bool, bool, double, bool, Rcpp::Nullable<Rcpp::Vector<14, Rcpp::PreserveStorage> >)’:
ccc_repeated_mixed_model.cpp:947:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  947 |             for (size_t k = 0; k < tim_i.size(); ++k)
      |             ^~~
ccc_repeated_mixed_model.cpp:950:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  950 |               auto kp = unit_kappas(times_obs);
      |               ^~~~
ccc_repeated_mixed_model.cpp:959:11: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  959 |           for (size_t k = 0; k < tim_i.size(); ++k)
      |           ^~~
ccc_repeated_mixed_model.cpp:962:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  962 |             auto kp = unit_kappas(times_obs);
      |             ^~~~
ccc_repeated_mixed_model.cpp:1263:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1263 |         for (int k = 0; k < n_i; ++k)
      |         ^~~
ccc_repeated_mixed_model.cpp:1265:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1265 |           if ((int)idx.size() <= 1) continue;
      |           ^~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c concordance_corr.cpp -o concordance_corr.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c distance_correlation.cpp -o distance_correlation.o
In file included from concordance_corr.cpp:4:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
concordance_corr.cpp: In function ‘arma::mat ccc_cpp(const arma::mat&)’:
concordance_corr.cpp:23:13: warning: unused variable ‘n’ [-Wunused-variable]
   23 |   const int n = X.n_rows;
      |             ^
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c kendall_corr.cpp -o kendall_corr.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c partial_correlation.cpp -o partial_correlation.o
In file included from kendall_corr.cpp:8:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
In file included from partial_correlation.cpp:8:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pearson.cpp -o pearson.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c schafer_strimmer_shrinkage_correlation.cpp -o schafer_strimmer_shrinkage_correlation.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c spearman.cpp -o spearman.o
In file included from spearman.cpp:4:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c tetrachoric.cpp -o tetrachoric.o
In file included from tetrachoric.cpp:10:
matrixCorr_detail.h: In function ‘void matrixCorr_detail::timeseries::ar1::make_Cinv_by_method(const std::vector<int, std::allocator<int> >&, const std::vector<int, std::allocator<int> >&, int, double, arma::mat&)’:
matrixCorr_detail.h:1175:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1175 |     for (int k = 0; k < (int)tim_ord.size(); ++k)
      |     ^~~
matrixCorr_detail.h:1179:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1179 |       int s = 0;
      |       ^~~
tetrachoric.cpp: In function ‘void build_cutpoints(const Rcpp::NumericMatrix&, std::vector<double>&, std::vector<double>&)’:
tetrachoric.cpp:64:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   64 |   for (int i=0;i<R;++i)
      |   ^~~
tetrachoric.cpp:70:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   70 |     if (tot <= 0) stop("Empty table");
      |     ^~
tetrachoric.cpp: In function ‘double matrixCorr_polychoric_mle_cpp(Rcpp::NumericMatrix, double)’:
tetrachoric.cpp:177:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  177 |     for (int j=0;j<C;++j)
      |     ^~~
tetrachoric.cpp:180:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  180 |       std::vector<double> alpha, beta;
      |       ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c validate_corr_input.cpp -o validate_corr_input.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -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/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/matrixCorr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/matrixCorr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/matrixCorr/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)