Install log for 'matrixCorr'

* installing *source* package ‘matrixCorr’ ...
** this is package ‘matrixCorr’ version ‘0.8.4’
** 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 22.1.0 (https://github.com/llvm/llvm-project 4434dabb69916856b824f68a64b029c67175e532)’
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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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
clang++-22 -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -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
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 -L/usr/local/clang21/lib/clang/22/lib/x86_64-unknown-linux-gnu -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 -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
** 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)