* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘phyr’ ... ** this is package ‘phyr’ version ‘1.1.0’ ** package ‘phyr’ 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/RtmpxvRAqC/R.INSTALL12ddf94d6e05a0/phyr/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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c binaryPGLMM.cpp -o binaryPGLMM.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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c cor_phylo.cpp -o cor_phylo.o cor_phylo.cpp:76:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] 76 | if (!arma::is_finite(rcond_dbl) || rcond_dbl < rcond_threshold) return MAX_RETURN; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here 164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]] | ^ cor_phylo.cpp:81:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] 81 | if (!arma::is_finite(rcond_dbl) || rcond_dbl < rcond_threshold) return MAX_RETURN; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here 164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]] | ^ cor_phylo.cpp:89:14: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] 89 | if (!arma::is_finite(logdetV)) return MAX_RETURN; | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here 164 | [[deprecated("change arma::is_finite(val) to std::isfinite(val)")]] | ^ 3 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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pcd.cpp -o pcd.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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pglmm_binary.cpp -o pglmm_binary.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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c pglmm_gaussian.cpp -o pglmm_gaussian.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/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c psv.cpp -o psv.o clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o phyr.so RcppExports.o binaryPGLMM.o cor_phylo.o pcd.o pglmm_binary.o pglmm_gaussian.o psv.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxvRAqC/R.INSTALL12ddf94d6e05a0/phyr/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxvRAqC/R.INSTALL12ddf94d6e05a0/phyr/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxvRAqC/R.INSTALL12ddf94d6e05a0/phyr/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-phyr/00new/phyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (phyr)