############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf distinct.buildbin-libdir && mkdir distinct.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=distinct.buildbin-libdir distinct_1.12.2.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'distinct' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Perm.cpp -o Perm.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Perm_covariates.cpp -o Perm_covariates.o In file included from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:16, from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5, from Perm_covariates.cpp:2: F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 19 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 92 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 105 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 157 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 164 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 175 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 182 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 193 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 200 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 211 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 218 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 228 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 456 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 939 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 944 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 973 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 978 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1006 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1011 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1394 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1416 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1421 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1498 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1520 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1525 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1556 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1579 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1600 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1621 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1762 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1823 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1884 | #pragma omp critical | In file included from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:15: F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:42:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 42 | inline static type val; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:47:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 47 | inline static type val= NA_INTEGER; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:52:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 52 | inline static type val= NA_LOGICAL; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:57:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 57 | inline static type val= NA_REAL; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:62:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 62 | inline static type val = NA_STRING; | ^~~~~~ Perm_covariates.cpp: In function 'arma::vec my_rint_reg(const arma::mat&, const arma::vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)': Perm_covariates.cpp:189:16: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 189 | for(int i=0;i tol) { | ~~~^~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Perm_covariates_parallel.cpp -o Perm_covariates_parallel.o In file included from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:16, from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast.h:5, from Perm_covariates_parallel.cpp:2: F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:19: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 19 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:92: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 92 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:105: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 105 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:157: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 157 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:164: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 164 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:175: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 175 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:182: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 182 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:193: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 193 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:200: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 200 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:211: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 211 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:218: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 218 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:228: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 228 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/helpers.hpp:456: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 456 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:939: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 939 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:944: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 944 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:973: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 973 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:978: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 978 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1006: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1006 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1011: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1011 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1394: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1394 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1416: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1416 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1421: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1421 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1498: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1498 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1520: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1520 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1525: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1525 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1556: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1556 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1579: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1579 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1600: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1600 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1621: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1621 | #pragma omp parallel for | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1762: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1762 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1823: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1823 | #pragma omp critical | F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:1884: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 1884 | #pragma omp critical | In file included from F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/matrix.hpp:15: F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:42:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 42 | inline static type val; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:47:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 47 | inline static type val= NA_INTEGER; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:52:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 52 | inline static type val= NA_LOGICAL; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:57:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 57 | inline static type val= NA_REAL; | ^~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include/Rfast/types.hpp:62:17: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 62 | inline static type val = NA_STRING; | ^~~~~~ Perm_covariates_parallel.cpp: In function 'arma::vec my_rint_reg_parallel(const arma::mat&, const arma::vec&, Rcpp::IntegerVector, const unsigned int&, const unsigned int&, const double&, const unsigned int&)': Perm_covariates_parallel.cpp:189:16: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 189 | for(int i=0;i tol) { | ~~~^~~~~~~~~ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Perm_parallel.cpp -o Perm_parallel.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rfast/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -shared -s -static-libgcc -o distinct.dll tmp.def Perm.o Perm_covariates.o Perm_covariates_parallel.o Perm_parallel.o RcppExports.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/meat/distinct.buildbin-libdir/00LOCK-distinct/00new/distinct/libs/x64 ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'distinct' as distinct_1.12.2.zip * DONE (distinct)