* installing *source* package ‘hibayes’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 16.0.6 (11)’ using C++11 clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c Bayes.cpp -o Bayes.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c SBayesD.cpp -o SBayesD.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c SBayesS.cpp -o SBayesS.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c cg.cpp -o cg.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c cutwind.cpp -o cutwind.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c read_bed.cpp -o read_bed.o read_bed.cpp:142:9: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable] size_t n_bytes_read = static_cast(fread(buffer, 1, 3, fin)); ^ 1 warning generated. clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c rm.cpp -o rm.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c solver.cpp -o solver.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c stats.cpp -o stats.o clang++-16 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I'/srv/hornik/tmp/R-d-clang-16/library/Matrix/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_64BIT_WORD=1 -fopenmp -fpic -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c tXXmat.cpp -o tXXmat.o clang++-16 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o hibayes.so Bayes.o RcppExports.o SBayesD.o SBayesS.o cg.o cutwind.o read_bed.o rm.o solver.o stats.o tXXmat.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/hibayes.Rcheck/00LOCK-hibayes/00new/hibayes/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 (hibayes)