* installing *source* package ‘simer’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 16.0.6 (15)’ clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c data_converter.cpp -o data_converter.o In file included from data_converter.cpp:2: /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages] BOOST_PRAGMA_MESSAGE( ^ /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :138:2: note: expanded from here message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " " + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.") ^ data_converter.cpp:131:10: 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)); ^ 2 warnings generated. clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c emma.cpp -o emma.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c genotype.cpp -o genotype.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c impute.cpp -o impute.o impute.cpp:97:14: warning: unused variable 'r' [-Wunused-variable] size_t r = (block_start + j) / n; ^ impute.cpp:82:10: 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)); ^ 2 warnings generated. clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-16/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c pedigree.cpp -o pedigree.o clang++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-16/lib -Wl,-O1 -o simer.so RcppExports.o data_converter.o emma.o genotype.o impute.o pedigree.o -fopenmp -llapack -L/home/hornik/tmp/R-d-clang-16/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-clang-16/lib -lR installing to /srv/hornik/tmp/CRAN/simer.Rcheck/00LOCK-simer/00new/simer/libs ** R ** data ** 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 (simer)