* installing *source* package ‘simer’ ... ** using staged installation ** libs using C++ compiler: ‘Debian clang version 18.1.8 (11)’ clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c data_converter.cpp -o data_converter.o In file included from data_converter.cpp:2: /home/hornik/lib/R/Library/4.5/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] 36 | BOOST_PRAGMA_MESSAGE( | ^ /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' 24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) | ^ :454:2: note: expanded from here 454 | 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] 131 | size_t n_bytes_read = static_cast(fread(buffer, 1, 3, fin)); | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c emma.cpp -o emma.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c genotype.cpp -o genotype.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c impute.cpp -o impute.o impute.cpp:97:14: warning: unused variable 'r' [-Wunused-variable] 97 | size_t r = (block_start + j) / n; | ^ impute.cpp:82:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable] 82 | size_t n_bytes_read = static_cast(fread(buffer, 1, 3, fin)); | ^ 2 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c pedigree.cpp -o pedigree.o clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-18/lib -Wl,-O1 -o simer.so RcppExports.o data_converter.o emma.o genotype.o impute.o pedigree.o -llapack -L/home/hornik/tmp/R-d-clang-18/lib -lRblas -L/usr/lib/llvm-18/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-18/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/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)