* installing *source* package ‘simer’ ...
** package ‘simer’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_converter.cpp -o data_converter.o
In file included from data_converter.cpp:2:
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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 <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
BOOST_PRAGMA_MESSAGE(
^
/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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)))
^
<scratch space>:231:2: note: expanded from here
message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + 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<size_t>(fread(buffer, 1, 3, fin));
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c emma.cpp -o emma.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genotype.cpp -o genotype.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -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<size_t>(fread(buffer, 1, 3, fin));
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pedigree.cpp -o pedigree.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o simer.so RcppExports.o data_converter.o emma.o genotype.o impute.o pedigree.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/simer.Rcheck/00LOCK-simer/00new/simer/libs
** generating debug symbols (dSYM)
** 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)