* installing *source* package ‘GRAB’ ...
** package ‘GRAB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BGEN.cpp -o BGEN.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DenseGRM.cpp -o DenseGRM.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Main.cpp -o Main.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLINK.cpp -o PLINK.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c POLMM.cpp -o POLMM.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
BGEN.cpp:75:12: warning: unused variable 'CompressedSNPBlocks' [-Wunused-variable]
uint32_t CompressedSNPBlocks = flags&3; //Rcpp::Rcout << " CompressedSNPBlocks: " << CompressedSNPBlocks << std::endl;
^
BGEN.cpp:77:12: warning: unused variable 'Layout' [-Wunused-variable]
uint32_t Layout = (flags>>2)&0xf; //Rcpp::Rcout << " Layout: " << Layout << std::endl;
^
Main.cpp:582:18: warning: variable 'Beta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
} else if (t_method == "SPAGRM") {
^~~~~~~~~~~~~~~~~~~~
Main.cpp:591:23: note: uninitialized use occurs here
BetaVec.at(i) = Beta * (1 - 2 * flip); // Beta if flip = false, -1*Beta is flip = true
^~~~
Main.cpp:582:14: note: remove the 'if' if its condition is always false
} else if (t_method == "SPAGRM") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:579:18: warning: variable 'Beta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~
Main.cpp:591:23: note: uninitialized use occurs here
BetaVec.at(i) = Beta * (1 - 2 * flip); // Beta if flip = false, -1*Beta is flip = true
^~~~
Main.cpp:579:14: note: remove the 'if' if its condition is always false
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:545:16: note: initialize the variable 'Beta' to silence this warning
double Beta, seBeta, pval, zScore, hwepval;
^
= 0.0
Main.cpp:582:18: warning: variable 'seBeta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
} else if (t_method == "SPAGRM") {
^~~~~~~~~~~~~~~~~~~~
Main.cpp:592:25: note: uninitialized use occurs here
seBetaVec.at(i) = seBeta;
^~~~~~
Main.cpp:582:14: note: remove the 'if' if its condition is always false
} else if (t_method == "SPAGRM") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:579:18: warning: variable 'seBeta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~
Main.cpp:592:25: note: uninitialized use occurs here
seBetaVec.at(i) = seBeta;
^~~~~~
Main.cpp:579:14: note: remove the 'if' if its condition is always false
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:545:24: note: initialize the variable 'seBeta' to silence this warning
double Beta, seBeta, pval, zScore, hwepval;
^
= 0.0
Main.cpp:579:18: warning: variable 'hwepval' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~
Main.cpp:593:26: note: uninitialized use occurs here
hwepvalVec.at(i) = hwepval;
^~~~~~~
Main.cpp:579:14: note: remove the 'if' if its condition is always false
} else if (t_method == "SPACox") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:576:11: warning: variable 'hwepval' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
if (t_method == "POLMM") {
^~~~~~~~~~~~~~~~~~~
Main.cpp:593:26: note: uninitialized use occurs here
hwepvalVec.at(i) = hwepval;
^~~~~~~
Main.cpp:576:7: note: remove the 'if' if its condition is always false
if (t_method == "POLMM") {
^~~~~~~~~~~~~~~~~~~~~~~~~~
Main.cpp:545:47: note: initialize the variable 'hwepval' to silence this warning
double Beta, seBeta, pval, zScore, hwepval;
^
= 0.0
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SAGELD.cpp -o SAGELD.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPACox.cpp -o SPACox.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPAGRM.cpp -o SPAGRM.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPAmix.cpp -o SPAmix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c UTIL.cpp -o UTIL.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c WtCoxG.cpp -o WtCoxG.o
6 warnings generated.
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 GRAB.so BGEN.o DenseGRM.o Main.o PLINK.o POLMM.o RcppExports.o SAGELD.o SPACox.o SPAGRM.o SPAmix.o UTIL.o WtCoxG.o -lz -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/GRAB.Rcheck/00LOCK-GRAB/00new/GRAB/libs
** generating debug symbols (dSYM)
** 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 (GRAB)