* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘GRAB’ ...
** this is package ‘GRAB’ version ‘0.2.4’
** package ‘GRAB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 21.1.6 (2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnIU6SG/R.INSTALL1721c22d85a350/GRAB/src'
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c BGEN.cpp -o BGEN.o
BGEN.cpp:75:12: warning: unused variable 'CompressedSNPBlocks' [-Wunused-variable]
75 | uint32_t CompressedSNPBlocks = flags&3; //Rcpp::Rcout << " CompressedSNPBlocks: " << CompressedSNPBlocks << std::endl;
| ^~~~~~~~~~~~~~~~~~~
BGEN.cpp:77:12: warning: unused variable 'Layout' [-Wunused-variable]
77 | uint32_t Layout = (flags>>2)&0xf; //Rcpp::Rcout << " Layout: " << Layout << std::endl;
| ^~~~~~
2 warnings generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c DenseGRM.cpp -o DenseGRM.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c Main.cpp -o Main.o
Main.cpp:582:18: warning: variable 'Beta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
582 | } else if (t_method == "SPAGRM") {
| ^~~~~~~~~~~~~~~~~~~~
Main.cpp:591:23: note: uninitialized use occurs here
591 | 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
582 | } else if (t_method == "SPAGRM") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | pval = ptr_gSPAGRMobj->getMarkerPval(GVec, altFreq, zScore, hwepval);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 |
585 | } else {
| ~~~~~~~
Main.cpp:579:18: warning: variable 'Beta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~
Main.cpp:591:23: note: uninitialized use occurs here
591 | 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
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
580 | pval = ptr_gSPACoxobj->getMarkerPval(GVec, altFreq, zScore);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
581 |
582 | } else if (t_method == "SPAGRM") {
| ~~~~~~
Main.cpp:545:16: note: initialize the variable 'Beta' to silence this warning
545 | 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]
582 | } else if (t_method == "SPAGRM") {
| ^~~~~~~~~~~~~~~~~~~~
Main.cpp:592:25: note: uninitialized use occurs here
592 | seBetaVec.at(i) = seBeta;
| ^~~~~~
Main.cpp:582:14: note: remove the 'if' if its condition is always false
582 | } else if (t_method == "SPAGRM") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | pval = ptr_gSPAGRMobj->getMarkerPval(GVec, altFreq, zScore, hwepval);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 |
585 | } else {
| ~~~~~~~
Main.cpp:579:18: warning: variable 'seBeta' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~
Main.cpp:592:25: note: uninitialized use occurs here
592 | seBetaVec.at(i) = seBeta;
| ^~~~~~
Main.cpp:579:14: note: remove the 'if' if its condition is always false
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
580 | pval = ptr_gSPACoxobj->getMarkerPval(GVec, altFreq, zScore);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
581 |
582 | } else if (t_method == "SPAGRM") {
| ~~~~~~
Main.cpp:545:24: note: initialize the variable 'seBeta' to silence this warning
545 | 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]
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~
Main.cpp:593:26: note: uninitialized use occurs here
593 | hwepvalVec.at(i) = hwepval;
| ^~~~~~~
Main.cpp:579:14: note: remove the 'if' if its condition is always false
579 | } else if (t_method == "SPACox") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
580 | pval = ptr_gSPACoxobj->getMarkerPval(GVec, altFreq, zScore);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
581 |
582 | } else if (t_method == "SPAGRM") {
| ~~~~~~
Main.cpp:576:11: warning: variable 'hwepval' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
576 | if (t_method == "POLMM") {
| ^~~~~~~~~~~~~~~~~~~
Main.cpp:593:26: note: uninitialized use occurs here
593 | hwepvalVec.at(i) = hwepval;
| ^~~~~~~
Main.cpp:576:7: note: remove the 'if' if its condition is always false
576 | if (t_method == "POLMM") {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
577 | ptr_gPOLMMobj->getMarkerPval(GVec, Beta, seBeta, pval, altFreq, zScore);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
578 |
579 | } else if (t_method == "SPACox") {
| ~~~~~~
Main.cpp:545:47: note: initialize the variable 'hwepval' to silence this warning
545 | double Beta, seBeta, pval, zScore, hwepval;
| ^
| = 0.0
6 warnings generated.
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c PLINK.cpp -o PLINK.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c POLMM.cpp -o POLMM.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c RcppExports.cpp -o RcppExports.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c SAGELD.cpp -o SAGELD.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c SPACox.cpp -o SPACox.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c SPAGRM.cpp -o SPAGRM.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c SPAmix.cpp -o SPAmix.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c UTIL.cpp -o UTIL.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c WtCoxG.cpp -o WtCoxG.o
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-21/lib/clang/21/lib/linux -L/usr/lib/llvm-21/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnIU6SG/R.INSTALL1721c22d85a350/GRAB/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnIU6SG/R.INSTALL1721c22d85a350/GRAB/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnIU6SG/R.INSTALL1721c22d85a350/GRAB/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-GRAB/00new/GRAB/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 (GRAB)