* installing *source* package ‘GRAB’ ... ** this is package ‘GRAB’ version ‘0.2.4’ ** using staged installation ** libs using C++ compiler: ‘Debian clang version 21.1.6 (2)’ clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-d-clang-21/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-d-clang-21/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-d-clang-21/lib -lR installing to /srv/hornik/tmp/CRAN_pretest/GRAB.Rcheck/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)