* installing *source* package ‘pcadapt’ ... ** 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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 af.cpp -o af.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 bed-acc-xptr.cpp -o bed-acc-xptr.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 bed2matrix.cpp -o bed2matrix.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 clumping.cpp -o clumping.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 linear-regression.cpp -o linear-regression.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 nb-na.cpp -o nb-na.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 pedUtils.cpp -o pedUtils.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 prodMat.cpp -o prodMat.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 total-var.cpp -o total-var.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 vcfUtils.cpp -o vcfUtils.o vcfUtils.cpp:84:7: warning: variable 'na_tot' set but not used [-Wunused-but-set-variable] 84 | int na_tot = 0; | ^ 1 warning generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-18/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/srv/hornik/tmp/CRAN_pretest/Library/mmapcharr/include' -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/rmio/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 writebed.cpp -o writebed.o clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-18/lib -Wl,-O1 -o pcadapt.so RcppExports.o af.o bed-acc-xptr.o bed2matrix.o clumping.o linear-regression.o nb-na.o pedUtils.o prodMat.o total-var.o vcfUtils.o writebed.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/pcadapt.Rcheck/00LOCK-pcadapt/00new/pcadapt/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 (pcadapt)