* installing *source* package ‘hsphase’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 17.0.6 (5)’
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c FastDist.cpp -o FastDist.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c MAF.cpp -o MAF.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c Ohd.cpp -o Ohd.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c TypeConversion.cpp -o TypeConversion.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c block.cpp -o block.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c block4Phase.cpp -o block4Phase.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c co.cpp -o co.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c diag.cpp -o diag.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c hsp.cpp -o hsp.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c main.cpp -o main.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c memory.cpp -o memory.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c oh.cpp -o oh.o
clang++-17  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-17/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c swDetect.cpp -o swDetect.o
clang++-17 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-17/lib -Wl,-O1 -o hsphase.so FastDist.o MAF.o Ohd.o TypeConversion.o block.o block4Phase.o co.o diag.o hsp.o main.o memory.o oh.o swDetect.o -llapack -L/home/hornik/tmp/R-d-clang-17/lib -lRblas -L/usr/lib/llvm-17/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-17/lib -lR
installing to /srv/hornik/tmp/CRAN/hsphase.Rcheck/00LOCK-hsphase/00new/hsphase/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (hsphase)