* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘pcadapt’ ...
** package ‘pcadapt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpSoVyPR/R.INSTALL21254a2b46676d/pcadapt/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c af.cpp -o af.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed-acc-xptr.cpp -o bed-acc-xptr.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bed2matrix.cpp -o bed2matrix.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c clumping.cpp -o clumping.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linear-regression.cpp -o linear-regression.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c nb-na.cpp -o nb-na.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pedUtils.cpp -o pedUtils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c prodMat.cpp -o prodMat.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c vcfUtils.cpp -o vcfUtils.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/mmapcharr/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmio/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c writebed.cpp -o writebed.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/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 vcfUtils.o writebed.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpSoVyPR/R.INSTALL21254a2b46676d/pcadapt/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpSoVyPR/R.INSTALL21254a2b46676d/pcadapt/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpSoVyPR/R.INSTALL21254a2b46676d/pcadapt/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
* creating tarball
packaged installation of ‘pcadapt’ as ‘pcadapt_4.3.5_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (pcadapt)