Install log for 'pcadapt'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘pcadapt’ ...
** this is package ‘pcadapt’ version ‘4.4.1’
** package ‘pcadapt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 21.1.5 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFqqVhG/R.INSTALL10b1671139007/pcadapt/src'
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 af.cpp -o af.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 bed-acc-xptr.cpp -o bed-acc-xptr.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 bed2matrix.cpp -o bed2matrix.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 clumping.cpp -o clumping.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 linear-regression.cpp -o linear-regression.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 nb-na.cpp -o nb-na.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 pedUtils.cpp -o pedUtils.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 prodMat.cpp -o prodMat.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 total-var.cpp -o total-var.o
clang++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 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++-21 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/mmapcharr/include' -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/rmio/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 writebed.cpp -o writebed.o
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/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 total-var.o vcfUtils.o writebed.o -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/RtmpFqqVhG/R.INSTALL10b1671139007/pcadapt/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFqqVhG/R.INSTALL10b1671139007/pcadapt/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFqqVhG/R.INSTALL10b1671139007/pcadapt/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/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
* DONE (pcadapt)