* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘SKAT’ ...
** package ‘SKAT’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 18.1.4 (1)’
make[1]: Entering directory '/tmp/RtmpekTtn4/R.INSTALL10f01ba1b5042/SKAT/src'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_ComputeExact.cpp -o Binary_ComputeExact.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_ComputeExactMC.cpp -o Binary_ComputeExactMC.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_ComputeExactSKATO.cpp -o Binary_ComputeExactSKATO.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_HyperGeo.cpp -o Binary_HyperGeo.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_Permu_SKAT.cpp -o Binary_Permu_SKAT.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_global.cpp -o Binary_global.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c Binary_resampling.cpp -o Binary_resampling.o
Binary_resampling.cpp:196:15: warning: variable 'ncase' set but not used [-Wunused-but-set-variable]
  196 |         int i, n, m, ncase, idx;
      |                      ^
Binary_resampling.cpp:196:22: warning: variable 'idx' set but not used [-Wunused-but-set-variable]
  196 |         int i, n, m, ncase, idx;
      |                             ^
2 warnings generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c bed_reader.cpp -o bed_reader.o
bed_reader.cpp:623:6: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
  623 |         int flag = 0;
      |             ^
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c interface_new.cpp -o interface_new.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c interface_to_R.cpp -o interface_to_R.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c kernel_func.cpp -o kernel_func.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c mwo_reader.cpp -o mwo_reader.o
mwo_reader.cpp:231:9: warning: variable 'snp_id_ch_ind' set but not used [-Wunused-but-set-variable]
  231 |         size_t snp_id_ch_ind = 0;
      |                ^
mwo_reader.cpp:377:9: warning: variable 'snp_id_ch_ind' set but not used [-Wunused-but-set-variable]
  377 |         size_t snp_id_ch_ind = 0;
      |                ^
2 warnings generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c qfc.cpp -o qfc.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic  -c setid_bim_index.cpp -o setid_bim_index.o
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o SKAT.so Binary_ComputeExact.o Binary_ComputeExactMC.o Binary_ComputeExactSKATO.o Binary_HyperGeo.o Binary_Permu_SKAT.o Binary_global.o Binary_resampling.o bed_reader.o interface_new.o interface_to_R.o kernel_func.o mwo_reader.o qfc.o setid_bim_index.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpekTtn4/R.INSTALL10f01ba1b5042/SKAT/src'
make[1]: Entering directory '/tmp/RtmpekTtn4/R.INSTALL10f01ba1b5042/SKAT/src'
make[1]: Leaving directory '/tmp/RtmpekTtn4/R.INSTALL10f01ba1b5042/SKAT/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-SKAT/00new/SKAT/libs
** R
** data
** 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 (SKAT)