* installing *source* package ‘SKAT’ ...
** this is package ‘SKAT’ version ‘2.2.5’
** package ‘SKAT’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 23.1.0’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/SKAT/src'
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_ComputeExact.cpp -o Binary_ComputeExact.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_ComputeExactMC.cpp -o Binary_ComputeExactMC.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_ComputeExactSKATO.cpp -o Binary_ComputeExactSKATO.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_HyperGeo.cpp -o Binary_HyperGeo.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_Permu_SKAT.cpp -o Binary_Permu_SKAT.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c Binary_global.cpp -o Binary_global.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -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.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -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;
| ^
In file included from bed_reader.cpp:47:
In file included from ./bed_reader.h:19:
In file included from ./setid_bim_index.h:24:
./NPsort.h:113:48: warning: unused function template 'sort' [-Wunused-template]
113 | template<class T, class Comp > static void sort(const T* dat, size_t* idx, size_t size, Comp c=Comp() ){
| ^~~~
./NPsort.h:118:35: warning: unused function template 'sort' [-Wunused-template]
118 | template<class T> static void sort(const T* dat, size_t* idx, size_t size){
| ^~~~
3 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c interface_new.cpp -o interface_new.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c interface_to_R.cpp -o interface_to_R.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c kernel_func.cpp -o kernel_func.o
In file included from interface_to_R.cpp:16:
In file included from ./bed_reader.h:19:
In file included from ./setid_bim_index.h:24:
./NPsort.h:113:48: warning: unused function template 'sort' [-Wunused-template]
113 | template<class T, class Comp > static void sort(const T* dat, size_t* idx, size_t size, Comp c=Comp() ){
| ^~~~
./NPsort.h:118:35: warning: unused function template 'sort' [-Wunused-template]
118 | template<class T> static void sort(const T* dat, size_t* idx, size_t size){
| ^~~~
2 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c mwo_reader.cpp -o mwo_reader.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c qfc.cpp -o qfc.o
qfc.cpp:73:68: warning: variable 'ndtsrt' set but not used [-Wunused-but-set-variable]
73 | extern double *lb; extern int *th; extern int r; extern BOOL ndtsrt;
| ^
qfc.cpp:230:26: warning: variable 'fail' set but not used [-Wunused-but-set-variable]
230 | extern BOOL ndtsrt,fail; extern int *th,*n; extern double *lb,*nc;
| ^
qfc.cpp:29:40: warning: variable 'ndtsrt' set but not used [-Wunused-but-set-global]
29 | static int count, r, lim; static BOOL ndtsrt, fail;
| ^
3 warnings generated.
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;
| ^
In file included from mwo_reader.cpp:20:
In file included from ./mwo_reader.h:22:
In file included from ./bed_reader.h:19:
In file included from ./setid_bim_index.h:24:
./NPsort.h:113:48: warning: unused function template 'sort' [-Wunused-template]
113 | template<class T, class Comp > static void sort(const T* dat, size_t* idx, size_t size, Comp c=Comp() ){
| ^~~~
./NPsort.h:118:35: warning: unused function template 'sort' [-Wunused-template]
118 | template<class T> static void sort(const T* dat, size_t* idx, size_t size){
| ^~~~
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang23/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23 -c setid_bim_index.cpp -o setid_bim_index.o
4 warnings generated.
In file included from setid_bim_index.cpp:24:
In file included from ./setid_bim_index.h:24:
./NPsort.h:118:35: warning: unused function template 'sort' [-Wunused-template]
118 | template<class T> static void sort(const T* dat, size_t* idx, size_t size){
| ^~~~
1 warning generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -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
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/SKAT/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/SKAT/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/SKAT/src'
installing to /data/localhost/ripley/R/packages/tests-clang/SKAT.Rcheck/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)