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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=0   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SPATest.cpp -o SPATest.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=0   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:76:27: warning: unused variable 'th_idx' [-Wunused-variable]
   76 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp:76:27: note: in definition of macro 'PARALLEL_FOR'
   76 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_get_sparse(SEXP)':
saige_fitnull.cpp:256:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_len_t' {aka 'int'} [-Wsign-compare]
  256 |         if (num > Rf_length(geno))
      |             ~~~~^~~~~~~~~~~~~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_fitnull.cpp:76:27: warning: unused variable 'th_idx' [-Wunused-variable]
   76 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp:76:27: note: in definition of macro 'PARALLEL_FOR'
   76 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const arma::dcolvec&, arma::dvec&)':
saige_fitnull.cpp:80:27: warning: unused variable 'th_idx' [-Wunused-variable]
   80 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp:80:27: note: in definition of macro 'PARALLEL_RANGE'
   80 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'void get_diag_sigma(const arma::dvec&, const arma::dvec&, arma::dvec&)':
saige_fitnull.cpp:80:27: warning: unused variable 'th_idx' [-Wunused-variable]
   80 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp:80:27: note: in definition of macro 'PARALLEL_RANGE'
   80 |                 const int th_idx = 0;  \
      |                           ^~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=0   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_main.cpp -o saige_main.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=0   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vectorization.cpp -o vectorization.o
g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)