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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SAIGEgds
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c saige_misc.cpp -o saige_misc.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c vec_ext_def.cpp -o vec_ext_def.o
vec_ext_def.cpp: In function ‘void vec_init_function()’:
vec_ext_def.cpp:33:20: warning: unused variable ‘VEC_ALGORITHM_AVX2’ [-Wunused-variable]
   33 |  extern const bool VEC_ALGORITHM_AVX2;
      |                    ^~~~~~~~~~~~~~~~~~
vec_ext_def.cpp:34:20: warning: unused variable ‘VEC_ALGORITHM_AVX512BW’ [-Wunused-variable]
   34 |  extern const bool VEC_ALGORITHM_AVX512BW;
      |                    ^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -lopenblas -lgfortran -lm -lgcc -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-SAIGEgds/00new/SAIGEgds/libs
** 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
** 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 (SAIGEgds)