############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SAIGEgds ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘SAIGEgds’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_fitnull.cpp -o saige_fitnull.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_fitnull.cpp:29: /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_main.cpp -o saige_main.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_main.cpp:30: /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_misc.cpp -o saige_misc.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_misc.cpp:25: /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/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:33:27: warning: unused variable 'VEC_ALGORITHM_AVX2' [-Wunused-variable] 33 | extern const bool VEC_ALGORITHM_AVX2; | ^~~~~~~~~~~~~~~~~~ vec_ext_def.cpp:34:27: warning: unused variable 'VEC_ALGORITHM_AVX512BW' [-Wunused-variable] 34 | extern const bool VEC_ALGORITHM_AVX512BW; | ^~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/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 -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -lgcc -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)