############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=SAIGEgds.buildbin-libdir SAIGEgds_2.9.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'SAIGEgds' ... ** this is package 'SAIGEgds' version '2.9.0' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_fitnull.cpp:29: F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': F:/biocbuild/bbs-3.22-bioc/R/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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; | ^~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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*]': F:/biocbuild/bbs-3.22-bioc/R/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_main.cpp:30: F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': F:/biocbuild/bbs-3.22-bioc/R/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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; | ^~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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*]': F:/biocbuild/bbs-3.22-bioc/R/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_misc.cpp -o saige_misc.o In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from saige.h:37, from saige_misc.cpp:25: F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': F:/biocbuild/bbs-3.22-bioc/R/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); | ~~~~~~~~~^~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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; | ^~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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*]': F:/biocbuild/bbs-3.22-bioc/R/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 ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ F:/biocbuild/bbs-3.22-bioc/R/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"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx2.cpp -o vec_ext_avx2.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_def.cpp -o vec_ext_def.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -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 saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/libs/x64 -lRcppParallel -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-bioc/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'GenomeInfoDb' for requests: 'seqnames', 'seqlevels' when loading 'SeqArray' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'GenomeInfoDb' for requests: 'seqnames', 'seqlevels' when loading 'SeqArray' ** testing if installed package can be loaded from final location No methods found in package 'GenomeInfoDb' for requests: 'seqnames', 'seqlevels' when loading 'SeqArray' ** testing if installed package keeps a record of temporary installation path * MD5 sums packaged installation of 'SAIGEgds' as SAIGEgds_2.9.0.zip * DONE (SAIGEgds)