############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SNPRelate ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'SNPRelate' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SNPRelate.c -o R_SNPRelate.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPRelate.cpp -o SNPRelate.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadPool.cpp -o ThreadPool.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dGenGWAS.cpp -o dGenGWAS.o In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\alloc_traits.h:33, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ext\alloc_traits.h:34, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\basic_string.h:39, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:53, from F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include/dType.h:55, from F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include/R_GDS.h:40, from F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include/R_GDS_CPP.h:40, from dGenGWAS.h:25, from dGenGWAS.cpp:22: In function 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = unsigned char; _Args = {}]', inlined from 'static _ForwardIterator std::__uninitialized_default_n_1::__uninit_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned char*; _Size = long long unsigned int]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_uninitialized.h:661:23, inlined from 'static _ForwardIterator std::__uninitialized_default_n_1::__uninit_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned char*; _Size = long long unsigned int]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_uninitialized.h:655:9, inlined from '_ForwardIterator std::__uninitialized_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned char*; _Size = long long unsigned int]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_uninitialized.h:701:20, inlined from '_ForwardIterator std::__uninitialized_default_n_a(_ForwardIterator, _Size, allocator<_Tp>&) [with _ForwardIterator = unsigned char*; _Size = long long unsigned int; _Tp = unsigned char]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_uninitialized.h:766:44, inlined from 'void std::vector<_Tp, _Alloc>::_M_default_initialize(size_type) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:1713:36, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:553:30, inlined from 'void GWAS::CdBaseWorkSpace::GetMissingRates(double*)' at dGenGWAS.cpp:132:30: c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_construct.h:119:7: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\x86_64-w64-mingw32.static.posix\bits\c++allocator.h:33, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\allocator.h:46, from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:41: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\alloc_traits.h:464:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:378:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:395:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:332:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]' at c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_vector.h:552:47, inlined from 'void GWAS::CdBaseWorkSpace::GetMissingRates(double*)' at dGenGWAS.cpp:132:30: c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\new_allocator.h:137:55: note: destination object of size 0 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dVect.cpp -o dVect.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genBeta.cpp -o genBeta.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genEIGMIX.cpp -o genEIGMIX.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genFst.cpp -o genFst.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genHWE.cpp -o genHWE.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBD.cpp -o genIBD.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBS.cpp -o genIBS.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genKING.cpp -o genKING.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genLD.cpp -o genLD.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genPCA.cpp -o genPCA.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'F:/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genSlideWin.cpp -o genSlideWin.o g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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-SNPRelate/00new/SNPRelate/libs/x64 ** R ** data *** moving datasets to lazyload DB ** 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 (SNPRelate)