############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=universalmotif.buildbin-libdir universalmotif_1.24.2.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'universalmotif' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c add_multifreq.cpp -o add_multifreq.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calc_complexity.cpp -o calc_complexity.o In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\x86_64-w64-mingw32.static.posix\bits\c++allocator.h:33, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\allocator.h:46, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\alloc_traits.h:39, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\ext\alloc_traits.h:34, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\hashtable_policy.h:39, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\hashtable.h:35, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\unordered_map.h:33, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\unordered_map:41, from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153, from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66, from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/RcppCommon.h:30, from F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include/Rcpp.h:27, from calc_complexity.cpp:1: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]', inlined from 'static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\alloc_traits.h:517:23, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:390:19, inlined from 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:369:15, inlined from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:738:7, inlined from 'double dust_cpp(const std::string&)' at calc_complexity.cpp:154:1: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\new_allocator.h:172:33: warning: 'void operator delete(void*)' called on pointer '' with nonzero offset [16, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = std::unique_ptr*> >]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = std::unique_ptr*> >]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\alloc_traits.h:482:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = std::unique_ptr*> >; _Alloc = std::allocator*> > >]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:381:33, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:378:7, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:335:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:557:47, inlined from 'double dust_cpp(const std::string&)' at calc_complexity.cpp:149:44: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compare_motifs.cpp -o compare_motifs.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_bkg.cpp -o get_bkg.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c motif_finder.cpp -o motif_finder.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c motif_peaks.cpp -o motif_peaks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c motif_pvalue.cpp -o motif_pvalue.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scan_sequences.cpp -o scan_sequences.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c shuffle_sequences.cpp -o shuffle_sequences.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trim_motifs.cpp -o trim_motifs.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c universalmotif-class.cpp -o universalmotif-class.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils-exported.cpp -o utils-exported.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppThread/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils-internal.cpp -o utils-internal.o g++ -shared -s -static-libgcc -o universalmotif.dll tmp.def RcppExports.o add_multifreq.o calc_complexity.o compare_motifs.o get_bkg.o motif_finder.o motif_peaks.o motif_pvalue.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/meat/universalmotif.buildbin-libdir/00LOCK-universalmotif/00new/universalmotif/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for 'convert_motifs' with signature 'motifs="MotifList"': no definition for class "MotifList" in method for 'convert_motifs' with signature 'motifs="TFFMFirst"': no definition for class "TFFMFirst" in method for 'convert_motifs' with signature 'motifs="PFMatrix"': no definition for class "PFMatrix" in method for 'convert_motifs' with signature 'motifs="PWMatrix"': no definition for class "PWMatrix" in method for 'convert_motifs' with signature 'motifs="ICMatrix"': no definition for class "ICMatrix" in method for 'convert_motifs' with signature 'motifs="XMatrixList"': no definition for class "XMatrixList" in method for 'convert_motifs' with signature 'motifs="pwm"': no definition for class "pwm" in method for 'convert_motifs' with signature 'motifs="pcm"': no definition for class "pcm" in method for 'convert_motifs' with signature 'motifs="pfm"': no definition for class "pfm" in method for 'convert_motifs' with signature 'motifs="PWM"': no definition for class "PWM" in method for 'convert_motifs' with signature 'motifs="Motif"': no definition for class "Motif" ** 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 * MD5 sums packaged installation of 'universalmotif' as universalmotif_1.24.2.zip * DONE (universalmotif)