############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'NanoMethViz' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++20 g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/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++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_cg.cpp -o count_cg.o g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c modbam.cpp -o modbam.o modbam.cpp: In function 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)': modbam.cpp:394:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 394 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ modbam.cpp:400:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 400 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '.') { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ modbam.cpp:437:21: warning: 'target_base' may be used uninitialized [-Wmaybe-uninitialized] 437 | if (seq.at(seq_ind) == target_base) { | ^~ modbam.cpp:368:14: note: 'target_base' was declared here 368 | char target_base; | ^~~~~~~~~~~ modbam.cpp:425:17: warning: 'parse_mode' may be used uninitialized [-Wmaybe-uninitialized] 425 | if (parse_mode == ParseMode::skip_low_prob) { | ^~ modbam.cpp:371:19: note: 'parse_mode' was declared here 371 | ParseMode parse_mode; | ^~~~~~~~~~ In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator.h:85, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:67, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/algorithm:60, from modbam.cpp:1: In function 'constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = char; _Args = {const char&}]', inlined from 'static constexpr void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = char; _Args = {const char&}; _Tp = char]' at C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/alloc_traits.h:539:21, inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char&}; _Tp = char; _Alloc = std::allocator]' at C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/vector.tcc:468:28, inlined from 'constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = char; _Alloc = std::allocator]' at C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_vector.h:1289:21, inlined from 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)' at modbam.cpp:430:46: C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_construct.h:97:14: warning: 'current_base' may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modbam.cpp: In function 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)': modbam.cpp:367:14: note: 'current_base' was declared here 367 | char current_base; | ^~~~~~~~~~~~ g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -shared -s -static-libgcc -o NanoMethViz.dll tmp.def RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.o -lz -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/R/library/00LOCK-NanoMethViz/00new/NanoMethViz/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (NanoMethViz)