############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf NanoMethViz.buildbin-libdir && mkdir NanoMethViz.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=NanoMethViz.buildbin-libdir NanoMethViz_3.3.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'NanoMethViz' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++20 g++ -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genome.cpp -o genome.o genome.cpp: In member function 'bool Genome::check_if_motif(const std::string&, int, const std::string&, int)': genome.cpp:43:21: warning: variable 'chrom_view' set but not used [-Wunused-but-set-variable] 43 | string_view chrom_view = this->bases_at(chrom, motif_start, motif_end); | ^~~~~~~~~~ g++ -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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:331:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 331 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ modbam.cpp:339:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 339 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '?') { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ modbam.cpp:363:17: warning: 'target_base' may be used uninitialized [-Wmaybe-uninitialized] 363 | if (seq.at(seq_ind) == target_base) { | ^~ modbam.cpp:305:14: note: 'target_base' was declared here 305 | char target_base; | ^~~~~~~~~~~ modbam.cpp:364:21: warning: 'parse_mode' may be used uninitialized [-Wmaybe-uninitialized] 364 | switch (parse_mode) { | ^~~~~~ modbam.cpp:308:19: note: 'parse_mode' was declared here 308 | ParseMode parse_mode; | ^~~~~~~~~~ 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++\bits\stl_iterator.h:85, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_algobase.h:67, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\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\13.3.0\include\c++\bits\alloc_traits.h:540:21, 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\13.3.0\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\13.3.0\include\c++\bits\stl_vector.h:1292:21, inlined from 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)' at modbam.cpp:368:50: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\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:304:14: note: 'current_base' was declared here 304 | char current_base; | ^~~~~~~~~~~~ g++ -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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 genome.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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/meat/NanoMethViz.buildbin-libdir/00LOCK-NanoMethViz/00new/NanoMethViz/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 'NanoMethViz' as NanoMethViz_3.3.0.zip * DONE (NanoMethViz)