############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data NanoMethViz ### ############################################################################## ############################################################################## * checking for file ‘NanoMethViz/DESCRIPTION’ ... OK * preparing ‘NanoMethViz’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++20 g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c count_cg.cpp -o count_cg.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -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 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 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 /usr/include/c++/13/bits/stl_iterator.h:85, from /usr/include/c++/13/bits/stl_algobase.h:67, from /usr/include/c++/13/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 /usr/include/c++/13/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 /usr/include/c++/13/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 /usr/include/c++/13/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: /usr/include/c++/13/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"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c utils.cpp -o utils.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -hts -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR g++: error: unrecognized command-line option ‘-h’ make: *** [/home/biocbuild/bbs-3.21-bioc/R/share/make/shlib.mk:10: NanoMethViz.so] Error 1 ERROR: compilation failed for package ‘NanoMethViz’ * removing ‘/tmp/RtmpWYWN7n/Rinst11984a5d6ac2f3/NanoMethViz’ ----------------------------------- ERROR: package installation failed