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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL FLAMES
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'FLAMES' ...
** using non-staged installation via StagedInstall field
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c flexiplex.cpp -o flexiplex.o
flexiplex.cpp: In function 'unsigned int edit_distance(const std::string&, const std::string&, unsigned int&, int)':
flexiplex.cpp:118:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  118 |       if (min_value <= max_editd)
      |           ~~~~~~~~~~^~~~~~~~~~~~
flexiplex.cpp: In function 'Barcode get_barcode(const std::string&, const std::unordered_set<std::__cxx11::basic_string<char> >&, int, int, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&)':
flexiplex.cpp:224:19: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare]
  224 |     if (i_pattern >= subpattern_ends[i_subpattern]) {
flexiplex.cpp:285:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  285 |     if (editDistance == barcode.editd) {
      |         ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
flexiplex.cpp:287:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  287 |     } else if (editDistance < barcode.editd &&
      |                ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
flexiplex.cpp:288:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  288 |                editDistance <= barcode_max_editd) { // if best so far, update
      |                ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
flexiplex.cpp: In function 'std::vector<Barcode> big_barcode_search(const std::string&, const std::unordered_set<std::__cxx11::basic_string<char> >&, int, int, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&)':
flexiplex.cpp:350:29: warning: comparison of integer expressions of different signedness: 'const int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long long unsigned int'} [-Wsign-compare]
  350 |       if (barcode.flank_end == std::string::npos) {
      |           ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
flexiplex.cpp: In function 'void print_stats(const std::string&, const std::vector<Barcode>&, std::ostream&)':
flexiplex.cpp:375:38: warning: comparison of integer expressions of different signedness: 'const int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long long unsigned int'} [-Wsign-compare]
  375 |                << (barcode.flank_end == std::string::npos ? "True" : "False")
      |                    ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
flexiplex.cpp: In function 'void print_read(const std::string&, const std::string&, const std::string&, const std::vector<Barcode>&, std::ofstream&, std::unordered_set<std::__cxx11::basic_string<char> >&, bool)':
flexiplex.cpp:400:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Barcode>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  400 |   for (int b = 0; b < vec_bc.size(); b++) {
      |                   ~~^~~~~~~~~~~~~~~
flexiplex.cpp:410:32: warning: comparison of integer expressions of different signedness: 'const int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long long unsigned int'} [-Wsign-compare]
  410 |     if (vec_bc.at(b).flank_end == std::string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
flexiplex.cpp:415:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Barcode>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  415 |     for (int f = 0; f < vec_bc.size(); f++) {
      |                     ~~^~~~~~~~~~~~~~~
flexiplex.cpp: In function 'int flexiplex(Rcpp::String, Rcpp::String, bool, int, int, Rcpp::StringVector, Rcpp::String, Rcpp::String, Rcpp::String, int)':
flexiplex.cpp:634:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<SearchResult> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  634 |     for (int t = 0; t < sr_v.size();
      |                     ~~^~~~~~~~~~~~~
flexiplex.cpp:639:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SearchResult>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  639 |       for (int r = 0; r < sr_v[t].size(); r++) { // loop over the reads
      |                       ~~^~~~~~~~~~~~~~~~
flexiplex.cpp:641:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Barcode>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  641 |         for (int b = 0; b < sr_v[t][r].vec_bc_for.size(); b++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flexiplex.cpp:643:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Barcode>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  643 |         for (int b = 0; b < sr_v[t][r].vec_bc_rev.size(); b++)
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o
g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o flexiplex.o utility/edlib-1.2.7/edlib.o F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/FLAMES/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
* DONE (FLAMES)