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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL screenCounter
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘screenCounter’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_combo_barcodes_paired.cpp -o count_combo_barcodes_paired.o
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5,
                 from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6,
                 from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4,
                 from count_combo_barcodes_paired.cpp:3:
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘bool kaori::MismatchTrie::is_optimal(int, size_t, size_t&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:163:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |                 if (v < maxed) {
      |                     ~~^~~~~~~
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘std::pair<int, int> kaori::AnyMismatches::search(const char*, size_t, int, int, int&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable ‘found’ [-Wunused-variable]
  279 |                 bool found = false;
      |                      ^~~~~
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6,
                 from ../inst/include/kaori/handlers/CombinatorialBarcodesPairedEnd.hpp:4,
                 from count_combo_barcodes_paired.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘void kaori::fill_library(const std::vector<const char*>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, Trie&, bool, bool) [with Trie = kaori::AnyMismatches]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:123:21:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:40:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |             for (int j = 0; j < len; ++j) {
      |                             ~~^~~~~
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: variable ‘it’ set but not used [-Wunused-but-set-variable]
   45 |         auto it = exact.find(current);
      |              ^~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_combo_barcodes_single.cpp -o count_combo_barcodes_single.o
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5,
                 from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5,
                 from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘bool kaori::MismatchTrie::is_optimal(int, size_t, size_t&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:163:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |                 if (v < maxed) {
      |                     ~~^~~~~~~
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘std::pair<int, int> kaori::AnyMismatches::search(const char*, size_t, int, int, int&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable ‘found’ [-Wunused-variable]
  279 |                 bool found = false;
      |                      ^~~~~
count_combo_barcodes_single.cpp: In function ‘Rcpp::List count_combo_barcodes_single(std::string, std::string, int, Rcpp::List, int, bool, int)’:
count_combo_barcodes_single.cpp:43:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   43 |     for (size_t o = 0; o < options.size(); ++o) {
      |                        ~~^~~~~~~~~~~~~~~~
In file included from ../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:5,
                 from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘void kaori::fill_library(const std::vector<const char*>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, Trie&, bool, bool) [with Trie = kaori::AnyMismatches]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:123:21:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:40:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |             for (int j = 0; j < len; ++j) {
      |                             ~~^~~~~
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: variable ‘it’ set but not used [-Wunused-but-set-variable]
   45 |         auto it = exact.find(current);
      |              ^~
In file included from count_combo_barcodes_single.cpp:3:
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp: In instantiation of ‘kaori::CombinatorialBarcodesSingleEnd<max_size, num_variable>::CombinatorialBarcodesSingleEnd(const char*, size_t, int, const std::array<kaori::BarcodePool, num_variable>&, int) [with long unsigned int max_size = 32; long unsigned int num_variable = 2; size_t = long unsigned int]’:
count_combo_barcodes_single.cpp:23:49:   required from ‘Rcpp::List count_combo_barcodes_single_(Reader&, std::string, int, const std::array<kaori::BarcodePool, num_variable>&, int, bool, int) [with long unsigned int N = 32; long unsigned int V = 2; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_combo_barcodes_single.cpp:51:53:   required from here
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable ‘len’ [-Wunused-variable]
   69 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable ‘len’ [-Wunused-variable]
   78 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp: In instantiation of ‘kaori::CombinatorialBarcodesSingleEnd<max_size, num_variable>::CombinatorialBarcodesSingleEnd(const char*, size_t, int, const std::array<kaori::BarcodePool, num_variable>&, int) [with long unsigned int max_size = 64; long unsigned int num_variable = 2; size_t = long unsigned int]’:
count_combo_barcodes_single.cpp:23:49:   required from ‘Rcpp::List count_combo_barcodes_single_(Reader&, std::string, int, const std::array<kaori::BarcodePool, num_variable>&, int, bool, int) [with long unsigned int N = 64; long unsigned int V = 2; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_combo_barcodes_single.cpp:53:53:   required from here
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable ‘len’ [-Wunused-variable]
   69 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable ‘len’ [-Wunused-variable]
   78 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp: In instantiation of ‘kaori::CombinatorialBarcodesSingleEnd<max_size, num_variable>::CombinatorialBarcodesSingleEnd(const char*, size_t, int, const std::array<kaori::BarcodePool, num_variable>&, int) [with long unsigned int max_size = 128; long unsigned int num_variable = 2; size_t = long unsigned int]’:
count_combo_barcodes_single.cpp:23:49:   required from ‘Rcpp::List count_combo_barcodes_single_(Reader&, std::string, int, const std::array<kaori::BarcodePool, num_variable>&, int, bool, int) [with long unsigned int N = 128; long unsigned int V = 2; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_combo_barcodes_single.cpp:55:54:   required from here
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable ‘len’ [-Wunused-variable]
   69 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable ‘len’ [-Wunused-variable]
   78 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp: In instantiation of ‘kaori::CombinatorialBarcodesSingleEnd<max_size, num_variable>::CombinatorialBarcodesSingleEnd(const char*, size_t, int, const std::array<kaori::BarcodePool, num_variable>&, int) [with long unsigned int max_size = 256; long unsigned int num_variable = 2; size_t = long unsigned int]’:
count_combo_barcodes_single.cpp:23:49:   required from ‘Rcpp::List count_combo_barcodes_single_(Reader&, std::string, int, const std::array<kaori::BarcodePool, num_variable>&, int, bool, int) [with long unsigned int N = 256; long unsigned int V = 2; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_combo_barcodes_single.cpp:57:54:   required from here
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:69:24: warning: unused variable ‘len’ [-Wunused-variable]
   69 |                 size_t len = current.second - current.first;
      |                        ^~~
../inst/include/kaori/handlers/CombinatorialBarcodesSingleEnd.hpp:78:24: warning: unused variable ‘len’ [-Wunused-variable]
   78 |                 size_t len = current.second - current.first;
      |                        ^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_dual_barcodes.cpp -o count_dual_barcodes.o
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5,
                 from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘bool kaori::MismatchTrie::is_optimal(int, size_t, size_t&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:163:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |                 if (v < maxed) {
      |                     ~~^~~~~~~
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘std::pair<int, int> kaori::AnyMismatches::search(const char*, size_t, int, int, int&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable ‘found’ [-Wunused-variable]
  279 |                 bool found = false;
      |                      ^~~~~
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘void kaori::fill_library(const std::vector<const char*>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, Trie&, bool, bool) [with Trie = kaori::AnyMismatches]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:123:21:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:40:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |             for (int j = 0; j < len; ++j) {
      |                             ~~^~~~~
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: variable ‘it’ set but not used [-Wunused-but-set-variable]
   45 |         auto it = exact.find(current);
      |              ^~
In file included from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/DualBarcodes.hpp: In instantiation of ‘kaori::DualBarcodes<max_size>::DualBarcodes(const char*, size_t, bool, const kaori::BarcodePool&, int, const char*, size_t, bool, const kaori::BarcodePool&, int, bool) [with long unsigned int max_size = 32; size_t = long unsigned int]’:
count_dual_barcodes.cpp:31:28:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:116:46:   required from here
../inst/include/kaori/handlers/DualBarcodes.hpp:105:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |                 for (int j = 0; j < len1; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp:114:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  114 |                 for (int j = 0; j < len2; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp: In instantiation of ‘kaori::DualBarcodes<max_size>::DualBarcodes(const char*, size_t, bool, const kaori::BarcodePool&, int, const char*, size_t, bool, const kaori::BarcodePool&, int, bool) [with long unsigned int max_size = 64; size_t = long unsigned int]’:
count_dual_barcodes.cpp:31:28:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 64; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:118:46:   required from here
../inst/include/kaori/handlers/DualBarcodes.hpp:105:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |                 for (int j = 0; j < len1; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp:114:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  114 |                 for (int j = 0; j < len2; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp: In instantiation of ‘kaori::DualBarcodes<max_size>::DualBarcodes(const char*, size_t, bool, const kaori::BarcodePool&, int, const char*, size_t, bool, const kaori::BarcodePool&, int, bool) [with long unsigned int max_size = 128; size_t = long unsigned int]’:
count_dual_barcodes.cpp:31:28:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 128; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:120:47:   required from here
../inst/include/kaori/handlers/DualBarcodes.hpp:105:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |                 for (int j = 0; j < len1; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp:114:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  114 |                 for (int j = 0; j < len2; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp: In instantiation of ‘kaori::DualBarcodes<max_size>::DualBarcodes(const char*, size_t, bool, const kaori::BarcodePool&, int, const char*, size_t, bool, const kaori::BarcodePool&, int, bool) [with long unsigned int max_size = 256; size_t = long unsigned int]’:
count_dual_barcodes.cpp:31:28:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 256; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:122:47:   required from here
../inst/include/kaori/handlers/DualBarcodes.hpp:105:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |                 for (int j = 0; j < len1; ++j) {
      |                                 ~~^~~~~~
../inst/include/kaori/handlers/DualBarcodes.hpp:114:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  114 |                 for (int j = 0; j < len2; ++j) {
      |                                 ~~^~~~~~
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘void kaori::fill_library(const std::vector<const char*>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, Trie&, bool, bool) [with Trie = kaori::SegmentedMismatches<2>]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:298:21:   required from ‘kaori::SegmentedBarcodeSearch<num_segments>::SegmentedBarcodeSearch(const kaori::BarcodePool&, std::array<int, V>, std::array<int, V>, bool, bool) [with long unsigned int num_segments = 2]’
../inst/include/kaori/handlers/DualBarcodes.hpp:126:18:   required from ‘kaori::DualBarcodes<max_size>::DualBarcodes(const char*, size_t, bool, const kaori::BarcodePool&, int, const char*, size_t, bool, const kaori::BarcodePool&, int, bool) [with long unsigned int max_size = 32; size_t = long unsigned int]’
count_dual_barcodes.cpp:31:28:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:116:46:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:40:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |             for (int j = 0; j < len; ++j) {
      |                             ~~^~~~~
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: variable ‘it’ set but not used [-Wunused-but-set-variable]
   45 |         auto it = exact.find(current);
      |              ^~
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘static bool kaori::HasMore<total, position>::check(const std::array<int, V>&, const std::array<int, V>&) [with long unsigned int total = 2; long unsigned int position = 0]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:378:59:   required from ‘static void kaori::SegmentedBarcodeSearch<num_segments>::Methods::update(kaori::SegmentedBarcodeSearch<num_segments>::State&, const SegmentedResult&, const std::array<int, V>&) [with long unsigned int num_segments = 2; kaori::SegmentedBarcodeSearch<num_segments>::SegmentedResult = kaori::SegmentedMismatches<2>::Result]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:70:28:   required from ‘void kaori::matcher_in_the_rye(const string&, const Cache&, const Trie&, Result&, const Mismatch&, const Mismatch&) [with Methods = kaori::SegmentedBarcodeSearch<2>::Methods; Cache = std::unordered_map<std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result, std::hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result> > >; Trie = kaori::SegmentedMismatches<2>; Result = kaori::SegmentedBarcodeSearch<2>::State; Mismatch = std::array<int, 2>; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:421:40:   required from ‘void kaori::SegmentedBarcodeSearch<num_segments>::search(const string&, kaori::SegmentedBarcodeSearch<num_segments>::State&, std::array<int, V>) const [with long unsigned int num_segments = 2; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/DualBarcodes.hpp:228:26:   required from ‘bool kaori::DualBarcodes<max_size>::process_first(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/handlers/DualBarcodes.hpp:311:21:   required from ‘bool kaori::DualBarcodes<max_size>::process(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/process_data.hpp:303:48:   required from ‘void kaori::process_paired_end_data(byteme::Reader*, byteme::Reader*, Handler&, int, int) [with Handler = kaori::DualBarcodes<32>]’
count_dual_barcodes.cpp:38:35:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:116:46:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:253:83: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  253 |         return (HasMore<total, position + 1>::check(left, right) | left[position] > right[position]);
      |                                                                    ~~~~~~~~~~~~~~~^~~~~~~~
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5,
                 from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../MismatchTrie.hpp: In instantiation of ‘kaori::SegmentedMismatches<num_segments>::Result kaori::SegmentedMismatches<num_segments>::search(const char*, size_t, size_t, kaori::SegmentedMismatches<num_segments>::Result, const std::array<int, V>&, int&) const [with long unsigned int num_segments = 2; size_t = long unsigned int]’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:389:22:   required from ‘kaori::SegmentedMismatches<num_segments>::Result kaori::SegmentedMismatches<num_segments>::search(const char*, const std::array<int, V>&) const [with long unsigned int num_segments = 2]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:73:38:   required from ‘void kaori::matcher_in_the_rye(const string&, const Cache&, const Trie&, Result&, const Mismatch&, const Mismatch&) [with Methods = kaori::SegmentedBarcodeSearch<2>::Methods; Cache = std::unordered_map<std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result, std::hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result> > >; Trie = kaori::SegmentedMismatches<2>; Result = kaori::SegmentedBarcodeSearch<2>::State; Mismatch = std::array<int, 2>; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:421:40:   required from ‘void kaori::SegmentedBarcodeSearch<num_segments>::search(const string&, kaori::SegmentedBarcodeSearch<num_segments>::State&, std::array<int, V>) const [with long unsigned int num_segments = 2; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/DualBarcodes.hpp:228:26:   required from ‘bool kaori::DualBarcodes<max_size>::process_first(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/handlers/DualBarcodes.hpp:311:21:   required from ‘bool kaori::DualBarcodes<max_size>::process(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/process_data.hpp:303:48:   required from ‘void kaori::process_paired_end_data(byteme::Reader*, byteme::Reader*, Handler&, int, int) [with Handler = kaori::DualBarcodes<32>]’
count_dual_barcodes.cpp:38:35:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:116:46:   required from here
../inst/include/kaori/handlers/../MismatchTrie.hpp:447:26: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const value_type’ {aka ‘const int’} [-Wsign-compare]
  447 |             if (next_pos == boundaries[segment_id]) {
      |                 ~~~~~~~~~^~~~~~~~~~~~~~
../inst/include/kaori/handlers/../MismatchTrie.hpp:465:22: warning: unused variable ‘found’ [-Wunused-variable]
  465 |                 bool found = false;
      |                      ^~~~~
In file included from ../inst/include/kaori/handlers/DualBarcodes.hpp:5,
                 from count_dual_barcodes.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘static bool kaori::HasMore<total, position>::check(const std::array<int, V>&, const std::array<int, V>&) [with long unsigned int total = 2; long unsigned int position = 1]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:253:52:   required from ‘static bool kaori::HasMore<total, position>::check(const std::array<int, V>&, const std::array<int, V>&) [with long unsigned int total = 2; long unsigned int position = 0]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:378:59:   required from ‘static void kaori::SegmentedBarcodeSearch<num_segments>::Methods::update(kaori::SegmentedBarcodeSearch<num_segments>::State&, const SegmentedResult&, const std::array<int, V>&) [with long unsigned int num_segments = 2; kaori::SegmentedBarcodeSearch<num_segments>::SegmentedResult = kaori::SegmentedMismatches<2>::Result]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:70:28:   required from ‘void kaori::matcher_in_the_rye(const string&, const Cache&, const Trie&, Result&, const Mismatch&, const Mismatch&) [with Methods = kaori::SegmentedBarcodeSearch<2>::Methods; Cache = std::unordered_map<std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result, std::hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, kaori::SegmentedMismatches<2>::Result> > >; Trie = kaori::SegmentedMismatches<2>; Result = kaori::SegmentedBarcodeSearch<2>::State; Mismatch = std::array<int, 2>; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/../BarcodeSearch.hpp:421:40:   required from ‘void kaori::SegmentedBarcodeSearch<num_segments>::search(const string&, kaori::SegmentedBarcodeSearch<num_segments>::State&, std::array<int, V>) const [with long unsigned int num_segments = 2; std::string = std::__cxx11::basic_string<char>]’
../inst/include/kaori/handlers/DualBarcodes.hpp:228:26:   required from ‘bool kaori::DualBarcodes<max_size>::process_first(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/handlers/DualBarcodes.hpp:311:21:   required from ‘bool kaori::DualBarcodes<max_size>::process(kaori::DualBarcodes<max_size>::State&, const std::pair<const char*, const char*>&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/process_data.hpp:303:48:   required from ‘void kaori::process_paired_end_data(byteme::Reader*, byteme::Reader*, Handler&, int, int) [with Handler = kaori::DualBarcodes<32>]’
count_dual_barcodes.cpp:38:35:   required from ‘Rcpp::List count_dual_barcodes_(Reader&, std::string, bool, const kaori::BarcodePool&, int, Reader&, std::string, bool, const kaori::BarcodePool&, int, bool, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_dual_barcodes.cpp:116:46:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:253:83: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  253 |         return (HasMore<total, position + 1>::check(left, right) | left[position] > right[position]);
      |                                                                    ~~~~~~~~~~~~~~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_random_barcodes.cpp -o count_random_barcodes.o
In file included from count_random_barcodes.cpp:3:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’:
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<32>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:45:35:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable ‘found’ [-Wunused-variable]
  111 |         bool found = false;
      |              ^~~~~
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 64]’:
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<64>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 64; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:47:35:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable ‘found’ [-Wunused-variable]
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 128]’:
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<128>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 128; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:49:36:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable ‘found’ [-Wunused-variable]
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 256]’:
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<256>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 256; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:51:36:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:111:14: warning: unused variable ‘found’ [-Wunused-variable]
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::reverse_match(const char*, size_t, kaori::RandomBarcodeSingleEnd<max_size>::State&) const [with long unsigned int max_size = 32; size_t = long unsigned int]’:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:123:21:   required from ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 32]’
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<32>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 32; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:45:35:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:98:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   98 |         for (int j = 0; j < len; ++j) {
      |                         ~~^~~~~
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::reverse_match(const char*, size_t, kaori::RandomBarcodeSingleEnd<max_size>::State&) const [with long unsigned int max_size = 64; size_t = long unsigned int]’:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:123:21:   required from ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 64]’
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<64>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 64; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:47:35:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:98:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::reverse_match(const char*, size_t, kaori::RandomBarcodeSingleEnd<max_size>::State&) const [with long unsigned int max_size = 128; size_t = long unsigned int]’:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:123:21:   required from ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 128]’
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<128>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 128; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:49:36:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:98:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp: In instantiation of ‘void kaori::RandomBarcodeSingleEnd<max_size>::reverse_match(const char*, size_t, kaori::RandomBarcodeSingleEnd<max_size>::State&) const [with long unsigned int max_size = 256; size_t = long unsigned int]’:
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:123:21:   required from ‘void kaori::RandomBarcodeSingleEnd<max_size>::process(kaori::RandomBarcodeSingleEnd<max_size>::State&, const std::pair<const char*, const char*>&) const [with long unsigned int max_size = 256]’
../inst/include/kaori/process_data.hpp:157:51:   required from ‘void kaori::process_single_end_data(byteme::Reader*, Handler&, int, int) [with Handler = kaori::RandomBarcodeSingleEnd<256>]’
count_random_barcodes.cpp:16:35:   required from ‘void count_random_barcodes_(Rcpp::List&, int&, Reader&, const string&, int, int, bool, int) [with long unsigned int N = 256; Reader = byteme::SomeFileReader; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’
count_random_barcodes.cpp:51:36:   required from here
../inst/include/kaori/handlers/RandomBarcodeSingleEnd.hpp:98:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_single_barcodes.cpp -o count_single_barcodes.o
In file included from ../inst/include/kaori/handlers/../BarcodeSearch.hpp:5,
                 from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6,
                 from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4,
                 from count_single_barcodes.cpp:3:
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘bool kaori::MismatchTrie::is_optimal(int, size_t, size_t&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:163:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |                 if (v < maxed) {
      |                     ~~^~~~~~~
../inst/include/kaori/handlers/../MismatchTrie.hpp: In member function ‘std::pair<int, int> kaori::AnyMismatches::search(const char*, size_t, int, int, int&) const’:
../inst/include/kaori/handlers/../MismatchTrie.hpp:279:22: warning: unused variable ‘found’ [-Wunused-variable]
  279 |                 bool found = false;
      |                      ^~~~~
In file included from ../inst/include/kaori/handlers/../SimpleSingleMatch.hpp:6,
                 from ../inst/include/kaori/handlers/SingleBarcodeSingleEnd.hpp:4,
                 from count_single_barcodes.cpp:3:
../inst/include/kaori/handlers/../BarcodeSearch.hpp: In instantiation of ‘void kaori::fill_library(const std::vector<const char*>&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, Trie&, bool, bool) [with Trie = kaori::AnyMismatches]’:
../inst/include/kaori/handlers/../BarcodeSearch.hpp:123:21:   required from here
../inst/include/kaori/handlers/../BarcodeSearch.hpp:40:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   40 |             for (int j = 0; j < len; ++j) {
      |                             ~~^~~~~
../inst/include/kaori/handlers/../BarcodeSearch.hpp:45:14: warning: variable ‘it’ set but not used [-Wunused-but-set-variable]
   45 |         auto it = exact.find(current);
      |              ^~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘kaori::BarcodePool format_pointers(const CharacterVector&)’:
utils.cpp:9:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
    9 |     for (size_t o = 0; o < options.size(); ++o) {
      |                        ~~^~~~~~~~~~~~~~~~
utils.cpp:13:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   13 |             if (size != LENGTH(current.get_sexp())) {
      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o screenCounter.so RcppExports.o count_combo_barcodes_paired.o count_combo_barcodes_single.o count_dual_barcodes.o count_random_barcodes.o count_single_barcodes.o utils.o -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-screenCounter/00new/screenCounter/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (screenCounter)