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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:screenCounter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings screenCounter_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/screenCounter.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘screenCounter/DESCRIPTION’ ... OK
* this is package ‘screenCounter’ version ‘1.0.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘screenCounter’ can be installed ... WARNING
Found the following significant warnings:
  ../inst/include/kaori/handlers/../BarcodeSearch.hpp:253:83: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/screenCounter.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘counting.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/screenCounter.Rcheck/00check.log’
for details.

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### Running command:
###
###   /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)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(screenCounter)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("screenCounter")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 264 ]
> 
> proc.time()
   user  system elapsed 
 14.940   0.553  15.731