##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘SingleR’ ...
** 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-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c find_classic_markers.cpp -o find_classic_markers.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
find_classic_markers.cpp: In function ‘Rcpp::List find_classic_markers(int, int, Rcpp::List, Rcpp::List, int, int)’:
find_classic_markers.cpp:9:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
    9 |     if (nref != labels.size()) {
      |         ~~~~~^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from ../inst/include/singlepp/singlepp.hpp:14,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
../inst/include/singlepp/ChooseClassicMarkers.hpp: In instantiation of ‘singlepp::Markers singlepp::ChooseClassicMarkers::run(const std::vector<const Matrix*>&, const std::vector<const Label*>&) const [with Matrix = tatami::Matrix<double, int>; Label = int; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
find_classic_markers.cpp:39:25:   required from here
../inst/include/singlepp/ChooseClassicMarkers.hpp:198:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  198 |                 for (int g = 0; g < ngenes; ++g, ++sIt) {
      |                                 ~~^~~~~~~~
../inst/include/singlepp/ChooseClassicMarkers.hpp:225:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  225 |                     for (int g = 0; g < ngenes; ++g, ++lptr, ++rptr, ++sIt) {
      |                                     ~~^~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c grouped_medians.cpp -o grouped_medians.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c integrate_build.cpp -o integrate_build.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c integrate_run.cpp -o integrate_run.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
integrate_run.cpp: In function ‘SEXPREC* integrate_run(Rcpp::RObject, Rcpp::List, SEXP, double, int)’:
integrate_run.cpp:13:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   13 |     for (size_t r = 0; r < results.size(); ++r) {
      |                        ~~^~~~~~~~~~~~~~~~
integrate_run.cpp:19:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   19 |     for (size_t r = 0; r < results.size(); ++r) {
      |                        ~~^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c prebuild.cpp -o prebuild.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
prebuild.cpp: In function ‘SEXPREC* prebuild(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::List, bool, int)’:
prebuild.cpp:18:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   18 |     for (size_t m = 0; m < markers.size(); ++m) {
      |                        ~~^~~~~~~~~~~~~~~~
prebuild.cpp:23:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   23 |         for (size_t n = 0; n < curmarkers.size(); ++n) {
      |                            ~~^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c run.cpp -o run.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from /home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
/home/biocbuild/bbs-3.19-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-SingleR/00new/SingleR/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 (SingleR)