############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SingleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘SingleR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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 std::vector&) const [with Matrix = tatami::Matrix; Label = int; singlepp::Markers = std::vector > >]’: find_classic_markers.cpp:39:44: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c prebuild.cpp -o prebuild.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c run.cpp -o run.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::fill_labels_in_use(const std::vector&, double, std::vector&)’: ../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 singlepp::replace_labels_in_use(const std::vector&, double, std::vector&)’: ../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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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 singlepp::FineTuner::run(singlepp::RankedVector&, const std::vector&, const Markers&, std::vector&, double, double) [with bool test = false; singlepp::RankedVector = std::vector, std::allocator > >; singlepp::Markers = std::vector > >]’: ../inst/include/singlepp/annotate_cells.hpp:101:86: 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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector kmeans::InitializeKmeansPP::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details kmeans::HartiganWong::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/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details kmeans::Kmeans::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize*, kmeans::Refine*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn::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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)