Back to Multiple platform build/check report for BioC 3.19: simplified long 

This page was generated on 20240509 11:41:28 0400 (Thu, 09 May 2024).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo1  Linux (Ubuntu 22.04.3 LTS)  x86_64  4.4.0 (20240424)  "Puppy Cup"  4748 
palomino3  Windows Server 2022 Datacenter  x64  4.4.0 (20240424 ucrt)  "Puppy Cup"  4484 
lconway  macOS 12.7.1 Monterey  x86_64  4.4.0 (20240424)  "Puppy Cup"  4514 
kunpeng2  Linux (openEuler 22.03 LTSSP1)  aarch64  4.4.0 beta (20240415 r86425)  "Puppy Cup"  4480 
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname p', except on Windows and Mac OS X 
Package 1994/2300  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
SingleR 2.6.0 (landing page) Aaron Lun
 nebbiolo1  Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  OK  WARNINGS  
palomino3  Windows Server 2022 Datacenter / x64  OK  OK  WARNINGS  OK  
lconway  macOS 12.7.1 Monterey / x86_64  OK  OK  WARNINGS  OK  
kunpeng2  Linux (openEuler 22.03 LTSSP1) / aarch64  OK  OK  WARNINGS  
kjohnson3  macOS 13.6.5 Ventura / arm64  see weekly results here  
To the developers/maintainers of the SingleR package:  Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to reflect on this report. See Troubleshooting Build Report for more information.  Use the following Renviron settings to reproduce errors and warnings.  If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.  See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. 
Package: SingleR 
Version: 2.6.0 
Command: /home/biocbuild/R/Rbeta20240415_r86425/bin/R CMD INSTALL SingleR 
StartedAt: 20240508 20:58:12 0000 (Wed, 08 May 2024) 
EndedAt: 20240508 21:00:27 0000 (Wed, 08 May 2024) 
EllapsedTime: 135.0 seconds 
RetCode: 0 
Status: OK 
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/Rbeta20240415_r86425/bin/R CMD INSTALL SingleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary’ * 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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include' I/usr/local/include fPIC g O2 Wall c RcppExports.cpp o RcppExports.o g++ std=gnu++17 I"/home/biocbuild/R/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 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’} [Wsigncompare] 9  if (nref != labels.size()) {  ~~~~~^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 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:39:44: 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’} [Wsigncompare] 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’} [Wsigncompare] 225  for (int g = 0; g < ngenes; ++g, ++lptr, ++rptr, ++sIt) {  ~~^~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 58  if (i != best_index && next_score < val) {  ~~^~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 138  size_t NR = curref.index>ndim();  ^~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 58  if (i != best_index && next_score < val) {  ~~^~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 138  size_t NR = curref.index>ndim();  ^~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 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’} [Wsigncompare] 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’} [Wsigncompare] 19  for (size_t r = 0; r < results.size(); ++r) {  ~~^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 138  size_t NR = curref.index>ndim();  ^~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include' I/usr/local/include fPIC g O2 Wall c prebuild.cpp o prebuild.o In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 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’} [Wsigncompare] 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’} [Wsigncompare] 23  for (size_t n = 0; n < curmarkers.size(); ++n) {  ~~^~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 138  size_t NR = curref.index>ndim();  ^~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/include" DNDEBUG I../inst/include/ I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/Rcpp/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/beachmat/include' I'/home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include' I/usr/local/include fPIC g O2 Wall c run.cpp o run.o In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 163  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 77  #pragma omp parallel for  In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 49  #pragma omp parallel for  /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas] 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’ [Wsigncompare] 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’ [Wsigncompare] 58  if (i != best_index && next_score < val) {  ~~^~~~~~~~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 116  for (INDEX_t i = 1; i < ncenters; ++i) {  ~~^~~~~~~~~~ /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [Wsigncompare] 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:101:86: required from here ../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [Wunusedvariable] 138  size_t NR = curref.index>ndim();  ^~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [Wunusedbutsetvariable] 73  INDEX_t counter = 0;  ^~~~~~~ In file included from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7, from /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/R/Rbeta20240415_r86425/sitelibrary/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/Rbeta20240415_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/Rbeta20240415_r86425/lib lR installing to /home/biocbuild/R/Rbeta20240415_r86425/sitelibrary/00LOCKSingleR/00new/SingleR/libs ** R ** inst ** bytecompile 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)