This page was generated on 20240328 11:37:06 0400 (Thu, 28 Mar 2024).
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### Running command:
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### /home/biocbuild/bbs3.19bioc/R/bin/R CMD INSTALL SingleR
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* installing to library ‘/home/biocbuild/bbs3.19bioc/R/sitelibrary’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.01ubuntu1~22.04) 11.4.0’
using C++17
g++ std=gnu++17 I"/home/biocbuild/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include' I/usr/local/include fpic g O2 Wall c RcppExports.cpp o RcppExports.o
g++ std=gnu++17 I"/home/biocbuild/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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:39:25: required from here
../inst/include/singlepp/ChooseClassicMarkers.hpp:198:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include' I/usr/local/include fpic g O2 Wall c prebuild.cpp o prebuild.o
In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/include" DNDEBUG I../inst/include/ I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/Rcpp/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/beachmat/include' I'/home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include' I/usr/local/include fpic g O2 Wall c run.cpp o run.o
In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
163  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
77  #pragma omp parallel for

In file included from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [Wunknownpragmas]
49  #pragma omp parallel for

/home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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:101:36: 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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs3.19bioc/R/sitelibrary/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/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/bbs3.19bioc/R/lib L/usr/local/lib o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o L/home/biocbuild/bbs3.19bioc/R/lib lR
installing to /home/biocbuild/bbs3.19bioc/R/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)