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

This page was generated on 20240328 11:37:06 0400 (Thu, 28 Mar 2024).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo1  Linux (Ubuntu 22.04.3 LTS)  x86_64  R Under development (unstable) (20240318 r86148)  "Unsuffered Consequences"  4708 
palomino3  Windows Server 2022 Datacenter  x64  R Under development (unstable) (20240316 r86144 ucrt)  "Unsuffered Consequences"  4446 
lconway  macOS 12.7.1 Monterey  x86_64  R Under development (unstable) (20240318 r86148)  "Unsuffered Consequences"  4471 
kunpeng2  Linux (openEuler 22.03 LTSSP1)  aarch64  R Under development (unstable) (20240319 r86153)  "Unsuffered Consequences"  4426 
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 1970/2270  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
SingleR 2.5.2 (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  
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. 
Package: SingleR 
Version: 2.5.2 
Command: /home/biocbuild/bbs3.19bioc/R/bin/R CMD check install=check:SingleR.installout.txt library=/home/biocbuild/bbs3.19bioc/R/sitelibrary timings SingleR_2.5.2.tar.gz 
StartedAt: 20240328 02:48:54 0400 (Thu, 28 Mar 2024) 
EndedAt: 20240328 02:54:59 0400 (Thu, 28 Mar 2024) 
EllapsedTime: 365.2 seconds 
RetCode: 0 
Status: WARNINGS 
CheckDir: SingleR.Rcheck 
Warnings: 1 
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.19bioc/R/bin/R CMD check install=check:SingleR.installout.txt library=/home/biocbuild/bbs3.19bioc/R/sitelibrary timings SingleR_2.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs3.19bioc/meat/SingleR.Rcheck’ * using R Under development (unstable) (20240318 r86148) * using platform: x86_64pclinuxgnu * R was compiled by gcc (Ubuntu 11.4.01ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.01ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF8 * checking for file ‘SingleR/DESCRIPTION’ ... OK * this is package ‘SingleR’ version ‘2.5.2’ * package encoding: UTF8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SingleR’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.01ubuntu1~22.04) 11.4.0’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 5.8Mb subdirectories of 1Mb or more: libs 5.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION metainformation ... OK * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for nonASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd crossreferences ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs3.19bioc/R/sitelibrary/SingleR/libs/SingleR.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotScoreDistribution 8.624 0.236 8.860 plotDeltaDistribution 5.297 0.151 5.449 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking rebuilding of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs3.19bioc/meat/SingleR.Rcheck/00check.log’ for details.
SingleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs3.19bioc/R/bin/R CMD INSTALL SingleR ### ############################################################################## ############################################################################## * 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)
SingleR.Rcheck/tests/testthat.Rout
R Under development (unstable) (20240318 r86148)  "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64pclinuxgnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(SingleR) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > test_check("SingleR") Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep [ FAIL 0  WARN 5  SKIP 0  PASS 303 ] [ FAIL 0  WARN 5  SKIP 0  PASS 303 ] > > proc.time() user system elapsed 68.904 2.656 118.871
SingleR.Rcheck/SingleREx.timings
name  user  system  elapsed  
SingleR  1.460  0.092  1.552  
aggregateReference  1.855  0.040  1.895  
classifySingleR  0.138  0.012  0.150  
combineCommonResults  0.384  0.028  0.412  
combineRecomputedResults  0.369  0.013  0.381  
getClassicMarkers  0.143  0.000  0.144  
getDeltaFromMedian  0.232  0.016  0.248  
matchReferences  0.394  0.000  0.394  
mockData  0.026  0.000  0.026  
plotDeltaDistribution  5.297  0.151  5.449  
plotScoreDistribution  8.624  0.236  8.860  
plotScoreHeatmap  2.381  0.040  2.420  
pruneScores  0.269  0.008  0.278  
rebuildIndex  0.075  0.000  0.076  
trainSingleR  1.202  0.032  1.235  