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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1994/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 2.6.0  (landing page)
Aaron Lun
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: RELEASE_3_19
git_last_commit: 1999dd0
git_last_commit_date: 2024-04-30 11:16:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for SingleR on palomino3

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.

raw results


Summary

Package: SingleR
Version: 2.6.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SingleR_2.6.0.tar.gz
StartedAt: 2024-06-17 12:02:42 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 12:14:35 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 712.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SingleR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SingleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SingleR_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SingleR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SingleR/DESCRIPTION' ... OK
* this is package 'SingleR' version '2.6.0'
* package encoding: UTF-8
* 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 whether package 'SingleR' can be installed ... WARNING
Found the following significant warnings:
  F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.19-bioc/meat/SingleR.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII 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 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 cross-references ... 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/SingleR/libs/x64/SingleR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 10.45   0.19   10.64
plotDeltaDistribution  5.83   3.81    9.67
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/SingleR.Rcheck/00check.log'
for details.


Installation output

SingleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'SingleR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_classic_markers.cpp -o find_classic_markers.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from find_classic_markers.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
find_classic_markers.cpp: In function 'Rcpp::List find_classic_markers(int, int, Rcpp::List, Rcpp::List, int, int)':
find_classic_markers.cpp:9:14: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
    9 |     if (nref != labels.size()) {
      |         ~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
In file included from ../inst/include/singlepp/singlepp.hpp:14:
../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 long unsigned int'} [-Wsign-compare]
  198 |                 for (int g = 0; g < ngenes; ++g, ++sIt) {
      |                                 ~~^~~~~~~~
../inst/include/singlepp/ChooseClassicMarkers.hpp:225:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  225 |                     for (int g = 0; g < ngenes; ++g, ++lptr, ++rptr, ++sIt) {
      |                                     ~~^~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c grouped_medians.cpp -o grouped_medians.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from grouped_medians.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c integrate_build.cpp -o integrate_build.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_build.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c integrate_run.cpp -o integrate_run.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from integrate_run.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
integrate_run.cpp: In function 'SEXPREC* integrate_run(Rcpp::RObject, Rcpp::List, SEXP, double, int)':
integrate_run.cpp:13:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   13 |     for (size_t r = 0; r < results.size(); ++r) {
      |                        ~~^~~~~~~~~~~~~~~~
integrate_run.cpp:19:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   19 |     for (size_t r = 0; r < results.size(); ++r) {
      |                        ~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c prebuild.cpp -o prebuild.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from prebuild.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
prebuild.cpp: In function 'SEXPREC* prebuild(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::List, bool, int)':
prebuild.cpp:18:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   18 |     for (size_t m = 0; m < markers.size(); ++m) {
      |                        ~~^~~~~~~~~~~~~~~~
prebuild.cpp:23:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   23 |         for (size_t n = 0; n < curmarkers.size(); ++n) {
      |                            ~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include/  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c run.cpp -o run.o
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
                 from ../inst/include/singlepp/BasicBuilder.hpp:6,
                 from ../inst/include/singlepp/Classifier.hpp:8,
                 from ../inst/include/singlepp/singlepp.hpp:10,
                 from utils.h:11,
                 from run.cpp:1:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  163 |         #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:6:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   77 |                 #pragma omp parallel for
      | 
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:19:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   49 |     #pragma omp parallel for
      | 
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   92 |     #pragma omp parallel for
      | 
In file included from ../inst/include/singlepp/annotate_cells.hpp:11,
                 from ../inst/include/singlepp/BasicScorer.hpp:8,
                 from ../inst/include/singlepp/Classifier.hpp:9:
../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 long unsigned int'} and 'int' [-Wsign-compare]
   32 |         if (i != best_label && next_score < val) {
      |             ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function 'std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)':
../inst/include/singlepp/fine_tune.hpp:58:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |         if (i != best_index && next_score < val) {
      |             ~~^~~~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]':
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  116 |         for (INDEX_t i = 1; i < ncenters; ++i) {
      |                             ~~^~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
  133 |             for (INDEX_t c = 0; c < ncenters; ++c) {
      |                                 ~~^~~~~~~~~~
../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 singlepp::Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]':
../inst/include/singlepp/annotate_cells.hpp:101:36:   required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable 'NR' [-Wunused-variable]
  138 |                 size_t NR = curref.index->ndim();
      |                        ^~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of 'std::vector<Index_> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25:   required from 'CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable 'counter' set but not used [-Wunused-but-set-variable]
   73 |             INDEX_t counter = 0;
      |                     ^~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of 'void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26:   required from 'kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60:   required from 'knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]'
../inst/include/singlepp/BasicBuilder.hpp:107:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  344 |                     if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
      |                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:8,
                 from F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/knncolle.hpp:12:
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1188:30:   required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1410:24:   required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:969:46:   required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/knncolle/Annoy/Annoy.hpp:98:26:   required from 'knncolle::Annoy<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_INDEX_t, INTERNAL_DATA_t>::Annoy(INDEX_t, INDEX_t, const INPUT*, int, double) [with INPUT = double; DISTANCE = Annoy::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_INDEX_t = int; INTERNAL_DATA_t = float]'
../inst/include/singlepp/BasicBuilder.hpp:97:127:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                   |
      |                                   std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:64: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                              ~~^
      |                                                                |
      |                                                                long int
      |                                                              %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1309 |           children_indices[0].size(), children_indices[1].size());
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                               |
      |                                                               std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1308:88: note: format string is defined here
 1308 |         annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
      |                                                                                      ~~^
      |                                                                                        |
      |                                                                                        long int
      |                                                                                      %lld
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1069:8:   required from here
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                                                                      |
      |                                                                                      std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
   81 |   #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
      |                                                                  ^~~~~~~~~~~
F:/biocbuild/bbs-3.19-bioc/R/library/BiocNeighbors/include/annoy/annoylib.h:1118:48: note: format string is defined here
 1118 |     if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
      |                                              ~~^
      |                                                |
      |                                                long unsigned int
      |                                              %llu
g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-SingleR/00new/SingleR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleR)

Tests output

SingleR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 on-line 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 6 | SKIP 0 | PASS 303 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 303 ]
> 
> proc.time()
   user  system elapsed 
  73.75   20.45  202.17 

Example timings

SingleR.Rcheck/SingleR-Ex.timings

nameusersystemelapsed
SingleR1.580.121.70
aggregateReference2.180.172.34
classifySingleR0.170.000.17
combineCommonResults0.570.020.58
combineRecomputedResults0.510.050.56
getClassicMarkers0.220.000.22
getDeltaFromMedian0.230.000.25
matchReferences0.330.010.34
mockData0.010.000.01
plotDeltaDistribution5.833.819.67
plotScoreDistribution10.45 0.1910.64
plotScoreHeatmap2.950.203.20
pruneScores0.360.000.36
rebuildIndex0.080.000.10
trainSingleR1.260.371.66