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INSTALL report for SingleR on tokay1

This page was generated on 2021-05-06 12:33:39 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SingleR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1726/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.4.1  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SingleR
Branch: RELEASE_3_12
Last Commit: 5b9704c
Last Changed Date: 2021-02-02 03:46:49 -0400 (Tue, 02 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SingleR
Version: 1.4.1
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SingleR_1.4.1.tar.gz && rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleR.buildbin-libdir SingleR_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SingleR_1.4.1.zip && rm SingleR_1.4.1.tar.gz SingleR_1.4.1.zip
StartedAt: 2021-05-05 17:57:41 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 17:59:22 -0400 (Wed, 05 May 2021)
EllapsedTime: 101.4 seconds
RetCode: 0
Status:   OK   

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SingleR_1.4.1.tar.gz && rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SingleR.buildbin-libdir SingleR_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SingleR_1.4.1.zip && rm SingleR_1.4.1.tar.gz SingleR_1.4.1.zip
###
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100 98329  100 98329    0     0  1863k      0 --:--:-- --:--:-- --:--:-- 1920k

install for i386

* installing *source* package 'SingleR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
             for (size_t j=0; j<internals.size(); ++j) {
                              ~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(Rcpp::RObject, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:41:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]':
fine_tune_de.cpp:54:95:   required from here
fine_tuner.h:39:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_de.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]':
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:39:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_sd.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c recompute_scores.cpp -o recompute_scores.o
recompute_scores.cpp: In function 'Rcpp::RObject recompute_scores(Rcpp::List, Rcpp::RObject, Rcpp::IntegerMatrix, Rcpp::List, Rcpp::List, double)':
recompute_scores.cpp:38:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (Labels.nrow()!=nref) {
         ~~~~~~~~~~~~~^~~~~~
recompute_scores.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (Labels.ncol()!=ncells) {
         ~~~~~~~~~~~~~^~~~~~~~
recompute_scores.cpp:45:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'int'} and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
     if (Genes.size()!=nref) {
         ~~~~~~~~~~~~^~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from recompute_scores.cpp:2:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = unsigned int; size_t = unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/SingleR.buildbin-libdir/00LOCK-SingleR/00new/SingleR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SingleR'
    finding HTML links ... done
    SingleR                                 html  
    finding level-2 HTML links ... done

    aggregateReference                      html  
    classifySingleR                         html  
    combineCommonResults                    html  
    combineRecomputedResults                html  
    datasets                                html  
    getClassicMarkers                       html  
    getDeltaFromMedian                      html  
    matchReferences                         html  
    mockData                                html  
    plotDeltaDistribution                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkbPHPh/R.INSTALL14d4297711a3/SingleR/man/plotDeltaDistribution.Rd:47: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
    plotScoreDistribution                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkbPHPh/R.INSTALL14d4297711a3/SingleR/man/plotScoreDistribution.Rd:58: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
    plotScoreHeatmap                        html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkbPHPh/R.INSTALL14d4297711a3/SingleR/man/plotScoreHeatmap.Rd:70: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpkbPHPh/R.INSTALL14d4297711a3/SingleR/man/plotScoreHeatmap.Rd:222: file link 'grid.arrange' in package 'gridExtra' does not exist and so has been treated as a topic
    pruneScores                             html  
    trainSingleR                            html  
** 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

install for x64

* installing *source* package 'SingleR' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor 'de_markers::de_markers(Rcpp::List)':
fine_tune_de.cpp:6:27: 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]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: 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]
             for (size_t j=0; j<internals.size(); ++j) {
                              ~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function 'Rcpp::List fine_tune_label_de(Rcpp::RObject, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)':
fine_tune_de.cpp:41:23: 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]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]':
fine_tune_de.cpp:54:95:   required from here
fine_tuner.h:39:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_de.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function 'Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)':
fine_tune_sd.cpp:46:23: 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]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:
fine_tuner.h: In instantiation of 'tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]':
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:39:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_sd.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c recompute_scores.cpp -o recompute_scores.o
recompute_scores.cpp: In function 'Rcpp::RObject recompute_scores(Rcpp::List, Rcpp::RObject, Rcpp::IntegerMatrix, Rcpp::List, Rcpp::List, double)':
recompute_scores.cpp:38:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (Labels.nrow()!=nref) {
         ~~~~~~~~~~~~~^~~~~~
recompute_scores.cpp:41:22: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (Labels.ncol()!=ncells) {
         ~~~~~~~~~~~~~^~~~~~~~
recompute_scores.cpp:45:21: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
     if (Genes.size()!=nref) {
         ~~~~~~~~~~~~^~~~~~
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from recompute_scores.cpp:2:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from 'beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from 'std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
         if (nnz != x.size()) {
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from 'beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]':
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from 'beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from 'beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]'
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
C:/Users/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare]
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o SingleR.dll tmp.def RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/SingleR.buildbin-libdir/SingleR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SingleR' as SingleR_1.4.1.zip
* DONE (SingleR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SingleR' successfully unpacked and MD5 sums checked