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### Running command:
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### 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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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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
