############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DropletUtils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘DropletUtils’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c downsample_run.cpp -o downsample_run.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c encode_sequences.cpp -o encode_sequences.o encode_sequences.cpp: In function 'Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)': encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 8 | for (size_t i=0; i::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 36 | return std::unique_ptr(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 38 | return std::unique_ptr(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 40 | return std::unique_ptr(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c get_cell_barcodes.cpp -o get_cell_barcodes.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c group_cells.cpp -o group_cells.o group_cells.cpp: In function 'Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)': group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 10 | if (N!=gems.size()) { | ~^~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c hashed_deltas.cpp -o hashed_deltas.o In file included from /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/beachmat.h:24, from hashed_deltas.cpp:2: /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 36 | return std::unique_ptr(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 38 | return std::unique_ptr(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 40 | return std::unique_ptr(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long unsigned int'} and 'R_xlen_t' {aka 'long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.4.1/site-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 unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::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 unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.4.1/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -c montecarlo_pval.cpp -o montecarlo_pval.o In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/size_type.hpp:20, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/range/size.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:29, from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/random.hpp:70, from montecarlo_pval.cpp:3: /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - montecarlo_pval.cpp: In function 'Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)': montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare] 99 | if (higher