Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD check --install=check:scuttle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scuttle_1.20.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scuttle.Rcheck’* using R version 4.5.0 (2025-04-11)* using platform: aarch64-unknown-linux-gnu* R was compiled by    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0    GNU Fortran (GCC) 14.2.0* running under: openEuler 24.03 (LTS)* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘scuttle/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘scuttle’ version ‘1.20.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘scuttle’ can be installed ... OK* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’* checking C++ specification ... NOTE  Specified C++11: please drop specification unless essential* checking installed package size ... INFO  installed size is  8.8Mb  sub-directories of 1Mb or more:    libs   8.3Mb* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  addPerCellQCMetrics.Rd: SummarizedExperiment-class, rowData, colData  aggregateAcrossCells.Rd: colData, SingleCellExperiment-class,    SummarizedExperiment-class, reducedDims, altExps, DataFrame-class,    applySCE  aggregateAcrossFeatures.Rd: SummarizedExperiment-class  calculateAverage.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, BiocParallelParam-class,    DelayedMatrix-class, sizeFactors  calculateCPM.Rd: SummarizedExperiment-class,    SingleCellExperiment-class  calculateFPKM.Rd: SummarizedExperiment-class,    SingleCellExperiment-class  calculateTPM.Rd: SummarizedExperiment-class,    SingleCellExperiment-class  computePooledFactors.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, sizeFactors  computeSpikeFactors.Rd: SingleCellExperiment-class, altExps, altExp,    sizeFactors  downsampleBatches.Rd: SummarizedExperiment-class, List-class  downsampleMatrix.Rd: RealizationSink-class, dgCMatrix-class,    DelayedMatrix-class  fitLinearModel.Rd: BiocParallelParam-class  geometricSizeFactors.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, BiocParallelParam-class,    DelayedArray-class, sizeFactors  librarySizeFactors.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, BiocParallelParam-class,    DelayedArray-class, sizeFactors  logNormCounts.Rd: SingleCellExperiment-class,    SummarizedExperiment-class, BiocParallelParam-class, applySCE,    sizeFactors  makePerCellDF.Rd: SingleCellExperiment-class, altExp, rowData  makePerFeatureDF.Rd: SingleCellExperiment-class  medianSizeFactors.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, sizeFactors  mockSCE.Rd: SingleCellExperiment-class, colData, altExps,    SingleCellExperiment  normalizeCounts.Rd: SingleCellExperiment-class,    SummarizedExperiment-class, DelayedMatrix-class,    BiocParallelParam-class, sizeFactors  numDetectedAcrossCells.Rd: SummarizedExperiment-class,    DataFrame-class, SingleCellExperiment-class, colData,    BiocParallelParam-class  numDetectedAcrossFeatures.Rd: SummarizedExperiment-class,    BiocParallelParam-class  perCellQCFilters.Rd: DataFrame-class  perCellQCMetrics.Rd: SingleCellExperiment-class,    SummarizedExperiment-class, BiocParallelParam-class,    DataFrame-class  perFeatureQCMetrics.Rd: SummarizedExperiment-class,    SingleCellExperiment-class, BiocParallelParam-class,    DataFrame-class  quickPerCellQC.Rd: DataFrame-class, SummarizedExperiment-class,    colData  readSparseCounts.Rd: readMM  sumCountsAcrossCells.Rd: SummarizedExperiment-class, DataFrame-class,    SingleCellExperiment-class, colData, BiocParallelParam-class,    colsum  sumCountsAcrossFeatures.Rd: SummarizedExperiment-class,    BiocParallelParam-class  summarizeAssayByGroup.Rd: SummarizedExperiment-class,    DataFrame-class, colData, BiocParallelParam-class  uniquifyDataFrameByGroup.Rd: DataFrame-class, colData, DFrame-classPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking line endings in C/C++/Fortran sources/headers ... OK* checking line endings in Makefiles ... OK* checking compilation flags in Makevars ... OK* checking for GNU extensions in Makefiles ... OK* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK* checking use of PKG_*FLAGS in Makefiles ... OK* checking compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                      user system elapsedcomputePooledFactors 7.369  0.095   7.485* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘testthat.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 3 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/scuttle.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/R/R/bin/R CMD INSTALL scuttle###############################################################################################################################################################* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’* installing *source* package ‘scuttle’ ...** this is package ‘scuttle’ version ‘1.20.0’** using staged installation** libsusing C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’using C++11/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c cumulative_prop.cpp -o cumulative_prop.oIn file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24,                 from cumulative_prop.cpp:2:/home/biocbuild/R/R-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   36 |             return std::unique_ptr<M>(new integer_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   38 |             return std::unique_ptr<M>(new double_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   40 |             return std::unique_ptr<M>(new logical_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c downsample_counts.cpp -o downsample_counts.oIn file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24,                 from downsample_counts.cpp:2:/home/biocbuild/R/R-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   36 |             return std::unique_ptr<M>(new integer_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   38 |             return std::unique_ptr<M>(new double_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   40 |             return std::unique_ptr<M>(new logical_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c fit_linear_model.cpp -o fit_linear_model.oIn file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24,                 from fit_linear_model.cpp:2:/home/biocbuild/R/R-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   36 |             return std::unique_ptr<M>(new integer_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   38 |             return std::unique_ptr<M>(new double_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   40 |             return std::unique_ptr<M>(new logical_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c pool_size_factors.cpp -o pool_size_factors.opool_size_factors.cpp: In function ‘Rcpp::List pool_size_factors(Rcpp::RObject, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector)’:pool_size_factors.cpp:56:15: 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]   56 |     if (ngenes!=pseudo_cell.size()) {      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~pool_size_factors.cpp:61:22: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]   61 |     if (order.size() < ncells*2-1)  {      |         ~~~~~~~~~~~~~^~~~~~~~~~~~pool_size_factors.cpp:170:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]  170 |                     for (auto i=0; i<n; ++i, ++val, ++rows) {      |                                    ~^~In file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24,                 from pool_size_factors.cpp:2:/home/biocbuild/R/R-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   36 |             return std::unique_ptr<M>(new integer_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   38 |             return std::unique_ptr<M>(new double_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   40 |             return std::unique_ptr<M>(new logical_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c sparse_summarize.cpp -o sparse_summarize.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c sum_counts.cpp -o sum_counts.oIn file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11,                 from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24,                 from sum_counts.cpp:2:/home/biocbuild/R/R-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   36 |             return std::unique_ptr<M>(new integer_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   38 |             return std::unique_ptr<M>(new double_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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>]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   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>]’  561 |     lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) {      |                                              ^~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’   40 |             return std::unique_ptr<M>(new logical_SparseArraySeed(block));      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here   65 |         auto ptr = read_lin_sparse_block_raw<lin_matrix>(block);      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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 unsigned int]’  596 |         return reader.template get_row<const int*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here  595 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) {      |                                   ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/home/biocbuild/R/R-4.5.0/site-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 unsigned int; size_t = long unsigned int]’:/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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 unsigned int]’  650 |         return core.template get_row<OUT>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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 unsigned int]’  602 |         return reader.template get_row<const double*>(r, work_x, work_i, first, last);      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here  601 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) {      |                                      ^~~~~~~/home/biocbuild/R/R-4.5.0/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<size_t>(i[idex]) == r) {      |                 ~~~~~^~~~~~~/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sparse_summarize.o sum_counts.o utils.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lRinstalling to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-scuttle/00new/scuttle/libs** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (scuttle)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-unknown-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(scuttle)Loading required package: SingleCellExperimentLoading required package: SummarizedExperimentLoading required package: MatrixGenericsLoading required package: matrixStatsAttaching package: 'MatrixGenerics'The following objects are masked from 'package:matrixStats':    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,    colWeightedMeans, colWeightedMedians, colWeightedSds,    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,    rowWeightedSds, rowWeightedVarsLoading required package: GenomicRangesLoading required package: stats4Loading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minLoading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SeqinfoLoading required package: BiobaseWelcome to Bioconductor    Vignettes contain introductory material; view with    'browseVignettes()'. To cite Bioconductor, see    'citation("Biobase")', and for packages 'citation("pkgname")'.Attaching package: 'Biobase'The following object is masked from 'package:MatrixGenerics':    rowMediansThe following objects are masked from 'package:matrixStats':    anyMissing, rowMedians> test_check("scuttle")Loading required package: MatrixAttaching package: 'Matrix'The following object is masked from 'package:S4Vectors':    expandLoading required package: S4ArraysLoading required package: abindAttaching package: 'S4Arrays'The following object is masked from 'package:abind':    abindThe following object is masked from 'package:base':    rowsumLoading required package: SparseArrayAttaching package: 'DelayedArray'The following objects are masked from 'package:base':    apply, scale, sweep[ FAIL 0 | WARN 13 | SKIP 0 | PASS 1707 ][ FAIL 0 | WARN 13 | SKIP 0 | PASS 1707 ]> > proc.time()   user  system elapsed 135.046   8.483 170.518