##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DropletUtils_1.29.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DropletUtils.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 ‘DropletUtils/DESCRIPTION’ ... OK
* this is package ‘DropletUtils’ version ‘1.29.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DropletUtils’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ambientContribMaximum.Rd: SummarizedExperiment-class,
    BiocParallelParam-class
  ambientContribNegative.Rd: SummarizedExperiment-class
  ambientContribSparse.Rd: SummarizedExperiment-class,
    BiocParallelParam-class
  ambientProfileBimodal.Rd: SummarizedExperiment-class,
    medianSizeFactors
  ambientProfileEmpty.Rd: dgTMatrix-class, dgCMatrix-class,
    SummarizedExperiment-class, BiocParallelParam-class
  barcodeRanks.Rd: SummarizedExperiment-class, BiocParallelParam-class,
    DataFrame-class
  chimericDrops.Rd: DataFrame-class
  cleanTagCounts.Rd: SummarizedExperiment-class, isOutlier,
    DataFrame-class
  defaultDrops.Rd: SummarizedExperiment-class
  emptyDrops.Rd: dgTMatrix-class, dgCMatrix-class,
    SummarizedExperiment-class, BiocParallelParam-class,
    goodTuringProportions
  emptyDropsCellRanger.Rd: SummarizedExperiment-class,
    BiocParallelParam-class, DataFrame-class
  hashedDrops.Rd: SummarizedExperiment-class, DataFrame-class, metadata
  read10xCounts.Rd: SingleCellExperiment-class, DelayedArray-class,
    BiocParallelParam-class, TENxMatrix-class, splitAltExps
  read10xMolInfo.Rd: DataFrame-class
  removeAmbience.Rd: SummarizedExperiment-class, DataFrame-class,
    sumCountsAcrossCells, RealizationSink-class,
    BiocParallelParam-class
  swappedDrops.Rd: HDF5Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package 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 ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.5.0/site-library/DropletUtils/libs/DropletUtils.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘DropletUtils’ ...
** this is package ‘DropletUtils’ version ‘1.29.4’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/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++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c downsample_run.cpp -o downsample_run.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function ‘Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)’:
encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
    8 |     for (size_t i=0; i<output.size(); ++i) {
      |                      ~^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c find_chimeric.cpp -o find_chimeric.o
find_chimeric.cpp: In function ‘Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)’:
find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   28 |     for (size_t i=0; i<nmolecules; ++i, ++uIt) {
      |                      ~^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c find_swapped.cpp -o find_swapped.o
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 find_swapped.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<_Tp> 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<_Tp> 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<_Tp> 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++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c get_cell_barcodes.cpp -o get_cell_barcodes.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function ‘Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)’:
group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   10 |     if (N!=gems.size()) {
      |         ~^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c hashed_deltas.cpp -o hashed_deltas.o
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 hashed_deltas.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<_Tp> 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<_Tp> 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<_Tp> 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++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:30,
                 from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/random.hpp:71,
                 from montecarlo_pval.cpp:3:
/home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
montecarlo_pval.cpp: In function ‘Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)’:
montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   99 |             if (higher<curlen) {
      |                 ~~~~~~^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c rand_custom.cpp -o rand_custom.o
rand_custom.cpp: In function ‘void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)’:
rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    8 |     if (seeds.size()!=N) {
      |         ~~~~~~~~~~~~^~~
rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   14 |     if (streams.size()!=N) {
      |         ~~~~~~~~~~~~~~^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c read_mm.cpp -o read_mm.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -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'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/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++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o DropletUtils.so RcppExports.o downsample_run.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o read_mm.o utils.o /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-DropletUtils/00new/DropletUtils/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 (DropletUtils)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(DropletUtils)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, 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.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("DropletUtils")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1021 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1021 ]
> 
> proc.time()
   user  system elapsed 
232.863   6.531 237.068