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This page was generated on 2026-03-14 11:33 -0400 (Sat, 14 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4837
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" 4050
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 632/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DropletUtils 1.31.0  (landing page)
Jonathan Griffiths
Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 2026)
git_url: https://git.bioconductor.org/packages/DropletUtils
git_branch: devel
git_last_commit: 92de364
git_last_commit_date: 2025-10-29 10:42:43 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    ERROR  
See other builds for DropletUtils in R Universe.

CHECK results for DropletUtils on nebbiolo1

To the developers/maintainers of the DropletUtils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DropletUtils.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DropletUtils
Version: 1.31.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DropletUtils_1.31.0.tar.gz
StartedAt: 2026-03-13 23:07:55 -0400 (Fri, 13 Mar 2026)
EndedAt: 2026-03-13 23:14:30 -0400 (Fri, 13 Mar 2026)
EllapsedTime: 395.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DropletUtils.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DropletUtils_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/DropletUtils.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-14 03:07:55 UTC
* checking for file ‘DropletUtils/DESCRIPTION’ ... OK
* this is package ‘DropletUtils’ version ‘1.31.0’
* 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 ... 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... INFO
  installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/DropletUtils/libs/DropletUtils.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/DropletUtils.Rcheck/00check.log’
for details.

Installation output

DropletUtils.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DropletUtils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DropletUtils’ ...
** this is package ‘DropletUtils’ version ‘1.31.0’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/scuttle/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/scuttle/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c downsample_run.cpp -o downsample_run.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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) {
      |                      ~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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) {
      |                      ~^~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from find_swapped.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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()) {
      |         ~^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from hashed_deltas.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/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>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/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]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.23-bioc/R/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]
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/scuttle/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c montecarlo_pval.cpp -o montecarlo_pval.o
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) {
      |                 ~~~~~~^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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) {
      |         ~~~~~~~~~~~~~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/scuttle/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c read_mm.cpp -o read_mm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/scuttle/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/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)

Tests output

DropletUtils.Rcheck/tests/testthat.Rout


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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 1017 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1017 ]
> 
> proc.time()
   user  system elapsed 
180.884   4.606 182.647

Example timings

DropletUtils.Rcheck/DropletUtils-Ex.timings

nameusersystemelapsed
ambientContribMaximum1.0830.0101.093
ambientContribNegative0.0240.0000.024
ambientContribSparse0.0320.0000.032
ambientProfileBimodal0.0050.0000.005
ambientProfileEmpty0.0880.0280.116
barcodeRanks0.2320.0170.249
chimericDrops0.1620.0130.176
cleanTagCounts0.0520.0020.054
defaultDrops0.0780.0110.089
downsampleReads0.1050.0260.131
emptyDrops1.3500.0061.356
emptyDropsCellRanger2.2260.2002.426
encodeSequences0.0010.0000.000
get10xMolInfoStats0.1080.0040.112
hashedDrops0.1270.0030.129
makeCountMatrix0.0050.0020.007
read10xCounts0.3340.0020.336
read10xMolInfo0.0880.0040.091
removeAmbience0.2640.0230.288
swappedDrops0.3730.0010.374
write10xCounts0.0900.0000.089