##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scran.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scran_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/scran.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-22 01:50:20 UTC
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.41.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scran’ can be installed ... NOTE
Found the following notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/Users/biocbuild/bbs-3.24-bioc/meat/scran.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* checking installed package size ... OK
* 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 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:
  buildSNNGraph.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class, reducedDims, makeSNNGraph,
    makeKNNGraph, BiocSingularParam-class, BiocParallelParam-class,
    graph, cluster_walktrap
  clusterCells.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class, BlusterParam-class, clusterRows
  combineBlocks.Rd: DataFrame-class, combineParallelPValues
  combineMarkers.Rd: DataFrame-class, BiocParallelParam-class,
    List-class, combineParallelPValues
  combineVar.Rd: DataFrame-class, combineParallelPValues
  computeSumFactors.Rd: pooledSizeFactors, computePooledFactors,
    sizeFactors
  correlateGenes.Rd: DataFrame-class
  correlateNull.Rd: BiocParallelParam-class
  correlatePairs.Rd: SummarizedExperiment-class,
    BiocParallelParam-class, DataFrame-class, parallelStouffer
  cyclone.Rd: SummarizedExperiment-class, BiocParallelParam-class
  decideTestsPerLabel.Rd: decideTests, List-class
  defunct.Rd: bootstrapStability, pairwiseModularity, neighborPurity,
    clusterRows, NNGraphParam-class, TwoStepParam-class, pairwiseRand
  denoisePCA.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, DataFrame-class,
    BiocSingularParam-class, BiocParallelParam-class, reducedDimNames,
    assays, reducedDims, LowRankMatrix-class, runSVD
  findMarkers.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, colLabels, DataFrame-class,
    BiocParallelParam-class
  fitTrendPoisson.Rd: BiocParallelParam-class
  fitTrendVar.Rd: weightedLowess
  fixedPCA.Rd: SingleCellExperiment-class, reducedDimNames, assays,
    BiocSingularParam-class, BiocParallelParam-class, reducedDims,
    LowRankMatrix-class
  gene_selection.Rd: Rle-class, SingleCellExperiment-class,
    calculateAverage
  getClusteredPCs.Rd: clusterRows, BlusterParam-class, makeSNNGraph,
    cluster_walktrap, DataFrame-class, List-class, runPCA
  getMarkerEffects.Rd: DataFrame-class
  getTopHVGs.Rd: DataFrame-class, SummarizedExperiment-class
  getTopMarkers.Rd: DataFrame-class, List-class
  modelGeneCV2.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, combineParallelPValues,
    BiocParallelParam-class, librarySizeFactors, sizeFactors,
    DataFrame-class
  modelGeneCV2WithSpikes.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, altExp, combineParallelPValues,
    BiocParallelParam-class, DataFrame-class, librarySizeFactors,
    sizeFactors
  modelGeneVar.Rd: SummarizedExperiment-class, combineParallelPValues,
    BiocParallelParam-class, DataFrame-class
  modelGeneVarByPoisson.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, combineParallelPValues,
    BiocParallelParam-class, librarySizeFactors, sizeFactors,
    DataFrame-class
  modelGeneVarWithSpikes.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, altExp, combineParallelPValues,
    BiocParallelParam-class, DataFrame-class, librarySizeFactors,
    sizeFactors
  multiMarkerStats.Rd: DataFrame-class, List-class
  pairwiseBinom.Rd: colLabels, BiocParallelParam-class,
    DataFrame-class, binomTest
  pairwiseTTests.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, colLabels, BiocParallelParam-class,
    DataFrame-class, logNormCounts
  pairwiseWilcox.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, colLabels, BiocParallelParam-class,
    DataFrame-class
  pseudoBulkDGE.Rd: DataFrame-class, makeContrasts, glmTreat, treat,
    voomWithQualityWeights, sumCountsAcrossCells, voom, List-class,
    topTags, topTable, metadata, filterByExpr
  pseudoBulkSpecific.Rd: treat, List-class, DataFrame-class
  quickCluster.Rd: SummarizedExperiment-class, NNGraphParam,
    HclustParam, BiocSingularParam-class, BiocParallelParam-class,
    dgCMatrix-class, calculateAverage
  quickSubCluster.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BlusterParam-class, clusterRows,
    reducedDims, List-class, metadata
  sandbag.Rd: SummarizedExperiment-class
  scaledColRanks.Rd: BiocParallelParam-class
  scoreMarkers.Rd: SummarizedExperiment-class, BiocParallelParam-class,
    correctGroupSummary
  summaryMarkerStats.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, colLabels, DataFrame-class,
    sumCountsAcrossCells, BiocParallelParam-class, List-class
  testLinearModel.Rd: SummarizedExperiment-class,
    combineParallelPValues, BiocParallelParam-class, lmFit,
    fitLinearModel, DataFrame-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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
  Warning in .local(x, ...) : 'pairwiseBinom' is deprecated.
  Warning in .local(x, ...) : 'numDetectedAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in combineVar(results1, results2) : 'combineVar' is deprecated.
  Warning in computeMinRank(lfcs) : 'computeMinRank' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(means, vars) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fixedPCA(sce, subset.row = hvgs) : 'fixedPCA' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in getTopHVGs(stats) : 'getTopHVGs' is deprecated.
  Warning in getTopHVGs(sce) : 'getTopHVGs' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseBinom' is deprecated.
  Warning in .local(x, ...) : 'numDetectedAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'pairwiseBinom' is deprecated.
  Warning in .local(x, ...) : 'numDetectedAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
  Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in getTopHVGs(dec, prop = 0.2) : 'getTopHVGs' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in getTopHVGs(dec, prop = 0.2) : 'getTopHVGs' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
  Warning in getTopHVGs(dec, prop = 0.2) : 'getTopHVGs' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'buildSNNGraph' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'sumCountsAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'numDetectedAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'sumCountsAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'numDetectedAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/scran.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scran
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘scran’ ...
** this is package ‘scran’ version ‘1.41.1’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c choose_effect_size.cpp -o choose_effect_size.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c combine_rho.cpp -o combine_rho.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_blocked_stats.cpp -o compute_blocked_stats.o
In file included from compute_blocked_stats.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  218 |     virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  236 |     virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  254 |     virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  272 |     virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  287 |     sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  304 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  321 |     sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  338 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_residual_stats.cpp -o compute_residual_stats.o
In file included from compute_residual_stats.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  218 |     virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  236 |     virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  254 |     virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  272 |     virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  287 |     sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  304 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  321 |     sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  338 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_rho_null.cpp -o compute_rho_null.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cyclone_scores.cpp -o cyclone_scores.o
In file included from cyclone_scores.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  218 |     virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  236 |     virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  254 |     virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  272 |     virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  287 |     sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  304 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  321 |     sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  338 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c overlap_exprs.cpp -o overlap_exprs.o
In file included from overlap_exprs.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  218 |     virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  236 |     virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  254 |     virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  272 |     virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
      |                                              ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  287 |     sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  304 |     sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
      |                                   ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
  321 |     sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   52 |     virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
   81 |     virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
      |                           ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
  338 |     sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
      |                                      ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   66 |     virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
      |                        ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
   95 |     virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
      |                           ^
overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [-Wunused-variable]
  202 |     const size_t ngroups=groups.size();
      |                  ^~~~~~~
9 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scuttle/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rand_custom.cpp -o rand_custom.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-scran/00new/scran/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 (scran)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scran)
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

Loading required package: scuttle
> test_check("scran")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

[ FAIL 0 | WARN 2833 | SKIP 1 | PASS 4307 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Mac (1): 'test-cyclone.R:10:1'

[ FAIL 0 | WARN 2833 | SKIP 1 | PASS 4307 ]
> 
> proc.time()
   user  system elapsed 
101.889   2.162 127.781