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### Running command:
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###   /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_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.35.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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, makeSNNGraph,
    makeKNNGraph, SummarizedExperiment-class, reducedDims,
    BiocSingularParam-class, BiocParallelParam-class, graph,
    cluster_walktrap
  clusterCells.Rd: SingleCellExperiment-class, clusterRows,
    SummarizedExperiment-class, BlusterParam-class
  combineBlocks.Rd: DataFrame-class, combineParallelPValues
  combineMarkers.Rd: DataFrame-class, BiocParallelParam-class,
    List-class, combineParallelPValues
  combinePValues.Rd: combineParallelPValues
  combineVar.Rd: DataFrame-class, combineParallelPValues
  computeSumFactors.Rd: pooledSizeFactors, computePooledFactors,
    sizeFactors
  convertTo.Rd: SingleCellExperiment-class
  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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in combinePValues(p1, p2, p3) : 'combinePValues' 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On Mac (1): 'test-cyclone.R:10:1'
  • monocle is a little broken because of clusterApply (1): 'test-convert.R:71:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-altrep.R:63:5'): buildSNNGraph with irlba runs properly on sparse matrices ──
  g1[] not identical to g2[].
  Attributes: < Component "i": Numeric: lengths (9718, 9712) differ >
  Attributes: < Component "p": Mean relative difference: 0.0007949093 >
  Attributes: < Component "x": Numeric: lengths (9718, 9712) differ >
  
  [ FAIL 1 | WARN 192 | SKIP 2 | PASS 4451 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/scran.Rcheck/00check.log’
for details.