Running ‘testthat.R’ [81s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  Loading required package: SeuratObject
  Loading required package: sp
  
  Attaching package: 'SeuratObject'
  
  The following objects are masked from 'package:base':
  
      intersect, t
  
  > #
  > # # Run tests for 'v3'
  > # message('Run tests for v3 assay')
  > # options(Seurat.object.assay.version = 'v3')
  > # test_check("Seurat")
  > 
  > # Run tests for 'v5'
  > message('Run tests for v5 assay')
  Run tests for v5 assay
  > options(Seurat.object.assay.version = 'v5')
  > test_check("Seurat")
  
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  Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
  
  Number of nodes: 80
  Number of edges: 525
  
  Running Louvain algorithm...
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Maximum modularity in 10 random starts: 0.8255
  Number of communities: 6
  Elapsed time: 0 seconds
  Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
  
  Number of nodes: 80
  Number of edges: 525
  
  Running Louvain algorithm...
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Maximum modularity in 10 random starts: 0.8255
  Number of communities: 6
  Elapsed time: 0 seconds
  Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
  
  Number of nodes: 80
  Number of edges: 525
  
  Running Louvain algorithm with multilevel refinement...
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Maximum modularity in 10 random starts: 0.8255
  Number of communities: 6
  Elapsed time: 0 seconds
  Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
  
  Number of nodes: 80
  Number of edges: 525
  
  Running smart local moving algorithm...
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Maximum modularity in 10 random starts: 0.8255
  Number of communities: 6
  Elapsed time: 0 seconds
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
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  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
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    |======================================================================| 100%
  Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
  
  Number of nodes: 80
  Number of edges: 2045
  
  Running Louvain algorithm...
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Maximum modularity in 10 random starts: -0.0613
  Number of communities: 64
  Elapsed time: 0 seconds
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
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  [ FAIL 6 | WARN 1 | SKIP 29 | PASS 708 ]
  
  ══ Skipped tests (29) ══════════════════════════════════════════════════════════
  • On CRAN (29): 'test_differential_expression.R:307:3',
    'test_differential_expression.R:349:3',
    'test_differential_expression.R:455:3', 'test_dimensional_reduction.R:55:3',
    'test_integratedata.R:111:3', 'test_integration.R:74:3',
    'test_integration.R:105:3', 'test_integration.R:136:3',
    'test_integration.R:170:3', 'test_integration.R:202:3',
    'test_integration.R:234:3', 'test_integration.R:264:3',
    'test_integration.R:306:3', 'test_integration.R:335:3',
    'test_integration.R:365:3', 'test_integration5.R:38:3',
    'test_integration5.R:331:3', 'test_objects.R:6:3',
    'test_preprocessing.R:140:3', 'test_preprocessing.R:158:3',
    'test_preprocessing.R:433:3', 'test_preprocessing.R:554:3',
    'test_read_mtx.R:4:3', 'test_read_mtx.R:18:3', 'test_transferdata.R:65:3',
    'test_transferdata.R:88:3', 'test_transferdata.R:100:3',
    'test_transferdata.R:112:3', 'test_transferdata.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_sketching.R:41:3'): SketchData defaults work ───────────────────
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:41:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  ── Error ('test_sketching.R:92:3'): SketchData with multiple layers works ──────
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:92:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  ── Error ('test_sketching.R:124:3'): SketchData with a different number of cells per layer works ──
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:124:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  ── Error ('test_sketching.R:184:3'): SketchData with specified features works ──
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:184:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  ── Error ('test_sketching.R:212:3'): SketchData with specified features and multiple layers works ──
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:212:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  ── Error ('test_sketching.R:247:3'): SketchData when setting your own variable features and specifying features works ──
  Error in `irlba(A = object, nv = 50, nu = 0, verbose = FALSE)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(...) at test_sketching.R:247:3
    2. │ └─base::withCallingHandlers(...)
    3. └─Seurat::SketchData(...)
    4.   ├─Seurat::LeverageScore(...)
    5.   └─Seurat:::LeverageScore.Seurat(...)
    6.     ├─Seurat::LeverageScore(...)
    7.     └─Seurat:::LeverageScore.StdAssay(...)
    8.       ├─Seurat::LeverageScore(...)
    9.       └─Seurat:::LeverageScore.default(...)
   10.         └─irlba::irlba(A = object, nv = 50, nu = 0, verbose = FALSE)
  
  [ FAIL 6 | WARN 1 | SKIP 29 | PASS 708 ]
  Error: Test failures
  Execution halted