Running ‘testthat.R’ [71s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  Loading required package: ggplot2
  Loading required package: cowplot
  
  Attaching package: 'cowplot'
  
  The following object is masked from 'package:ggplot2':
  
      ggsave
  
  Loading required package: Matrix
  > 
  > test_check("Seurat")
  Running CCA
  Merging objects
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
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    |======================================================================| 100%
  Rescaling group 1
  
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    |======================================================================| 100%
  Rescaling group 2
  
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    |======================================================================| 100%
  Aligning dimension 1
  Aligning dimension 2
  Aligning dimension 3
  Aligning dimension 4
  Aligning dimension 5
  Calculating for group1 
  	 Separating group1 cells
  	 Running Dimensional Reduction 
  Calculating for group2 
  	 Separating group2 cells
  	 Running Dimensional Reduction 
  [1] "Computing CC 1"
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
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    |======================================================================| 100%
  Computing nearest neighbor graph
  Computing SNN
  ── 1. Failure: Row merging done correctly (@test_data_manipulation.R#22)  ──────
  m3[1, 14] not equal to -0.17.
  1/1 mismatches
  [1] 0 - -0.17 == 0.17
  
  ── 2. Failure: Row merging done correctly (@test_data_manipulation.R#23)  ──────
  m3[3, 2] not equal to -1.4.
  1/1 mismatches
  [1] 0 - -1.4 == 1.4
  
  ── 3. Error: Row merging done correctly (@test_data_manipulation.R#24)  ────────
  index larger than maximal 13
  1: expect_equal(m3[14, 18], -0.43) at testthat/test_data_manipulation.R:24
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: m3[14, 18]
  5: m3[14, 18]
  6: callGeneric(x, i = i, j = j, drop = TRUE)
  7: eval(call, parent.frame())
  8: eval(call, parent.frame())
  9: x[i = i, j = j, drop = TRUE]
  10: x[i = i, j = j, drop = TRUE]
  11: subCsp_ij(x, i, j, drop = drop)
  12: intI(i, n = d[1], dn[[1]], give.dn = FALSE)
  13: stop(gettextf("index larger than maximal %d", n), domain = NA)
  
  ── 4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70)
  x[1] not equal to "GCAGCTCTGTTTCT".
  1/1 mismatches
  x[1]: "GGCCGATGTACTCT"
  y[1]: "GCAGCTCTGTTTCT"
  
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
    |                                                                            
    |                                                                      |   0%
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    |======================================================================| 100%
  
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    |======================================================================| 100%
  
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    |======================================================================| 100%
  
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    |======================================================================| 100%
  Calculating gene means
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variance to mean ratios
  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%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
  ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
  
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    |======================================================================| 100%
  Calculating gene means
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variance to mean ratios
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Running CCA
  Merging objects
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
    |                                                                            
    |                                                                      |   0%
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    |======================================================================| 100%
  Running CCA
  ── 5. Failure: CCA returns the expected cell.embeddings matrix values when run o
  abs(unname(c3@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
  1/1 mismatches
  [1] 0.534 - 0.311 == 0.224
  
  ── 6. Failure: CCA returns the expected cell.embeddings matrix values when run o
  abs(unname(c3@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
  1/1 mismatches
  [1] 0.404 - 0.606 == -0.202
  
  ── 7. Failure: CCA returns the expected cell.embeddings matrix values when run o
  abs(unname(c4@dr$cca@cell.embeddings[1, 1])) not equal to 0.3108733.
  1/1 mismatches
  [1] 0.534 - 0.311 == 0.224
  
  ── 8. Failure: CCA returns the expected cell.embeddings matrix values when run o
  abs(unname(c4@dr$cca@cell.embeddings[14, 3])) not equal to 0.6064297.
  1/1 mismatches
  [1] 0.404 - 0.606 == -0.202
  
  Computing nearest neighbor graph
  Computing SNN
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 8
  1. Failure: Row merging done correctly (@test_data_manipulation.R#22) 
  2. Failure: Row merging done correctly (@test_data_manipulation.R#23) 
  3. Error: Row merging done correctly (@test_data_manipulation.R#24) 
  4. Failure: max.cells.per.ident downsamples properly (@test_interaction.R#70) 
  5. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#228) 
  6. Failure: CCA returns the expected cell.embeddings matrix values when run on two objects (@test_seurat_object.R#229) 
  7. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#234) 
  8. Failure: CCA returns the expected cell.embeddings matrix values when run on single object (@test_seurat_object.R#235) 
  
  Error: testthat unit tests failed
  Execution halted