Running ‘testthat.R’ [24s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(countland)
  > 
  > test_check("countland")
  countland object
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  Performing spectral clustering on dot products...
      done.
  countland object
  after removing empty cells and genes
  the count matrix has 3 genes (rows)
      and 3 cells (columns)
  the fraction of entries that are nonzero is 0.6667
  Calculating dot products between rows...
      done.
  Performing spectral embedding on dot products...
      done.
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1001 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.407
  countland object
  after removing empty cells and genes
  the count matrix has 7 genes (rows)
      and 10 cells (columns)
  the fraction of entries that are nonzero is 0.4429
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  subsampling 641 genes to a max total counts of 10
  'as(<dgCMatrix>, "dgTMatrix")' is deprecated.
  Use 'as(., "TsparseMatrix")' instead.
  See help("Deprecated") and help("Matrix-deprecated").
  subsampling all cells to a standard sequencing depth of 10
  subsampling 641 genes to a max total counts of 10
  subsampling all cells to a standard sequencing depth of 10
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  after subsetting and removing empty cells and genes,
  after removing empty cells and genes
  new number of genes: 25
  new number of cells: 100
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  after subsetting and removing empty cells and genes,
  after removing empty cells and genes
  new number of genes: 805
  new number of cells: 25
  countland object
  after removing empty cells and genes
  the count matrix has 1000 genes (rows)
      and 100 cells (columns)
  the fraction of entries that are nonzero is 0.4074
  new number of genes: 1000
  new number of cells: 100
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-countland_embed.R:20:3'): function ScikitManifoldSpectralEmbedding, returns correct values ──
  embed[[2]][1, 1] (`actual`) not equal to 0.02515773 (`expected`).
  
    `actual`: 0.023
  `expected`: 0.025
  ── Failure ('test-countland_embed.R:21:3'): function ScikitManifoldSpectralEmbedding, returns correct values ──
  embed[[2]][1, 2] (`actual`) not equal to 0.04247028 (`expected`).
  
    `actual`: -0.03
  `expected`:  0.04
  ── Failure ('test-countland_embed.R:22:3'): function ScikitManifoldSpectralEmbedding, returns correct values ──
  embed[[2]][3, 2] (`actual`) not equal to -0.01595493 (`expected`).
  
    `actual`:  0.03
  `expected`: -0.02
  ── Error ('test-countland_shared_counts.R:6:3'): function SharedCounts, returns correct value ──
  Error in `apply(combX[spectral_cluster$cluster == x, ], 2, sum)`: dim(X) must have a positive length
  Backtrace:
      ▆
   1. └─countland::SharedCounts(C, n_clusters = 2, n_cells = 10, subsample = F) at test-countland_shared_counts.R:6:3
   2.   ├─methods::as(...)
   3.   │ └─methods:::.class1(object)
   4.   ├─base::do.call(...)
   5.   └─base::lapply(...)
   6.     └─countland (local) FUN(X[[i]], ...)
   7.       └─base::apply(combX[spectral_cluster$cluster == x, ], 2, sum)
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted