Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(CRMetrics)
  > 
  > test_check("CRMetrics")
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Adding list of 4 count matrices.
  Running preprocessing using pagoda2...
  3000 cells, 10000 genes; normalizing ... 
  Using plain model 
  Winsorizing ... 
  log scale ... 
  done.
  
  calculating variance fit ...
   using gam 
  0 overdispersed genes ... 0
  persisting ... 
  done.
  running PCA using 3000 OD genes .
  .
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests.R:34:3'): Check preprocessing ─────────────────────────────────
  Error in `irlba(x, nv = nPcs, nu = 0, center = cm, right_only = FALSE, 
      fastpath = fastpath, maxit = maxit, reorth = TRUE, ...)`: function 'as_cholmod_sparse' not provided by package 'Matrix'
  Backtrace:
      ▆
   1. └─crm$doPreprocessing(min.transcripts.per.cell = 0, min.cells.per.gene = 0) at tests.R:34:3
   2.   └─base::lapply(...)
   3.     └─pagoda2 (local) FUN(X[[i]], ...)
   4.       └─p2$calculatePcaReduction(...)
   5.         └─irlba::irlba(...)
  ── Error ('tests.R:41:3'): Check embedding object ──────────────────────────────
  Error in `crm$createEmbedding(arg.embedGraph = list(method = "largeVis"))`: No preprocessed count matrices found, please run doPreprocessing.
  Backtrace:
      ▆
   1. └─crm$createEmbedding(arg.embedGraph = list(method = "largeVis")) at tests.R:41:3
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted