Running ‘testthat.R’ [10s/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(aPEAR)
  > 
  > test_check("aPEAR")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-prepareEnrichment.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cluster.R:5:3'): spectral clustering returns correct data format ──
  Error in `spectral(sim, verbose = FALSE)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::spectral(sim, verbose = FALSE) at test-cluster.R:5:3
  ── Error ('test-cluster.R:55:3'): pathwayClusters returns something for all implemented methods ──
  Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::pathwayClusters(sim, method = "s") at test-cluster.R:55:3
   2.   └─aPEAR:::spectral(sim, verbose)
  ── Error ('test-cluster.R:63:3'): pathwayClusters filters out by cluster size ──
  Error in `spectral(sim, verbose)`: Package Spectrum is required to use "spectral" clustering method.
  Backtrace:
      ▆
   1. └─aPEAR:::pathwayClusters(sim, method = "s", minClusterSize = 13) at test-cluster.R:63:3
   2.   └─aPEAR:::spectral(sim, verbose)
  
  [ FAIL 3 | WARN 4 | SKIP 1 | PASS 101 ]
  Error: Test failures
  Execution halted