Running ‘testthat.R’ [9s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RAMClustR)
  > 
  > test_check("RAMClustR")
  plotting findmain annotation results 
  finished 
  87.5% of features move forward
  ma MSdata 
  df phenoData 
  Features which failed to demonstrate signal intensity of at least 3 fold greater in QC samples than in blanks were removed from the feature dataset. 6 of 48 features were removed.MSdata :  33 passed the CV filter 
  Features were filtered based on their qc sample CV values. Only features with CV vaules less than or equal to 0.5 in MSdata set were retained. 9 of 42 features were removed.Features were normalized by linearly regressing run order versus qc feature intensities to account for instrument signal intensity drift. Only features with a regression pvalue less than 0.05 and an r-squared greater than 0.1 were corrected.  Of 42 features, 0 was corrected for run order effects.replaced 12 of 192 total feature values ( 6 % ) 
  Calculating ramclustR similarity using 3 nblocks.
  1  
   RAMClust feature similarity matrix calculated and stored.
  fastcluster based clustering complete 
  dynamicTreeCut based pruning complete 
  RAMClust has condensed 33 features into 4 spectra 
  collapsing feature into spectral signal intensities 
  Calculating ramclustR similarity using 3 nblocks.
  1  
   RAMClust feature similarity matrix calculated and stored.
  fastcluster based clustering complete 
  dynamicTreeCut based pruning complete 
  RAMClust has condensed 33 features into 6 spectra 
  collapsing feature into spectral signal intensities 
  organizing dataset 
  replaced 0 of 609 total feature values ( 0 % ) 
    normalizing dataset 
  Calculating ramclustR similarity using 3 nblocks.
  1  
   RAMClust feature similarity matrix calculated and stored.
  fastcluster based clustering complete 
  dynamicTreeCut based pruning complete 
  RAMClust has condensed 203 features into 22 spectra 
  collapsing feature into spectral signal intensities 
  writing msp formatted spectra 
  msp file complete 
  [ FAIL 1 | WARN 10 | SKIP 4 | PASS 19 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • xcms cannot be loaded (4): 'test-rc.get.xcms.data.R:2:3',
    'test-stepwise-workflow.R:2:3', 'test-workflow-comparison.R:2:3',
    'test.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-do.findmain.R:10:3'): RAMClustR do.findmain ──────────────────
  `actual` not equal to `expected`.
  Component "M.ann.findmain": Component 1: Attributes: < Component "scores": Attributes: < Component "row.names": Modes: character, numeric > >
  Component "M.ann.findmain": Component 1: Attributes: < Component "scores": Attributes: < Component "row.names": target is character, current is numeric > >
  Component "M.ann.findmain": Component 2: Attributes: < Component "scores": Attributes: < Component "row.names": Modes: character, numeric > >
  Component "M.ann.findmain": Component 2: Attributes: < Component "scores": Attributes: < Component "row.names": target is character, current is numeric > >
  Component "M.ann.findmain": Component 3: Attributes: < Component "scores": Attributes: < Component "row.names": Modes: character, numeric > >
  Component "M.ann.findmain": Component 3: Attributes: < Component "scores": Attributes: < Component "row.names": target is character, current is numeric > >
  Component "M.ann.findmain": Component 4: Attributes: < Component "scores": Attributes: < Component "row.names": Modes: character, numeric > >
  Component "M.ann.findmain": Component 4: Attributes: < Component "scores": Attributes: < Component "row.names": target is character, current is numeric > >
  
  [ FAIL 1 | WARN 10 | SKIP 4 | PASS 19 ]
  Error: Test failures
  Execution halted