Running ‘testthat.R’ [52s/228s]
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 
  organizing dataset 
  [ FAIL 5 | WARN 10 | SKIP 0 | PASS 17 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rc.get.xcms.data.R:7:3'): RAMClustR rc.get.xcms.data ───────────
  Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable
  Backtrace:
      ▆
   1. └─RAMClustR::rc.get.xcms.data(xcmsObj = xdata) at test-rc.get.xcms.data.R:7:3
  ── Error ('test-stepwise-workflow.R:11:3'): RAMClustR workflow with xcms works ──
  Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable
  Backtrace:
      ▆
   1. └─RAMClustR::rc.get.xcms.data(xcmsObj = xdata) at test-stepwise-workflow.R:11:3
  ── Error ('test-workflow-comparison.R:8:3'): RAMClustR workflow comparison test ──
  Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable
  Backtrace:
      ▆
   1. └─RAMClustR::ramclustR(xcmsObj = xdata, maxt = 20, sr = 0.5) at test-workflow-comparison.R:8:3
   2.   └─RAMClustR::rc.get.xcms.data(...)
  ── Error ('test.R:11:3'): RAMClustR with xcms works ────────────────────────────
  Error in `xcmsObj@phenoData[[1]]`: this S4 class is not subsettable
  Backtrace:
      ▆
   1. └─RAMClustR::ramclustR(xcmsObj = xdata, maxt = 20, sr = 0.5, mzdec = 4) at test.R:11:3
   2.   └─RAMClustR::rc.get.xcms.data(...)
  ── Error ('test.R:24:3'): RAMClustR with csv works ─────────────────────────────
  Error in `gzfile(file, "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readRDS(file.path("testdata", "test_csv.rds")) at test.R:24:3
   2.   └─base::gzfile(file, "rb")
  
  [ FAIL 5 | WARN 10 | SKIP 0 | PASS 17 ]
  Error: Test failures
  Execution halted