Running ‘testthat.R’ [67s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmartR)
  > 
  > test_check("pmartR")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 2571 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (6): 'test_diffexp_seq.R:4:3', 'test_imd_anova.R:5:3',
    'test_imd_anova_paired.R:5:3', 'test_plots.R:15:3', 'test_trelliPlots.R:4:3',
    'test_trelliPlots_seqData.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_dispersion_est.R:39:3'): dispersion_est returns the correct data frame and attributes ──
  Error in `dispersion_est(seqdata_grp, method = "DESeq2")`: package 'DESeq2' required for DESeq2 processing
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(dispersion_est(seqdata_grp, method = "DESeq2")) at test_dispersion_est.R:39:3
   2. │ └─base::withCallingHandlers(...)
   3. └─pmartR::dispersion_est(seqdata_grp, method = "DESeq2")
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 2571 ]
  Deleting unused snapshots:
  • plots/plot-corres.svg
  • plots/plot-cvfilt-log-scale.svg
  • plots/plot-cvfilt.svg
  • plots/plot-datares-bw-theme.svg
  • plots/plot-datares-palette.svg
  • plots/plot-datares.svg
  • plots/plot-dimres.svg
  • plots/plot-imdanovafilt.svg
  • plots/plot-isobaricnormres-bw-theme.svg
  • plots/plot-isobaricnormres-global-normalized.svg
  • plots/plot-isobaricnormres-palette.svg
  • plots/plot-isobaricnormres.svg
  • plots/plot-isobaricpepdata.svg
  • plots/plot-lipiddata.svg
  • plots/plot-metabdata.svg
  • plots/plot-moleculefilt-cumulative.svg
  • plots/plot-moleculefilt.svg
  • plots/plot-nares-bar-group-color.svg
  • plots/plot-nares-bar-group-order.svg
  • plots/plot-nares-scatter.svg
  • plots/plot-nmrdata.svg
  • plots/plot-nmrnormres-2.svg
  • plots/plot-nmrnormres-color-by.svg
  • plots/plot-nmrnormres.svg
  • plots/plot-normres.svg
  • plots/plot-pepdata.svg
  • plots/plot-prodata.svg
  • plots/plot-proteomicsfilt-redundancy.svg
  • plots/plot-proteomicsfilt.svg
  • plots/plot-rmdfilt.svg
  • plots/plot-rnafilt.svg
  • plots/plot-seqdata.svg
  • plots/plot-spansres-bw-theme.svg
  • plots/plot-spansres-color-high-color-low.svg
  • plots/plot-spansres.svg
  • plots/plot-statres-anova-volcano.svg
  • plots/plot-statres-anova.svg
  • plots/plot-statres-combined-volcano.svg
  • plots/plot-statres-combined.svg
  • plots/plot-statres-gtest.svg
  • plots/plot-totalcountfilt.svg
  Error: Test failures
  Execution halted