Package: pmartR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [34s/34s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(pmartR)
    > 
    > test_check("pmartR")
    [ FAIL 1 | WARN 11 | SKIP 11 | PASS 2376 ]
    
    ══ Skipped tests (11) ══════════════════════════════════════════════════════════
    • On CRAN (11): 'test_as_trelliData.R:4:3', 'test_as_trelliData.R:361:3',
      'test_as_trelliData_edata.R:4:3', 'test_as_trelliData_summary.R:4:3',
      'test_diffexp_seq.R:4:3', 'test_imd_anova.R:5:3',
      'test_imd_anova_paired.R:5:3', 'test_plots.R:49:3', 'test_trelliPlots.R:4:3',
      'test_trelliPlots_seqData.R:4:3', 'test_trelli_pvalue_filter.R:4:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_dispersion_est.R:43:3'): dispersion_est returns the correct data frame and attributes ──
    Error in `validObject(.Object)`: invalid class "DESeqDataSet" object: superclass "ExpData" not defined in the environment of the object's class
    Backtrace:
         ▆
      1. ├─base::suppressWarnings(dispersion_est(seqdata_grp, method = "DESeq2")) at test_dispersion_est.R:43:3
      2. │ └─base::withCallingHandlers(...)
      3. └─pmartR::dispersion_est(seqdata_grp, method = "DESeq2")
      4.   ├─base::suppressWarnings(...)
      5.   │ └─base::withCallingHandlers(...)
      6.   └─DESeq2::DESeqDataSetFromMatrix(...)
      7.     └─DESeq2::DESeqDataSet(se, design = design, ignoreRank)
      8.       └─methods::new("DESeqDataSet", se, design = design)
      9.         ├─methods::initialize(value, ...)
     10.         └─methods::initialize(value, ...)
     11.           └─methods::validObject(.Object)
    
    [ FAIL 1 | WARN 11 | SKIP 11 | PASS 2376 ]
    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-n-biomolecule-bar.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