Running ‘testthat.R’ [117s/196s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OlinkAnalyze)
  > 
  > test_check("OlinkAnalyze")
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Site
  ANOVA model fit to each assay: NPX~Site
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Time
  ANOVA model fit to each assay: NPX~Time
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Site, Time
  ANOVA model fit to each assay: NPX~Site*Time
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Site
  Means estimated for each assay from ANOVA model:  NPX~Site
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Time
  Means estimated for each assay from ANOVA model:  NPX~Time
  Variables and covariates converted from character to factors: treatment2
  ANOVA model fit to each assay: NPX~treatment2
  Variables and covariates converted from character to factors: treatment2
  Means estimated for each assay from ANOVA model:  NPX~treatment2
  Using Max LOD as filter criteria...
  Using Plate LOD as filter criteria...
  Using Plate_LOD as filter criteria...
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables converted from character to factors: Site
  Kruskal model fit to each assay: NPX~Site
  Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables converted from character to factors: Time
  Friedman model fit to each assay: NPX~Time
  Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables converted from character to factors: Site
  Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed
  Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables converted from character to factors: Time
  Pairwise comparisons for Friedman test using paired Wilcoxon signed-rank test were performed
  Variables converted from character to factors: treatment2
  Kruskal model fit to each assay: NPX~treatment2
  Variables converted from character to factors: treatment2
  Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed
  Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variables and covariates converted from character to factors: Treatment, Time
  ANOVA model fit to each assay: NPX~Treatment*Time
  Random assignment of SAMPLES to plates
  
  Assigning subjects to plates
  
  .
  Random assignment of SUBJECTS to plates
  
  Assigning subjects to plates. 'study' column detected so keeping studies together during randomization. 
  
  Testing with 0 empty well(s) in the plate. 
  
  .
  study1 successful! 
  
  Testing with 0 empty well(s) in the plate. 
  
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  Testing with 3 empty well(s) in the plate. 
  
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  Testing with 4 empty well(s) in the plate. 
  
  .
  study2 successful! 
  
  Random assignment of SUBJECTS to plates
  
  Totally included 4 empty well(s) in first and/or intermediate plate(s) to accomplish the randomization.
  
  Please try another seed or increase the number of iterations if there are indications that another randomization might leave fewer empty wells.
  
  Assigning subjects to plates. 'study' column detected so keeping studies together during randomization. 
  
  Random assignment of SAMPLES to plates by study
  
  Assigning subjects to plates
  
  .
  Random assignment of SUBJECTS to plates
  
  Random assignment of SAMPLES to plates
  
  Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variable converted from character to factor: Treatment
  T-test is performed on Treated - Untreated.
  Variable converted from character to factor: Time
  Paired t-test is performed on Baseline - Week.6.
  Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variable converted from character to factor: Time
  Variable converted from character to factor: treatment1
  T-test is performed on control - treated.
  Target 96 data in wide form detected.
  QUANT data detected. Some downstream functions may not be supported.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Bridging normalization with subset normalization will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Bridging normalization with overlapping samples will be performed.
  Adding missing columns...
  Bridging normalization with overlapping samples will be performed.
  Loading required namespace: umap
  Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variable converted from character to factor: Treatment
  Mann-Whitney U Test is performed on Treated - Untreated.
  Variable converted from character to factor: Time
  Paired Mann-Whitney U Test is performed on Baseline - Week.6.
  Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2
  Variable converted from character to factor: Time
  Variable converted from character to factor: treatment1
  Mann-Whitney U Test is performed on control - treated.
  [ FAIL 1 | WARN 2 | SKIP 11 | PASS 183 ]
  
  ══ Skipped tests (11) ══════════════════════════════════════════════════════════
  • On CRAN (11): 'test-Olink_boxplot.R:1:1',
    'test-Olink_plate_randomizer.R:59:3', 'test-Read_NPX_data.R:39:3',
    'test-Volcano_plot.R:16:3', 'test-dist_plot.R:17:3',
    'test-linear_mixed_model.R:1:1', 'test-olink_Pathway_Enrichment.R:1:1',
    'test-olink_Pathway_Heatmap.R:1:1', 'test-olink_Pathway_Visualization.R:1:1',
    'test-olink_qc_plot.R:15:3', 'test-pca_plot.R:2:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Olink_ordinalRegression.R:9:1'): (code run outside of `test_that()`) ──
  Error: length of start is 83 should equal 82
  Backtrace:
       ▆
    1. ├─... %>% select(-id) at test-Olink_ordinalRegression.R:9:0
    2. ├─dplyr::select(., -id)
    3. ├─dplyr::arrange(., id, Assay)
    4. ├─dplyr::mutate(., id = as.character(OlinkID))
    5. ├─OlinkAnalyze::olink_ordinalRegression(df = npx_data1, variable = "Treatment:Time")
    6. │ ├─base::withCallingHandlers(...)
    7. │ └─... %>% dplyr::arrange(Adjusted_pval)
    8. ├─dplyr::arrange(., Adjusted_pval)
    9. ├─dplyr::select(...)
   10. ├─dplyr::select(., -covariates)
   11. ├─dplyr::ungroup(.)
   12. ├─dplyr::mutate(...)
   13. ├─dplyr::mutate(...)
   14. ├─dplyr::mutate(., Adjusted_pval = p.adjust(p.value, method = "fdr"))
   15. ├─dplyr::group_by(., covariates)
   16. ├─dplyr::mutate(., covariates = term %in% covariate_filter_string)
   17. ├─dplyr::filter(., !term %in% c("(Intercept)", "Residuals"))
   18. ├─dplyr::ungroup(.)
   19. ├─dplyr::do(...)
   20. ├─dplyr:::do.grouped_df(...)
   21. │ └─rlang::eval_tidy(args[[j]], mask)
   22. ├─generics::tidy(...)
   23. ├─car::Anova(...)
   24. └─ordinal::clm(as.formula(formula_string), data = ., threshold = "symmetric")
   25.   └─ordinal:::clm.fit.default(clm.struct)
   26.     └─ordinal:::set.start(...)
  
  [ FAIL 1 | WARN 2 | SKIP 11 | PASS 183 ]
  Deleting unused snapshots:
  • Olink_boxplot/boxplot-site-10prots.svg
  • Olink_boxplot/boxplot-site-2prots.svg
  • Olink_boxplot/boxplot-time-and-site.svg
  • Olink_boxplot/boxplot-time-with-coloroption.svg
  • Olink_boxplot/boxplot-time.svg
  • Volcano_plot/volcano-plot-with-coloroption.svg
  • dist_plot/distribution-plot-col-by-treatment.svg
  • linear_mixed_model/lmer-plot-more-prots-than-space.svg
  • linear_mixed_model/lmer-plot.svg
  • olink_Pathway_Heatmap/gsea-heatmap.svg
  • olink_Pathway_Heatmap/ora-heatmap-with-keyword.svg
  • olink_Pathway_Visualization/gsea-vis-with-keyword.svg
  • olink_Pathway_Visualization/gsea-visualization.svg
  • olink_Pathway_Visualization/ora-vis-with-keyword.svg
  • olink_Pathway_Visualization/ora-vis-with-terms.svg
  • olink_qc_plot/qc-plot-with-coloroption.svg
  • pca_plot/pca-basic-plotting.svg
  • pca_plot/pca-plot-color-by-treatment.svg
  • pca_plot/pca-plot-drop-assays-and-drop-samples.svg
  • pca_plot/pca-plot-internal-2.svg
  • pca_plot/pca-plot-internal-3.svg
  • pca_plot/pca-plot-internal-4.svg
  • pca_plot/pca-plot-internal.svg
  • pca_plot/pca-plot-label-outliers.svg
  • pca_plot/pca-plot-not-label-outliers.svg
  • pca_plot/pca-plot-panel-1.svg
  • pca_plot/pca-plot-panel-2.svg
  • pca_plot/pca-plot-with-loadings.svg
  • pca_plot/pca-plot.svg
  Error: Test failures
  Execution halted