Running 'testthat.R' [216s]
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
  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
  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, Site
  Means estimated for each assay from ANOVA model:  NPX~Treatment*Time+Site
  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
  Random assignment of SAMPLES to plates
  Assigning subjects to plates
  .Random assignment of SUBJECTS 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.
  QUANT data detected. Some downstream functions may not be supported.
  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 2 | WARN 2 | SKIP 10 | PASS 90 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Olink_bridgeselector.R:15:3'): olink_bridgeselector works ──────
  Error in `dplyr::filter(., stringr::str_detect(OlinkID, "OID[0-9]{5}"))`: i In argument: `stringr::str_detect(OlinkID, "OID[0-9]{5}")`.
  Caused by error in `stri_detect_regex()`:
  ! memory allocation error: failed to allocate 640000 bytes
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-Olink_bridgeselector.R:15:2
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. ├─OlinkAnalyze::olink_bridgeselector(...)
    8. │ └─... %>% ...
    9. ├─dplyr::filter(., stringr::str_detect(OlinkID, "OID[0-9]{5}"))
   10. ├─dplyr:::filter.data.frame(., stringr::str_detect(OlinkID, "OID[0-9]{5}"))
   11. │ └─dplyr:::filter_rows(.data, dots, by)
   12. │   └─dplyr:::filter_eval(...)
   13. │     ├─base::withCallingHandlers(...)
   14. │     └─mask$eval_all_filter(dots, env_filter)
   15. │       └─dplyr (local) eval()
   16. ├─stringr::str_detect(OlinkID, "OID[0-9]{5}")
   17. │ └─stringi::stri_detect_regex(...)
   18. └─base::.handleSimpleError(...)
   19.   └─dplyr (local) h(simpleError(msg, call))
   20.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  ── Error ('test-Olink_normalization.R:12:1'): (code run outside of `test_that()`) ──
  Error: cannot allocate vector of size 7.5 Mb
  Backtrace:
      ▆
   1. ├─... %>% pull(.) at test-Olink_normalization.R:12:0
   2. ├─dplyr::pull(.)
   3. ├─dplyr::filter(., !str_detect(., "CONTROL_SAMPLE"))
   4. ├─base::data.frame(.)
   5. └─base::intersect(npx_data1$SampleID, npx_data2$SampleID)
  
  [ FAIL 2 | WARN 2 | SKIP 10 | PASS 90 ]
  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