Running 'testthat.R' [231s/286s]
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
  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.
  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.
  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 10 | SKIP 13 | PASS 102 ]
  
  == Skipped tests ===============================================================
  * On CRAN (13)
  
  == Failed tests ================================================================
  -- Error ('test-Read_NPX_data.R:14'): Data loads correctly with 'read_NPX()' ---
  Error in `zip::unzip(zipfile = filename, files = files_to_extract, exdir = tmp_unzip_dir, 
      overwrite = TRUE)`: zip error: `Cannot create directory `Example_NPX_Data_zip.csv` to extract `/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/OlinkAnalyze/extdata/Example_NPX_Data_zip.zip` from arghive `§c`` in file `zip.c:198`
  Backtrace:
      x
   1. +-testthat::expect_error(...) at test-Read_NPX_data.R:14:2
   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::read_NPX(filename = zip_npx_file_fail_1)
   8.   \-OlinkAnalyze:::read_NPX_explore(filename = filename)
   9.     \-zip::unzip(...)
  
  [ FAIL 1 | WARN 10 | SKIP 13 | PASS 102 ]
  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-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-label-outliers.svg
  * pca_plot/pca-plot-panel-1.svg
  * pca_plot/pca-plot-panel-2.svg
  * pca_plot/pca-plot-with-loadings.svg
  Error: Test failures
  Execution halted