Running 'testthat.R' [238s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OlinkAnalyze)
  > 
  > test_check("OlinkAnalyze")
  Variables and covariates converted from character to factors: Site
  ANOVA model fit to each assay: NPX~Site
  Variables and covariates converted from character to factors: Time
  ANOVA model fit to each assay: NPX~Time
  Variables and covariates converted from character to factors: Site, Time
  ANOVA model fit to each assay: NPX~Site*Time
  Variables and covariates converted from character to factors: Site
  Means estimated for each assay from ANOVA model:  NPX~Site
  Variables and covariates converted from character to factors: Time
  Means estimated for each assay from ANOVA model:  NPX~Time
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Variables and covariates converted from character to factors: treatment2
  ANOVA model fit to each assay: NPX~treatment2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Variables and covariates converted from character to factors: treatment1
  ANOVA model fit to each assay: NPX~treatment1
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Variables and covariates converted from character to factors: treatment2
  Means estimated for each assay from ANOVA model:  NPX~treatment2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Variables and covariates converted from character to factors: treatment2
  Means estimated for each assay from ANOVA model:  NPX~treatment2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Using max LOD as filter criteria...
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Using plate LOD as filter criteria...
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Using plate LOD as filter criteria...
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Using plate LOD as filter criteria...
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  0 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  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
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  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
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  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
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Variables converted from character to factors: treatment2
  Kruskal model fit to each assay: NPX~treatment2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  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
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  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
  Means estimated for each assay from ANOVA model:  NPX~Treatment*Time
  Saving _problems/test-Olink_ordinalRegression-27.R
  Random assignment of SAMPLES to plates
  
  Assigning subjects to plates
  
  .
  Random assignment of SUBJECTS to plates
  
  `study` column detected in manifest. Optional study argument is set to "study".
  Assigning subjects to plates. 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 1 empty well(s) in the plate. 
  
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  Testing with 2 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.
  
  `study` column detected in manifest. Optional study argument is set to "study".
  Assigning subjects to plates. Multi-study project detected.
              Studies will be kept 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
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  T-test is performed on control - treated.
  Target 96 data in wide form detected.
  The tzdb package is not installed. Timezones will not be available to Arrow compute functions.
  
  Multiple quantification columns detected (NPX, PCNormalizedNPX, Count). NPX will be used for downstream analysis.
  
  i Outdated Data Analysis Reference ID and Software Version combination detected.
  > Re-export data using Panel Archive Version 1.5.0+ in NPX Map and use the newest version of the Fixed LOD file when calculating LOD (Version 6+).
  ! Failure to re-export may result in incorrect PC normalization across lots and Fixed LOD calculations.
  QUANT data detected. Some downstream functions may not be supported.
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Bridge normalization will be performed!
  Assay(s) from the following input dataset have been excluded from normalization:
  * 20200001: OID01216 and OID01217
  i Were marked as "EXCLUDED".
  Bridge normalization will be performed!
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  Duplicate SampleID(s) detected:
   CONTROL_SAMPLE_AS 1
   CONTROL_SAMPLE_AS 2
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  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
  8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column.
  Mann-Whitney U Test is performed on control - treated.
  [ FAIL 1 | WARN 0 | SKIP 41 | PASS 565 ]
  
  ══ Skipped tests (41) ══════════════════════════════════════════════════════════
  • On CRAN (14): 'test-Olink_boxplot.R:1:1',
    'test-Olink_plate_randomizer.R:63:3', 'test-Read_NPX_data.R:1:1',
    'test-Volcano_plot.R:17:3', 'test-dist_plot.R:23:3',
    'test-linear_mixed_model.R:1:1', 'test-npxProcessing.R:141:1',
    'test-olink_Pathway_Enrichment.R:1:1', 'test-olink_Pathway_Heatmap.R:1:1',
    'test-olink_Pathway_Visualization.R:1:1',
    'test-olink_bridgeability_plot.R:6:5',
    'test-olink_bridgeability_plot.R:93:5', 'test-olink_qc_plot.R:21:3',
    'test-pca_plot.R:2:1'
  • file.exists(test_path("data", "example_3k_data.rds")) is not TRUE (22):
    'test-olink_normalization.R:450:5', 'test-olink_normalization.R:496:5',
    'test-olink_normalization.R:869:5', 'test-olink_normalization.R:934:5',
    'test-olink_normalization.R:989:5', 'test-olink_normalization_product.R:7:5',
    'test-olink_normalization_product.R:129:5',
    'test-olink_normalization_product.R:335:5',
    'test-olink_normalization_product.R:467:5',
    'test-olink_normalization_product.R:599:5',
    'test-olink_normalization_product.R:670:5',
    'test-olink_normalization_product.R:956:5',
    'test-olink_normalization_product.R:1147:5',
    'test-olink_normalization_utils.R:327:5',
    'test-olink_normalization_utils.R:3478:5',
    'test-olink_normalization_utils.R:3609:5',
    'test-olink_normalization_utils.R:3901:5',
    'test-olink_normalization_utils.R:3973:5',
    'test-olink_normalization_utils.R:4022:5',
    'test-olink_normalization_utils.R:4197:5',
    'test-olink_normalization_utils.R:5243:5',
    'test-olink_normalization_utils.R:6688:5'
  • file.exists(test_path("data", "example_HT_data.rds")) is not TRUE (1):
    'test-olink_normalization_product.R:881:5'
  • file.exists(test_path("data", "ref_results_norm.rds")) is not TRUE (4):
    'test-olink_normalization.R:17:5', 'test-olink_normalization.R:125:5',
    'test-olink_normalization.R:237:5', 'test-olink_normalization.R:349:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Olink_ordinalRegression.R:17:3'): (code run outside of `test_that()`) ──
  Error in ``contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])`: contrasts can be applied only to factors with 2 or more levels
  Backtrace:
       ▆
    1. ├─... %>% select(-id) at test-Olink_ordinalRegression.R:17:3
    2. ├─dplyr::select(., -id)
    3. ├─dplyr::arrange(., id, contrast)
    4. ├─dplyr::mutate(., id = as.character(OlinkID))
    5. ├─OlinkAnalyze::olink_ordinalRegression_posthoc(...)
    6. │ ├─base::withCallingHandlers(...)
    7. │ └─... %>% dplyr::mutate(term = paste(effect, collapse = ":"))
    8. ├─dplyr::mutate(., term = paste(effect, collapse = ":"))
    9. ├─dplyr::ungroup(.)
   10. ├─dplyr::do(...)
   11. ├─dplyr:::do.grouped_df(...)
   12. │ └─rlang::eval_tidy(args[[1]], mask)
   13. ├─base::data.frame(...)
   14. ├─emmeans::emmeans(...)
   15. │ └─emmeans:::.chk.list(object, ...)
   16. └─ordinal::clm(as.formula(formula_string), data = .)
   17.   └─ordinal:::get_clmDesign(fullmf, terms.list, contrasts)
   18.     └─ordinal:::get_clmDM(...)
   19.       ├─stats::model.matrix(...)
   20.       └─stats::model.matrix.default(...)
   21.         └─stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
  
  [ FAIL 1 | WARN 0 | SKIP 41 | PASS 565 ]
  Error:
  ! Test failures.
  Execution halted