Running ‘testthat.R’ [130s/164s]
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.
  
  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