R Under development (unstable) (2024-09-23 r87189 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'q()' to quit R.

> 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: 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
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
NOTE: Results may be misleading due to involvement in interactions
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: 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

Assigning subjects to plates. 'study' column detected so keeping studies together during randomization. 

Testing with 0 empty well(s) in the plate. 

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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. 

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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
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.
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.
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 0 | WARN 1 | SKIP 28 | PASS 459 ]

══ Skipped tests (28) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-Olink_boxplot.R:1:1',
  'test-Olink_plate_randomizer.R:60:3', 'test-Read_NPX_data.R:52:5',
  'test-Volcano_plot.R:16:3', 'test-dist_plot.R:18:5',
  'test-linear_mixed_model.R:1:1', 'test-npxProcessing.R:121:3',
  '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:16:5',
  'test-pca_plot.R:2:1'
• file.exists("../data/example_3k_data.rds") is not TRUE (11):
  'test-olink_normalization.R:473:5',
  'test-olink_normalization_product.R:97:5',
  'test-olink_normalization_product.R:191:5',
  'test-olink_normalization_product.R:312:5',
  'test-olink_normalization_utils.R:146:5',
  'test-olink_normalization_utils.R:2414:5',
  'test-olink_normalization_utils.R:2480:5',
  'test-olink_normalization_utils.R:2544:5',
  'test-olink_normalization_utils.R:2590:5',
  'test-olink_normalization_utils.R:2709:5',
  'test-olink_normalization_utils.R:3754:5'
• file.exists("../data/ref_results_norm.rds") is not TRUE (4):
  'test-olink_normalization.R:17:5', 'test-olink_normalization.R:131:5',
  'test-olink_normalization.R:249:5', 'test-olink_normalization.R:367:5'
• file.exists(normalizePath("../data/example_3k_data.rds")) is not TRUE (1):
  'test-olink_normalization_product.R:6:5'

[ FAIL 0 | WARN 1 | SKIP 28 | PASS 459 ]
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
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
 150.43    6.23  156.78