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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 Duplicate SampleID(s) detected: sample1_1 sample2_1 sample4_1 MM55111 XY32341 MN86751 YY35111 UY45551 cs2_1 S81771 SA0F71 S52F71 S8FCB1 S7EF01 S897C1 S65FC1 NEG-SOAP-11 SFCC51 S4DFE1 S0C651 S15B31 SD4171 NEG-SOAP-12 S17811 S0D6D1 S16F21 S53B71 S161F1 S6D2C1 SA17C1 SD4DD1 SACD01 SAC111 PC-SOAP-11 SF14F1 S353F1 S14C51 SE8771 PC-SOAP-12 SCF7B1 S84D41 SA1DC1 S45E31 S1DB31 S38321 sample5_2 sample6_2 sample7_2 KJ23652 OO34092 VX55552 cs1_2 ZK43212 SD50562 MN86752 XW43972 YY35112 LH84092 SD8172 SA0F72 S52F72 SA33F2 S7EF02 S939C2 S65FC2 NEG-SOAP-21 SFCC52 S4DFE2 S275F2 S857F2 S87C02 S10642 S0C652 NEG-SOAP-22 SC17B2 S0D6D2 S16F22 SCF472 S53B72 NEG-SOAP-23 S161F2 S6D2C2 S35EB2 S445F2 SD13C2 SAC412 SAC112 PC-SOAP-21 SBE1D2 S353F2 S14C52 S10262 SE8772 SCF7B2 SA1DC2 S7BD12 S4E5F2 S45BF2 SD7702 S38322 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 Duplicate SampleID(s) detected: sample1_1 sample2_1 sample4_1 MM55111 XY32341 MN86751 YY35111 UY45551 cs2_1 S81771 SA0F71 S52F71 S8FCB1 S7EF01 S897C1 S65FC1 NEG-SOAP-11 SFCC51 S4DFE1 S0C651 S15B31 SD4171 NEG-SOAP-12 S17811 S0D6D1 S16F21 S53B71 S161F1 S6D2C1 SA17C1 SD4DD1 SACD01 SAC111 PC-SOAP-11 SF14F1 S353F1 S14C51 SE8771 PC-SOAP-12 SCF7B1 S84D41 SA1DC1 S45E31 S1DB31 S38321 sample5_2 sample6_2 sample7_2 KJ23652 OO34092 VX55552 cs1_2 ZK43212 SD50562 MN86752 XW43972 YY35112 LH84092 SD8172 SA0F72 S52F72 SA33F2 S7EF02 S939C2 S65FC2 NEG-SOAP-21 SFCC52 S4DFE2 S275F2 S857F2 S87C02 S10642 S0C652 NEG-SOAP-22 SC17B2 S0D6D2 S16F22 SCF472 S53B72 NEG-SOAP-23 S161F2 S6D2C2 S35EB2 S445F2 SD13C2 SAC412 SAC112 PC-SOAP-21 SBE1D2 S353F2 S14C52 S10262 SE8772 SCF7B2 SA1DC2 S7BD12 S4E5F2 S45BF2 SD7702 S38322 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 `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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 1 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 2 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 3 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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. 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 0 | SKIP 30 | PASS 463 ] ══ Skipped tests (30) ══════════════════════════════════════════════════════════ • 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:17:3', '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(test_path("data", "example_3k_data.rds")) is not TRUE (14): 'test-olink_normalization.R:474:5', 'test-olink_normalization.R:739:5', 'test-olink_normalization_product.R:7:5', 'test-olink_normalization_product.R:122:5', 'test-olink_normalization_product.R:218:5', 'test-olink_normalization_product.R:342:5', 'test-olink_normalization_product.R:469:5', 'test-olink_normalization_utils.R:146:5', 'test-olink_normalization_utils.R:2429:5', 'test-olink_normalization_utils.R:2523:5', 'test-olink_normalization_utils.R:2598:5', 'test-olink_normalization_utils.R:2645:5', 'test-olink_normalization_utils.R:2764:5', 'test-olink_normalization_utils.R:3810:5' • file.exists(test_path("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' [ FAIL 0 | WARN 0 | SKIP 30 | PASS 463 ] 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 107.46 3.54 111.07