Last updated on 2026-01-11 05:50:12 CET.
| Package | ERROR | OK |
|---|---|---|
| OlinkAnalyze | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
Version: 4.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5m/12m]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 4.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [296s/345s]
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
Flavor: r-devel-linux-x86_64-fedora-gcc