R version 4.6.0 alpha (2026-03-28 r89738 ucrt)
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> # This file is part of the standard testthat infrastructure
> library(testthat)
> library(pepdiff)

Attaching package: 'pepdiff'

The following object is masked from 'package:testthat':

    compare

> 
> test_check("pepdiff")
Note: Use read_pepdiff() and compare.pepdiff_data() for new analyses
Rank Product analysis for unpaired case 
 

 done  NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 1000.00 (95th percentile)
Flagged peptides: 0 (0.0%) above threshold

Interpretation: Deviance distribution looks good.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.00 (95th percentile)
Flagged peptides: 20 (100.0%) above threshold

Interpretation: Many peptides show poor fit. Consider using method = 'art'.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.00 (95th percentile)
Flagged peptides: 20 (100.0%) above threshold

Interpretation: Many peptides show poor fit. Consider using method = 'art'.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.00 (95th percentile)
Flagged peptides: 20 (100.0%) above threshold

Interpretation: Many peptides show poor fit. Consider using method = 'art'.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'

GLM Fit Diagnostics
-------------------
Peptides analyzed: 20 (all converged)
Median deviance: 0.40
Threshold: 0.91 (95th percentile)
Flagged peptides: 1 (5.0%) above threshold

Interpretation: Some peptides show elevated deviance. Check residual plots.
See vignette('checking_fit') for detailed guidance.

`geom_smooth()` using formula = 'y ~ x'
Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  Rank Product analysis for unpaired case 
 

 done  [ FAIL 0 | WARN 258 | SKIP 4 | PASS 388 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• ARTool is installed (1): 'test-models.R:168:3'
• Cannot test missing package without uninstalling - manual verification needed
  (2): 'test-rankprod.R:138:3', 'test-rankprod.R:145:3'
• Legacy compare requires old data format (1): 'test-legacy.R:7:3'

[ FAIL 0 | WARN 258 | SKIP 4 | PASS 388 ]
> 
> proc.time()
   user  system elapsed 
  60.51    6.25   63.29