##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:POMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings POMA_1.13.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.13.22’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘POMA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.getHelpFile’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PomaBatch: no visible global function definition for ‘is’
PomaBatch: no visible global function definition for ‘validObject’
PomaBoxplots: no visible global function definition for ‘is’
PomaBoxplots: no visible binding for global variable ‘sample_id’
PomaBoxplots: no visible binding for global variable ‘group_factor’
PomaBoxplots: no visible global function definition for ‘median’
PomaBoxplots: no visible binding for global variable ‘value’
PomaBoxplots: no visible global function definition for ‘reorder’
PomaBoxplots: no visible binding for global variable ‘median_rank’
PomaBoxplots: no visible binding for global variable ‘name’
PomaClust: no visible global function definition for ‘is’
PomaClust: no visible binding for global variable ‘clust’
PomaClust: no visible binding for global variable ‘V1’
PomaClust: no visible binding for global variable ‘V2’
PomaClust: no visible binding for global variable ‘Dim1’
PomaClust: no visible binding for global variable ‘Dim2’
PomaCorr: no visible global function definition for ‘is’
PomaCorr: no visible global function definition for ‘cor’
PomaCorr: no visible binding for global variable ‘column’
PomaCorr: no visible binding for global variable ‘cor’
PomaCorr: no visible binding for global variable ‘p’
PomaCorr: no visible global function definition for ‘p.adjust’
PomaCorr: no visible binding for global variable ‘pvalue’
PomaCorr: no visible binding for global variable ‘corr’
PomaCorr: no visible binding for global variable ‘feature1’
PomaCorr: no visible binding for global variable ‘name’
PomaCorr: no visible binding for global variable ‘value’
PomaCreateObject: no visible global function definition for
  ‘validObject’
PomaDESeq: no visible global function definition for ‘is’
PomaDESeq: no visible binding for global variable ‘padj’
PomaDESeq: no visible binding for global variable ‘adj_pvalue’
PomaDensity: no visible global function definition for ‘is’
PomaDensity: no visible binding for global variable ‘sample_id’
PomaDensity: no visible binding for global variable ‘group_factor’
PomaDensity: no visible binding for global variable ‘name’
PomaDensity: no visible binding for global variable ‘value’
PomaHeatmap: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘aggregate’
PomaImpute: no visible binding for global variable ‘group_factor’
PomaImpute: no visible global function definition for ‘validObject’
PomaLM: no visible global function definition for ‘is’
PomaLM: no visible global function definition for ‘lm’
PomaLM: no visible global function definition for ‘p.adjust’
PomaLM: no visible binding for global variable ‘p.value’
PomaLM: no visible binding for global variable ‘term’
PomaLM: no visible binding for global variable ‘estimate’
PomaLM: no visible binding for global variable ‘std.error’
PomaLM: no visible binding for global variable ‘statistic’
PomaLM: no visible binding for global variable ‘adj_pvalue’
PomaLM: no visible binding for global variable ‘pvalue’
PomaLM: no visible global function definition for ‘reorder’
PomaLM: no visible binding for global variable ‘feature’
PomaLM: no visible binding for global variable ‘std_err’
PomaLMM: no visible global function definition for ‘is’
PomaLMM : lmm_fun: no visible global function definition for ‘vcov’
PomaLMM : lmm_fun: no visible binding for global variable ‘vcov’
PomaLMM : lmm_fun: no visible binding for global variable ‘grp’
PomaLMM : lmm_fun: no visible binding for global variable
  ‘variance_percent’
PomaLMM: no visible binding for global variable ‘feature’
PomaLMM: no visible binding for global variable ‘name’
PomaLMM: no visible binding for global variable ‘value’
PomaLasso: no visible global function definition for ‘is’
PomaLasso: no visible binding for global variable ‘estimate’
PomaLasso: no visible binding for global variable ‘conf.low’
PomaLasso: no visible binding for global variable ‘conf.high’
PomaLasso: no visible global function definition for ‘predict’
PomaLasso: no visible binding for global variable ‘term’
PomaLimma: no visible global function definition for ‘is’
PomaLimma: no visible global function definition for ‘as.formula’
PomaLimma: no visible binding for global variable ‘P.Value’
PomaLimma: no visible binding for global variable ‘adj.P.Val’
PomaNorm: no visible global function definition for ‘is’
PomaNorm: no visible binding for global variable ‘var’
PomaNorm : <anonymous>: no visible global function definition for ‘sd’
PomaNorm: no visible global function definition for ‘validObject’
PomaOddsRatio: no visible global function definition for ‘is’
PomaOddsRatio: no visible binding for global variable ‘group’
PomaOddsRatio: no visible binding for global variable ‘OddsRatio’
PomaOddsRatio: no visible binding for global variable ‘feature’
PomaOddsRatio: no visible binding for global variable ‘upr’
PomaOddsRatio: no visible binding for global variable ‘lwr’
PomaOutliers: no visible global function definition for ‘is’
PomaOutliers: no visible binding for global variable ‘groups’
PomaOutliers: no visible global function definition for ‘quantile’
PomaOutliers: no visible global function definition for ‘IQR’
PomaOutliers: no visible binding for global variable ‘limit’
PomaOutliers: no visible binding for global variable ‘out’
PomaOutliers : find_hull: no visible global function definition for
  ‘chull’
PomaOutliers: no visible binding for global variable ‘group’
PomaOutliers: no visible binding for global variable ‘.’
PomaOutliers: no visible binding for global variable ‘PCoA1’
PomaOutliers: no visible binding for global variable ‘PCoA2’
PomaOutliers: no visible global function definition for ‘validObject’
PomaPCA: no visible global function definition for ‘is’
PomaPCA: no visible global function definition for ‘prcomp’
PomaPCA: no visible binding for global variable ‘PC1’
PomaPCA: no visible binding for global variable ‘PC2’
PomaPCA: no visible binding for global variable ‘group’
PomaPCA: no visible binding for global variable ‘sample_id’
PomaPCA: no visible global function definition for ‘reorder’
PomaPCA: no visible binding for global variable ‘comp’
PomaPCA: no visible binding for global variable ‘var_exp’
PomaPCA: no visible binding for global variable ‘feature’
PomaPCA: no visible binding for global variable ‘value’
PomaPCA: no visible binding for global variable ‘name’
PomaPCA: no visible binding for global variable ‘to_x’
PomaPCA: no visible binding for global variable ‘to_y’
PomaPCR: no visible global function definition for ‘is’
PomaPCR: no visible binding for global variable ‘PC1’
PomaPCR: no visible global function definition for ‘lm’
PomaPCR: no visible global function definition for ‘p.adjust’
PomaPCR: no visible binding for global variable ‘p.value’
PomaPCR: no visible binding for global variable ‘term’
PomaPCR: no visible binding for global variable ‘estimate’
PomaPCR: no visible binding for global variable ‘std.error’
PomaPCR: no visible binding for global variable ‘statistic’
PomaPCR: no visible binding for global variable ‘adj_pvalue’
PomaPCR: no visible binding for global variable ‘pvalue’
PomaPLS: no visible global function definition for ‘is’
PomaPLS: no visible binding for global variable ‘comp1’
PomaPLS: no visible binding for global variable ‘comp2’
PomaPLS: no visible binding for global variable ‘sample_id’
PomaPLS: no visible binding for global variable ‘feature’
PomaPLS: no visible global function definition for ‘reorder’
PomaPLS: no visible binding for global variable ‘value’
PomaPLS: no visible binding for global variable ‘name’
PomaPLS: no visible binding for global variable ‘component’
PomaPLS: no visible binding for global variable ‘error’
PomaPLS: no visible binding for global variable ‘feature_sd’
PomaPLS: no visible binding for global variable ‘sd’
PomaRandForest: no visible global function definition for ‘is’
PomaRandForest: no visible binding for global variable ‘OOB’
PomaRandForest: no visible binding for global variable
  ‘MeanDecreaseGini’
PomaRandForest: no visible global function definition for ‘reorder’
PomaRandForest: no visible binding for global variable ‘feature’
PomaRankProd: no visible global function definition for ‘is’
PomaRankProd: no visible binding for global variable ‘P.value’
PomaRankProd: no visible binding for global variable ‘gene.index’
PomaUMAP: no visible global function definition for ‘is’
PomaUMAP: no visible binding for global variable ‘clust’
PomaUMAP: no visible binding for global variable ‘UMAP1’
PomaUMAP: no visible binding for global variable ‘UMAP2’
PomaUnivariate: no visible global function definition for ‘is’
PomaUnivariate: no visible binding for global variable ‘group’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘t.test’
PomaUnivariate: no visible global function definition for ‘p.adjust’
PomaUnivariate: no visible binding for global variable ‘pvalue’
PomaUnivariate: no visible binding for global variable ‘feature’
PomaUnivariate: no visible binding for global variable ‘fold_change’
PomaUnivariate: no visible binding for global variable ‘diff_means’
PomaUnivariate: no visible binding for global variable ‘adj_pvalue’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘anova’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘aov’
PomaUnivariate: no visible global function definition for ‘TukeyHSD’
PomaUnivariate: no visible global function definition for ‘aov’
PomaUnivariate: no visible binding for global variable ‘adj.p.value’
PomaUnivariate: no visible global function definition for ‘as.formula’
PomaUnivariate: no visible binding for global variable ‘term’
PomaUnivariate: no visible binding for global variable ‘p.value’
PomaUnivariate: no visible binding for global variable ‘contrast’
PomaUnivariate: no visible binding for global variable ‘p adj’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘wilcox.test’
PomaUnivariate : <anonymous>: no visible global function definition for
  ‘kruskal.test’
PomaUnivariate: no visible binding for global variable ‘kw_rank_sum’
PomaUnivariate: no visible binding for global variable ‘Comparison’
PomaUnivariate: no visible binding for global variable ‘P.adj’
PomaVolcano: no visible global function definition for ‘quantile’
PomaVolcano: no visible binding for global variable ‘logFC’
PomaVolcano: no visible binding for global variable ‘pvalue’
PomaVolcano: no visible binding for global variable ‘feature’
create_mock_data: no visible global function definition for ‘runif’
create_mock_summarized_experiment: no visible global function
  definition for ‘runif’
help_extract: no visible global function definition for
  ‘capture.output’
make_legend: no visible binding for global variable ‘POMA’
title_extract: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  . Comparison Dim1 Dim2 IQR MeanDecreaseGini OOB OddsRatio P.Value
  P.adj P.value PC1 PC2 PCoA1 PCoA2 POMA TukeyHSD UMAP1 UMAP2 V1 V2
  adj.P.Val adj.p.value adj_pvalue aggregate anova aov as.formula
  capture.output chull clust column comp comp1 comp2 component
  conf.high conf.low contrast cor corr diff_means error estimate
  feature feature1 feature_sd fold_change gene.index group group_factor
  groups grp is kruskal.test kw_rank_sum limit lm logFC lwr median
  median_rank name out p p adj p.adjust p.value padj prcomp predict
  pvalue quantile reorder runif sample_id sd statistic std.error
  std_err t.test term to_x to_y upr validObject value var var_exp
  variance_percent vcov wilcox.test
Consider adding
  importFrom("grDevices", "chull")
  importFrom("methods", "is", "validObject")
  importFrom("stats", "IQR", "TukeyHSD", "aggregate", "anova", "aov",
             "as.formula", "cor", "kruskal.test", "lm", "median",
             "p.adjust", "prcomp", "predict", "quantile", "reorder",
             "runif", "sd", "t.test", "var", "vcov", "wilcox.test")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘POMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PomaUnivariate
> ### Title: Univariate Statistical Test
> ### Aliases: PomaUnivariate
> 
> ### ** Examples
> 
> data("st000336")
> 
> # Perform T-test
> st000336 %>% 
+ PomaImpute() %>% 
+ PomaUnivariate(method = "ttest")
method argument is empty. KNN will be used
Error in t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided",  : 
  cannot use 'paired' in formula method
Calls: %>% ... data.frame -> apply -> FUN -> t.test -> t.test.formula
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    7. │   └─POMA (local) FUN(newX[, i], ...)
    8. │     ├─stats::t.test(...)
    9. │     └─stats:::t.test.formula(...)
   10. ├─dplyr::as_tibble(.)
   11. ├─dplyr::arrange(., pvalue)
   12. ├─dplyr::select(...)
   13. ├─dplyr::mutate(...)
   14. ├─dplyr::bind_cols(., group_means, group_sd)
   15. │ └─rlang::list2(...)
   16. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
   17. └─tibble::rownames_to_column(., "feature")
  
  [ FAIL 7 | WARN 39 | SKIP 6 | PASS 202 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL POMA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘POMA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (POMA)

R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(POMA)
Welcome to POMA!
Version 1.13.22
POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
> 
> test_check("POMA")
Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  No genes called significant under class1 < class2 

No genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

No genes called significant under class1 > class2 

[ FAIL 7 | WARN 39 | SKIP 6 | PASS 202 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• This test is skipped. (6): 'test-PomaLMM.R:3:3', 'test-PomaLMM.R:12:3',
  'test-PomaLMM.R:18:3', 'test-PomaLMM.R:27:3', 'test-PomaLMM.R:34:3',
  'test-PomaLMM.R:40:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-PomaUnivariate.R:4:3'): PomaUnivariate handles valid SummarizedExperiment objects ──
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─POMA::PomaUnivariate(data, method = "ttest") at test-PomaUnivariate.R:4:3
  2. │ ├─... %>% dplyr::as_tibble()
  3. │ ├─base::data.frame(...)
  4. │ └─base::apply(...)
  5. │   └─POMA (local) FUN(newX[, i], ...)
  6. │     ├─stats::t.test(...)
  7. │     └─stats:::t.test.formula(...)
  8. ├─dplyr::as_tibble(.)
  9. ├─dplyr::arrange(., pvalue)
 10. ├─dplyr::select(...)
 11. ├─dplyr::mutate(...)
 12. ├─dplyr::bind_cols(., group_means, group_sd)
 13. │ └─rlang::list2(...)
 14. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 15. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaUnivariate.R:17:5'): PomaUnivariate handles different methods correctly for 2 groups ──
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─POMA::PomaUnivariate(data, method = method) at test-PomaUnivariate.R:17:5
  2. │ ├─... %>% dplyr::as_tibble()
  3. │ ├─base::data.frame(...)
  4. │ └─base::apply(...)
  5. │   └─POMA (local) FUN(newX[, i], ...)
  6. │     ├─stats::t.test(...)
  7. │     └─stats:::t.test.formula(...)
  8. ├─dplyr::as_tibble(.)
  9. ├─dplyr::arrange(., pvalue)
 10. ├─dplyr::select(...)
 11. ├─dplyr::mutate(...)
 12. ├─dplyr::bind_cols(., group_means, group_sd)
 13. │ └─rlang::list2(...)
 14. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 15. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaUnivariate.R:41:3'): PomaUnivariate handles paired, var_equal, and adjust parameters correctly ──
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─POMA::PomaUnivariate(data_binary_paired, method = "ttest", paired = TRUE) at test-PomaUnivariate.R:41:3
  2. │ ├─... %>% dplyr::as_tibble()
  3. │ ├─base::data.frame(...)
  4. │ └─base::apply(...)
  5. │   └─POMA (local) FUN(newX[, i], ...)
  6. │     ├─stats::t.test(...)
  7. │     └─stats:::t.test.formula(...)
  8. ├─dplyr::as_tibble(.)
  9. ├─dplyr::arrange(., pvalue)
 10. ├─dplyr::select(...)
 11. ├─dplyr::mutate(...)
 12. ├─dplyr::bind_cols(., group_means, group_sd)
 13. │ └─rlang::list2(...)
 14. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 15. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaVolcano.R:3:3'): PomaVolcano handles valid data frames ─────
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─... %>% dplyr::select(feature, fold_change, pvalue) at test-PomaVolcano.R:3:3
  2. ├─dplyr::select(., feature, fold_change, pvalue)
  3. ├─POMA::PomaUnivariate(.)
  4. │ ├─... %>% dplyr::as_tibble()
  5. │ ├─base::data.frame(...)
  6. │ └─base::apply(...)
  7. │   └─POMA (local) FUN(newX[, i], ...)
  8. │     ├─stats::t.test(...)
  9. │     └─stats:::t.test.formula(...)
 10. ├─dplyr::as_tibble(.)
 11. ├─dplyr::arrange(., pvalue)
 12. ├─dplyr::select(...)
 13. ├─dplyr::mutate(...)
 14. ├─dplyr::bind_cols(., group_means, group_sd)
 15. │ └─rlang::list2(...)
 16. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 17. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaVolcano.R:13:3'): PomaVolcano handles different pval_cutoff and log2fc_cutoff values ──
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─... %>% dplyr::select(feature, fold_change, pvalue) at test-PomaVolcano.R:13:3
  2. ├─dplyr::select(., feature, fold_change, pvalue)
  3. ├─POMA::PomaUnivariate(.)
  4. │ ├─... %>% dplyr::as_tibble()
  5. │ ├─base::data.frame(...)
  6. │ └─base::apply(...)
  7. │   └─POMA (local) FUN(newX[, i], ...)
  8. │     ├─stats::t.test(...)
  9. │     └─stats:::t.test.formula(...)
 10. ├─dplyr::as_tibble(.)
 11. ├─dplyr::arrange(., pvalue)
 12. ├─dplyr::select(...)
 13. ├─dplyr::mutate(...)
 14. ├─dplyr::bind_cols(., group_means, group_sd)
 15. │ └─rlang::list2(...)
 16. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 17. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaVolcano.R:23:3'): PomaVolcano handles labels parameter correctly ──
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─... %>% dplyr::select(feature, fold_change, pvalue) at test-PomaVolcano.R:23:3
  2. ├─dplyr::select(., feature, fold_change, pvalue)
  3. ├─POMA::PomaUnivariate(.)
  4. │ ├─... %>% dplyr::as_tibble()
  5. │ ├─base::data.frame(...)
  6. │ └─base::apply(...)
  7. │   └─POMA (local) FUN(newX[, i], ...)
  8. │     ├─stats::t.test(...)
  9. │     └─stats:::t.test.formula(...)
 10. ├─dplyr::as_tibble(.)
 11. ├─dplyr::arrange(., pvalue)
 12. ├─dplyr::select(...)
 13. ├─dplyr::mutate(...)
 14. ├─dplyr::bind_cols(., group_means, group_sd)
 15. │ └─rlang::list2(...)
 16. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 17. └─tibble::rownames_to_column(., "feature")
── Error ('test-PomaVolcano.R:33:3'): PomaVolcano handles custom axis labels ───
Error in `t.test.formula(x ~ group_factor, na.rm = TRUE, alternative = "two.sided", 
    var.equal = var_equal, paired = paired_samples)`: cannot use 'paired' in formula method
Backtrace:
     ▆
  1. ├─... %>% dplyr::select(feature, fold_change, pvalue) at test-PomaVolcano.R:33:3
  2. ├─dplyr::select(., feature, fold_change, pvalue)
  3. ├─POMA::PomaUnivariate(.)
  4. │ ├─... %>% dplyr::as_tibble()
  5. │ ├─base::data.frame(...)
  6. │ └─base::apply(...)
  7. │   └─POMA (local) FUN(newX[, i], ...)
  8. │     ├─stats::t.test(...)
  9. │     └─stats:::t.test.formula(...)
 10. ├─dplyr::as_tibble(.)
 11. ├─dplyr::arrange(., pvalue)
 12. ├─dplyr::select(...)
 13. ├─dplyr::mutate(...)
 14. ├─dplyr::bind_cols(., group_means, group_sd)
 15. │ └─rlang::list2(...)
 16. ├─dplyr::mutate(., adj_pvalue = p.adjust(pvalue, method = adjust))
 17. └─tibble::rownames_to_column(., "feature")

[ FAIL 7 | WARN 39 | SKIP 6 | PASS 202 ]
Error: Test failures
Execution halted