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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings POMA_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/POMA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.14.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
PomaUnivariate 39.292  0.200  39.492
PomaBoxplots   14.778  0.464  15.244
PomaPLS        14.149  0.231  14.420
PomaLMM        12.545  0.092  12.636
PomaBatch      11.256  0.444  11.699
PomaHeatmap     5.946  0.116   6.061
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL POMA
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 1.14.0
POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
> 
> test_check("POMA")
Rank Product analysis for unpaired case 
 

 done  Table1: 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  No genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

[ FAIL 0 | WARN 52 | SKIP 6 | PASS 209 ]

══ 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'

[ FAIL 0 | WARN 52 | SKIP 6 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
 54.731   1.305  56.027