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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1542/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POMA 1.10.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/POMA
git_branch: RELEASE_3_17
git_last_commit: ec14cae
git_last_commit_date: 2023-04-25 11:21:26 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for POMA on kjohnson2


To the developers/maintainers of the POMA package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: POMA
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2023-10-18 15:18:49 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 15:28:30 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 581.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: POMA.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/POMA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.10.0’
* 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 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PomaBoxplots: no visible global function definition for ‘is’
PomaBoxplots: no visible binding for global variable ‘ID’
PomaBoxplots: no visible binding for global variable ‘Group’
PomaBoxplots: no visible binding for global variable ‘value’
PomaBoxplots: no visible binding for global variable ‘name’
PomaClust: no visible global function definition for ‘is’
PomaClust: no visible binding for global variable ‘group’
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’
PomaCorr: no visible global function definition for ‘na.omit’
PomaCorr: no visible binding for global variable ‘est_corr’
PomaDESeq: no visible global function definition for ‘is’
PomaDESeq: no visible binding for global variable ‘padj’
PomaDensity: no visible global function definition for ‘is’
PomaDensity: no visible binding for global variable ‘ID’
PomaDensity: no visible binding for global variable ‘Group’
PomaDensity: no visible binding for global variable ‘value’
PomaDensity: no visible binding for global variable ‘name’
PomaEDA: no visible global function definition for ‘is’
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’
PomaImpute : <anonymous>: no visible global function definition for
  ‘median’
PomaImpute: no visible binding for global variable ‘group’
PomaImpute: no visible global function definition for ‘validObject’
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 binding for global variable ‘adj.P.Val’
PomaLimma: no visible global function definition for ‘as.formula’
PomaMultivariate: no visible global function definition for ‘is’
PomaMultivariate: no visible binding for global variable ‘PC1’
PomaMultivariate: no visible binding for global variable ‘PC2’
PomaMultivariate: no visible binding for global variable ‘Groups’
PomaMultivariate: no visible binding for global variable ‘ID’
PomaMultivariate: no visible global function definition for ‘reorder’
PomaMultivariate: no visible binding for global variable ‘component’
PomaMultivariate: no visible binding for global variable ‘pc_var_exp’
PomaMultivariate: no visible binding for global variable ‘feature’
PomaMultivariate: no visible binding for global variable ‘value’
PomaMultivariate: no visible binding for global variable ‘name’
PomaMultivariate: no visible binding for global variable ‘to_x’
PomaMultivariate: no visible binding for global variable ‘to_y’
PomaMultivariate: no visible binding for global variable ‘comp1’
PomaMultivariate: no visible binding for global variable ‘comp2’
PomaMultivariate: no visible binding for global variable ‘feature_sd’
PomaMultivariate: no visible binding for global variable ‘sd’
PomaMultivariate: no visible binding for global variable ‘value.var’
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 global function definition for ‘matches’
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 global function definition for ‘aggregate’
PomaOutliers : <anonymous>: no visible global function definition for
  ‘quantile’
PomaOutliers : <anonymous>: no visible global function definition for
  ‘IQR’
PomaOutliers: no visible binding for global variable ‘x’
PomaOutliers: no visible binding for global variable ‘out’
PomaOutliers: no visible binding for global variable ‘Groups’
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’
PomaPCR: no visible global function definition for ‘is’
PomaPCR: no visible global function definition for ‘prcomp’
PomaPCR: no visible binding for global variable ‘feature’
PomaPCR: no visible binding for global variable ‘PC1’
PomaPCR: no visible global function definition for ‘lm’
PomaRandForest: no visible global function definition for ‘is’
PomaRandForest: no visible binding for global variable ‘.’
PomaRandForest: no visible binding for global variable ‘Group’
PomaRandForest: no visible binding for global variable ‘OOB’
PomaRandForest: no visible binding for global variable
  ‘MeanDecreaseGini’
PomaRandForest: no visible binding for global variable ‘real_names’
PomaRandForest: no visible global function definition for ‘reorder’
PomaRandForest: no visible binding for global variable ‘feature’
PomaRandForest: no visible binding for global variable ‘new_names’
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’
PomaSummarizedExperiment: no visible global function definition for
  ‘validObject’
PomaUMAP: no visible global function definition for ‘is’
PomaUMAP: no visible binding for global variable ‘group’
PomaUMAP: no visible binding for global variable ‘UMAP1’
PomaUMAP: no visible binding for global variable ‘UMAP2’
PomaUMAP: no visible binding for global variable ‘clust’
PomaUnivariate: no visible global function definition for ‘is’
PomaUnivariate: no visible binding for global variable ‘group’
PomaUnivariate : stat_ttest: 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 ‘FC’
PomaUnivariate: no visible binding for global variable ‘diff_means’
PomaUnivariate: no visible binding for global variable ‘pvalueAdj’
PomaUnivariate : stat_aov: no visible global function definition for
  ‘anova’
PomaUnivariate : stat_aov: no visible global function definition for
  ‘aov’
PomaUnivariate: no visible global function definition for ‘colData’
PomaUnivariate: no visible global function definition for ‘anova’
PomaUnivariate: no visible global function definition for ‘aov’
PomaUnivariate: no visible global function definition for ‘as.formula’
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’
PomaVolcano: no visible global function definition for ‘is’
PomaVolcano: no visible binding for global variable ‘FC’
PomaVolcano: no visible binding for global variable ‘P.Value’
PomaVolcano: no visible binding for global variable ‘adj.P.Val’
PomaVolcano: no visible binding for global variable ‘log2FoldChange’
PomaVolcano: no visible binding for global variable ‘padj’
PomaVolcano: no visible binding for global variable ‘logFC’
PomaVolcano: no visible binding for global variable ‘pvalue’
PomaVolcano: no visible binding for global variable ‘threshold’
Undefined global functions or variables:
  . Dim1 Dim2 FC Group Groups ID IQR MeanDecreaseGini OOB OddsRatio
  P.Value P.value PC1 PC2 PCoA1 PCoA2 UMAP1 UMAP2 V1 V2 adj.P.Val
  aggregate anova aov as.formula chull clust colData column comp1 comp2
  component conf.high conf.low cor corr diff_means est_corr estimate
  feature feature1 feature_sd gene.index group is kruskal.test
  kw_rank_sum lm log2FoldChange logFC lwr matches median na.omit name
  new_names out p p.adjust padj pc_var_exp prcomp predict pvalue
  pvalueAdj quantile real_names reorder sd t.test term threshold to_x
  to_y upr validObject value value.var var wilcox.test x
Consider adding
  importFrom("grDevices", "chull")
  importFrom("methods", "is", "validObject")
  importFrom("stats", "IQR", "aggregate", "anova", "aov", "as.formula",
             "cor", "kruskal.test", "lm", "median", "na.omit",
             "p.adjust", "prcomp", "predict", "quantile", "reorder",
             "sd", "t.test", "var", "wilcox.test")
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
PomaMultivariate 27.858  0.439  41.699
PomaBoxplots     18.625  0.607  29.536
PomaVolcano       7.663  0.173  12.048
PomaDESeq         6.191  0.072   9.539
PomaDensity       4.609  0.083   7.204
PomaUMAP          3.226  0.037   5.003
* 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:
   done  Table1: Genes called significant under class1 < class2 
  
  Table2: Genes called significant under class1 > class2 
  
  [ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-PomaClust.R:49:3'): PomaClust works ──────────────────────────
  g$optimum_cluster_num not equal to h$optimum_cluster_num.
  1/1 mismatches
  [1] 8 - 9 == -1
  
  [ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/POMA.Rcheck/00check.log’
for details.


Installation output

POMA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

POMA.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 1.10.0
POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
For more detailed package information please visit https://pcastellanoescuder.github.io/POMA/
> 
> test_check("POMA")

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comp 1 

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comp 2 

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comp 3 

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comp 4 

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comp 1 

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comp 2 

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comp 3 

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comp 1 

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comp 2 

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comp 3 

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comp 4 

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comp 1 

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Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

Rank Product analysis for unpaired case 
 

 done  Table1: Genes called significant under class1 < class2 

Table2: Genes called significant under class1 > class2 

[ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-PomaClust.R:49:3'): PomaClust works ──────────────────────────
g$optimum_cluster_num not equal to h$optimum_cluster_num.
1/1 mismatches
[1] 8 - 9 == -1

[ FAIL 1 | WARN 692 | SKIP 0 | PASS 311 ]
Error: Test failures
Execution halted

Example timings

POMA.Rcheck/POMA-Ex.timings

nameusersystemelapsed
PomaBoxplots18.625 0.60729.536
PomaClust0.7170.0151.104
PomaCorr1.7540.0422.737
PomaDESeq6.1910.0729.539
PomaDensity4.6090.0837.204
PomaHeatmap2.6060.0844.082
PomaImpute0.0670.0030.089
PomaLasso2.4970.0663.258
PomaLimma0.3660.0070.474
PomaMultivariate27.858 0.43941.699
PomaNorm0.0860.0020.135
PomaOddsRatio0.3770.0070.585
PomaOutliers1.0230.0161.541
PomaPCR0.4080.0070.614
PomaRandForest0.5800.0130.865
PomaRankProd1.6820.0392.659
PomaSummarizedExperiment0.0350.0030.056
PomaUMAP3.2260.0375.003
PomaUnivariate1.5670.0362.475
PomaVolcano 7.663 0.17312.048