Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:37:57 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1573/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POMA 1.12.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/POMA
git_branch: RELEASE_3_18
git_last_commit: 6e2f5bc
git_last_commit_date: 2024-02-10 21:44:51 -0400 (Sat, 10 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for POMA on merida1


To the developers/maintainers of the POMA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/POMA.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-03-26 06:49:02 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 07:02:00 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 778.3 seconds
RetCode: 0
Status:   OK  
CheckDir: POMA.Rcheck
Warnings: 0

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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/POMA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.12.0’
* 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 53.434  0.432  59.776
PomaBoxplots     35.290  0.962  41.193
PomaVolcano      11.927  0.064  13.057
PomaDESeq        10.907  0.070  11.770
PomaDensity       5.996  0.240   6.866
PomaLasso         4.494  0.077   5.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/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-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)

Tests output

POMA.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 1.12.0
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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comp 2 

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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 0 | WARN 692 | SKIP 0 | PASS 312 ]

[ FAIL 0 | WARN 692 | SKIP 0 | PASS 312 ]
> 
> proc.time()
   user  system elapsed 
484.469  12.239 524.186 

Example timings

POMA.Rcheck/POMA-Ex.timings

nameusersystemelapsed
PomaBoxplots35.290 0.96241.193
PomaClust1.0290.0161.122
PomaCorr3.5210.0853.974
PomaDESeq10.907 0.07011.770
PomaDensity5.9960.2406.866
PomaHeatmap4.0330.1064.611
PomaImpute0.1240.0060.139
PomaLasso4.4940.0775.014
PomaLimma0.7220.0090.818
PomaMultivariate53.434 0.43259.776
PomaNorm0.1670.0050.189
PomaOddsRatio0.6180.0090.679
PomaOutliers1.5040.0141.626
PomaPCR0.7010.0120.756
PomaRandForest0.8720.0120.948
PomaRankProd3.2830.0463.832
PomaSummarizedExperiment0.0500.0040.060
PomaUMAP4.3380.0334.809
PomaUnivariate2.3570.0252.586
PomaVolcano11.927 0.06413.057