Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:08:09 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for POMA on machv2


To the developers/maintainers of the POMA package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1440/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POMA 1.4.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/POMA
git_branch: RELEASE_3_14
git_last_commit: c549d40
git_last_commit_date: 2021-10-26 13:01:27 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: POMA
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-01-23 16:34:11 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:45:52 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 700.4 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/POMA.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.4.0’
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
* 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 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 : <anonymous>: no visible global function definition for
  ‘kmeans’
PomaClust: no visible global function definition for ‘kmeans’
PomaClust: no visible global function definition for ‘dist’
PomaClust: no visible global function definition for ‘cmdscale’
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 ‘cor’
PomaCorr: no visible global function definition for ‘na.omit’
PomaCorr: no visible binding for global variable ‘corr’
PomaCorr: no visible binding for global variable ‘name’
PomaCorr: no visible binding for global variable ‘EstimatedCorr’
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’
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’
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 ‘coef’
PomaLasso: no visible global function definition for ‘predict’
PomaLasso: no visible binding for global variable ‘term’
PomaLimma: no visible global function definition for ‘model.matrix’
PomaLimma: no visible binding for global variable ‘adj.P.Val’
PomaLimma: no visible global function definition for ‘as.formula’
PomaMSnSetClass: no visible binding for global variable ‘group’
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
  ‘Principal_Component’
PomaMultivariate: no visible binding for global variable
  ‘Percent_Variance_Explained’
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 ‘Component’
PomaMultivariate: no visible binding for global variable ‘value’
PomaMultivariate: no visible binding for global variable ‘name’
PomaMultivariate: no visible binding for global variable ‘feature’
PomaMultivariate: no visible binding for global variable ‘features’
PomaMultivariate: no visible binding for global variable ‘features_sd’
PomaMultivariate: no visible binding for global variable ‘sd’
PomaNorm: no visible binding for global variable ‘var’
PomaNorm : <anonymous>: no visible global function definition for ‘sd’
PomaOddsRatio: no visible binding for global variable ‘Group’
PomaOddsRatio: no visible global function definition for ‘glm’
PomaOddsRatio: no visible global function definition for ‘binomial’
PomaOddsRatio: no visible global function definition for ‘coef’
PomaOddsRatio: no visible global function definition for
  ‘confint.default’
PomaOddsRatio: no visible binding for global variable ‘X2.5..’
PomaOddsRatio: no visible binding for global variable ‘X97.5..’
PomaOddsRatio: no visible binding for global variable ‘OddsRatio’
PomaOddsRatio: no visible binding for global variable ‘feature’
PomaOddsRatio: no visible binding for global variable ‘CIHigh’
PomaOddsRatio: no visible binding for global variable ‘CILow’
PomaOutliers: no visible global function definition for ‘dist’
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’
PomaRandForest: no visible binding for global variable ‘.’
PomaRandForest: no visible binding for global variable ‘OOB’
PomaRandForest: no visible global function definition for ‘reorder’
PomaRandForest: no visible binding for global variable ‘real_names’
PomaRandForest: no visible binding for global variable
  ‘MeanDecreaseGini’
PomaRankProd: no visible binding for global variable ‘gene.index’
PomaUnivariate: no visible binding for global variable ‘group’
PomaUnivariate : stat: 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 : stat2: no visible global function definition for
  ‘anova’
PomaUnivariate : stat2: no visible global function definition for ‘aov’
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’
PomaVolcano: no visible binding for global variable ‘FC’
PomaVolcano: no visible binding for global variable ‘pvalue’
PomaVolcano: no visible binding for global variable ‘threshold’
Undefined global functions or variables:
  . CIHigh CILow Component Dim1 Dim2 EstimatedCorr FC Group Groups ID
  IQR MeanDecreaseGini OOB OddsRatio PC1 PC2 PCoA1 PCoA2
  Percent_Variance_Explained Principal_Component V1 V2 X2.5.. X97.5..
  adj.P.Val aggregate anova aov as.formula binomial chull clust
  cmdscale coef comp1 comp2 conf.high conf.low confint.default cor corr
  dist estimate feature features features_sd gene.index glm group
  kmeans kruskal.test median model.matrix na.omit name out p.adjust
  predict pvalue quantile real_names reorder sd t.test term threshold
  to_x to_y value var wilcox.test x
Consider adding
  importFrom("grDevices", "chull")
  importFrom("stats", "IQR", "aggregate", "anova", "aov", "as.formula",
             "binomial", "cmdscale", "coef", "confint.default", "cor",
             "dist", "glm", "kmeans", "kruskal.test", "median",
             "model.matrix", "na.omit", "p.adjust", "predict",
             "quantile", "reorder", "sd", "t.test", "var", "wilcox.test")
to your NAMESPACE file.
* 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 38.085  0.212  38.349
PomaBoxplots     14.985  0.271  15.283
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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!
✔ 1.4.0 version
✔ POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
ℹ For more detailed package information please visit https://pcastellanoescuder.github.io/POMA/
> 
> test_check("POMA")

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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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comp 3 

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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 21 | SKIP 0 | PASS 320 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 320 ]
> 
> proc.time()
   user  system elapsed 
334.966   7.795 343.231 

Example timings

POMA.Rcheck/POMA-Ex.timings

nameusersystemelapsed
PomaBoxplots14.985 0.27115.283
PomaClust1.3180.0261.346
PomaCorr0.8640.2581.123
PomaDensity3.5500.0793.637
PomaHeatmap2.5740.0402.616
PomaImpute0.2440.0030.247
PomaLasso3.7110.0383.759
PomaLimma0.2130.0100.223
PomaMSnSetClass0.0940.0020.097
PomaMultivariate38.085 0.21238.349
PomaNorm0.1440.0020.145
PomaOddsRatio0.5320.0050.538
PomaOutliers1.4980.0081.509
PomaRandForest0.5570.0470.607
PomaUnivariate2.1890.0362.227
PomaVolcano0.6500.0040.654