Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:41 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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? 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 1478/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
POMA 1.6.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/POMA
git_branch: RELEASE_3_15
git_last_commit: 2ed1380
git_last_commit_date: 2022-04-26 12:07:02 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: POMA
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings POMA_1.6.0.tar.gz
StartedAt: 2022-10-18 21:10:33 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:17:43 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 429.7 seconds
RetCode: 0
Status:   OK  
CheckDir: POMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings POMA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/POMA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.6.0’
* 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
'library' or 'require' calls in package code:
  ‘ggraph’ ‘plotly’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 : <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 ‘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 ‘R’
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 ‘ggraph’
PomaCorr: no visible global function definition for ‘geom_edge_link’
PomaCorr: no visible global function definition for
  ‘scale_edge_colour_gradientn’
PomaCorr: no visible global function definition for ‘geom_node_point’
PomaCorr: no visible global function definition for ‘geom_node_label’
PomaCorr: no visible global function definition for ‘theme_graph’
PomaCorr: no visible global function definition for ‘na.omit’
PomaCorr: no visible binding for global variable ‘EstimatedCorr’
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 ‘coef’
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 ‘model.matrix’
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’
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 ‘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 ‘is’
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’
PomaOutliers: no visible global function definition for ‘validObject’
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 binding for global variable
  ‘group’
PomaSummarizedExperiment: no visible global function definition for
  ‘validObject’
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 ‘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 ‘pvalue’
PomaVolcano: no visible binding for global variable ‘threshold’
Undefined global functions or variables:
  . CIHigh CILow Dim1 Dim2 EstimatedCorr FC Group Groups ID IQR
  MeanDecreaseGini OOB OddsRatio P.value PC1 PC2 PCoA1 PCoA2 R V1 V2
  X2.5.. X97.5.. adj.P.Val aggregate anova aov as.formula binomial
  chull clust cmdscale coef column comp1 comp2 component conf.high
  conf.low confint.default cor diff_means dist estimate feature
  feature1 feature_sd gene.index geom_edge_link geom_node_label
  geom_node_point ggraph glm group is kmeans kruskal.test kw_rank_sum
  median model.matrix na.omit name new_names out p p.adjust pc_var_exp
  predict pvalue pvalueAdj quantile real_names reorder
  scale_edge_colour_gradientn sd t.test term theme_graph threshold to_x
  to_y validObject value var wilcox.test x
Consider adding
  importFrom("grDevices", "chull")
  importFrom("methods", "is", "validObject")
  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 (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 19.516  0.229  19.778
PomaBoxplots      6.479  0.167   6.647
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/POMA.Rcheck/00check.log’
for details.



Installation output

POMA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL POMA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1.6.0
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 676 | SKIP 0 | PASS 310 ]

[ FAIL 0 | WARN 676 | SKIP 0 | PASS 310 ]
> 
> proc.time()
   user  system elapsed 
191.028   2.405 193.474 

Example timings

POMA.Rcheck/POMA-Ex.timings

nameusersystemelapsed
PomaBoxplots6.4790.1676.647
PomaClust0.5120.0320.543
PomaCorr1.3040.0201.324
PomaDensity2.4570.0192.477
PomaHeatmap1.3370.0201.358
PomaImpute0.0610.0030.066
PomaLasso1.9820.0161.998
PomaLimma0.1490.0000.149
PomaMultivariate19.516 0.22919.778
PomaNorm0.0720.0040.075
PomaOddsRatio0.2600.0040.264
PomaOutliers0.6380.0040.642
PomaRandForest0.3430.0040.346
PomaSummarizedExperiment0.0170.0030.020
PomaUnivariate1.0790.0641.142
PomaVolcano0.4280.0080.436