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CHECK report for a4Base on malbec1

This page was generated on 2020-08-10 11:35:12 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE a4Base PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 2/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.37.0
Tobias Verbeke
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/a4Base
Branch: master
Last Commit: a12798d
Last Changed Date: 2020-04-27 14:25:17 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Base
Version: 1.37.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Base_1.37.0.tar.gz
StartedAt: 2020-08-09 23:28:32 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 23:31:25 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 173.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: a4Base.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Base_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘JavaGD’

Depends: includes the non-default packages:
  'grid', 'Biobase', 'AnnotationDbi', 'annaffy', 'mpm', 'genefilter',
  'limma', 'multtest', 'glmnet', 'a4Preproc', 'a4Core', 'gplots'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘a4Base’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 to packages already attached by Depends:
  ‘Biobase’ ‘grid’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Cairo’ ‘gridSVG’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘a4Preproc’ ‘annaffy’ ‘genefilter’ ‘glmnet’ ‘gplots’
  ‘grid’ ‘mpm’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
a4palette: no visible global function definition for ‘rgb’
a4palette: no visible global function definition for ‘rainbow’
addQuantilesColors: no visible global function definition for
  ‘quantile’
boxPlot: no visible global function definition for ‘boxplot’
boxPlot: no visible global function definition for ‘points’
boxPlot: no visible global function definition for ‘legend’
fTest: no visible global function definition for ‘rowFtests’
fTest: no visible global function definition for ‘mt.rawp2adjp’
filterVarInt: no visible global function definition for ‘pOverA’
filterVarInt : f2: no visible global function definition for ‘IQR’
filterVarInt: no visible global function definition for ‘filterfun’
filterVarInt: no visible global function definition for ‘genefilter’
grid.imageGrob: no visible global function definition for ‘grid.draw’
heatmap.expressionSet: no visible global function definition for ‘unit’
heatmap.expressionSet: no visible global function definition for ‘gpar’
heatmap.expressionSet: no visible global function definition for ‘rgb’
heatmap.expressionSet: no visible binding for global variable ‘dist’
heatmap.expressionSet : <anonymous>: no visible global function
  definition for ‘hclust’
heatmap.expressionSet: no visible global function definition for
  ‘as.dendrogram’
heatmap.expressionSet: no visible global function definition for
  ‘cutree’
heatmap.expressionSet: no visible global function definition for
  ‘reorder’
heatmap.expressionSet: no visible global function definition for
  ‘order.dendrogram’
heatmap.expressionSet: no visible global function definition for
  ‘aggregate’
heatmap.expressionSet: no visible global function definition for
  ‘col2rgb’
heatmap.expressionSet : <anonymous>: no visible global function
  definition for ‘colorpanel’
heatmap.expressionSet: no visible global function definition for
  ‘textGrob’
heatmap.expressionSet: no visible global function definition for
  ‘grid.layout’
heatmap.expressionSet: no visible global function definition for
  ‘grid.newpage’
heatmap.expressionSet: no visible global function definition for
  ‘convertUnit’
heatmap.expressionSet: no visible global function definition for
  ‘viewport’
heatmap.expressionSet: no visible global function definition for
  ‘pushViewport’
heatmap.expressionSet: no visible global function definition for
  ‘grid.text’
heatmap.expressionSet: no visible global function definition for
  ‘grid.rect’
heatmap.expressionSet: no visible global function definition for
  ‘popViewport’
heatmap.expressionSet: no visible global function definition for
  ‘unit.c’
heatmap.expressionSet: no visible global function definition for
  ‘grid.lines’
heatmap.expressionSet: no visible global function definition for
  ‘grid.xaxis’
histpvalueplotter: no visible global function definition for ‘hist’
histpvalueplotter: no visible global function definition for ‘abline’
histpvalueplotter: no visible global function definition for ‘legend’
imageGrob: no visible global function definition for ‘gTree’
imageGrob: no visible global function definition for ‘gList’
lassoReg: no visible global function definition for ‘glmnet’
limmaTwoLevels: no visible global function definition for
  ‘model.matrix’
logReg: no visible global function definition for ‘glm’
logReg: no visible global function definition for ‘fitted’
logReg: no visible global function definition for ‘par’
logReg: no visible global function definition for ‘lines’
logReg: no visible global function definition for ‘axis’
logReg: no visible global function definition for ‘box’
makeImageRect: no visible global function definition for ‘rectGrob’
makeImageRect: no visible global function definition for ‘gpar’
oaColors: no visible global function definition for ‘hcl’
oaColors: no visible global function definition for ‘rainbow’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘cor.test’
panel.cor: no visible global function definition for ‘symnum’
panel.cor: no visible global function definition for ‘text’
panel.plotSmoothScat: no visible global function definition for
  ‘points’
panel.plotSmoothScat: no visible global function definition for
  ‘densCols’
panel.plotSmoothScat: no visible global function definition for
  ‘abline’
plot1gene: no visible global function definition for ‘points’
plot1gene: no visible global function definition for ‘axis’
plot1gene: no visible global function definition for ‘mtext’
plot1gene: no visible global function definition for ‘lines’
plot1gene: no visible global function definition for ‘legend’
plotComb2Samples: no visible global function definition for ‘axis’
plotComb2Samples: no visible global function definition for ‘box’
plotComb2Samples: no visible global function definition for ‘densCols’
plotComb2Samples: no visible global function definition for ‘points’
plotComb2Samples: no visible global function definition for ‘text’
plotCombMultSamples: no visible global function definition for ‘pairs’
plotCombination2genes: no visible global function definition for
  ‘points’
plotCombination2genes: no visible global function definition for
  ‘legend’
plotLogRatio: no visible global function definition for ‘addGeneInfo’
plotLogRatio: no visible global function definition for ‘hclust’
plotLogRatio: no visible global function definition for ‘dist’
plotLogRatio : <anonymous>: no visible global function definition for
  ‘quantile’
plotLogRatio: no visible global function definition for ‘rainbow’
plotLogRatio: no visible global function definition for ‘x11’
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘pdf’
plotLogRatio: no visible global function definition for ‘png’
plotLogRatio: no visible global function definition for ‘CairoPNG’
plotLogRatio: no visible global function definition for ‘viewport’
plotLogRatio: no visible global function definition for ‘grid.layout’
plotLogRatio: no visible global function definition for ‘pushViewport’
plotLogRatio: no visible global function definition for ‘grid.rect’
plotLogRatio: no visible global function definition for ‘gpar’
plotLogRatio: no visible global function definition for ‘grid.text’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for ‘popViewport’
plotLogRatio: no visible global function definition for ‘colors’
plotLogRatio: no visible global function definition for ‘grid.lines’
plotLogRatio : <anonymous>: no visible global function definition for
  ‘grid.lines’
plotLogRatio : <anonymous>: no visible global function definition for
  ‘gpar’
plotLogRatio: no visible global function definition for ‘grid.segments’
plotLogRatio: no visible global function definition for
  ‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘gPath’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
plotLogRatio: no visible global function definition for ‘browseURL’
plotLogRatio: no visible global function definition for ‘dev.off’
probabilitiesPlot: no visible global function definition for ‘par’
probabilitiesPlot: no visible global function definition for ‘axis’
probabilitiesPlot: no visible global function definition for ‘abline’
probabilitiesPlot: no visible global function definition for ‘points’
probabilitiesPlot: no visible global function definition for ‘title’
probabilitiesPlot: no visible global function definition for ‘rgb’
probabilitiesPlot: no visible global function definition for ‘rect’
probabilitiesPlot: no visible global function definition for ‘barplot’
probe2gene: no visible global function definition for ‘aafSymbol’
probe2gene: no visible global function definition for ‘getText’
profilesPlot: no visible global function definition for ‘matplot’
profilesPlot: no visible global function definition for ‘axis’
profilesPlot: no visible global function definition for ‘legend’
tTest: no visible global function definition for ‘rowttests’
tTest: no visible global function definition for ‘mt.rawp2adjp’
tTest2 : ttestfun: no visible global function definition for ‘t.test’
tTest2: no visible global function definition for ‘rowttests’
tTest2: no visible global function definition for ‘mt.rawp2adjp’
volcanoplotter: no visible global function definition for
  ‘grid.newpage’
volcanoplotter: no visible global function definition for
  ‘plotViewport’
volcanoplotter: no visible global function definition for
  ‘pushViewport’
volcanoplotter: no visible global function definition for ‘textGrob’
volcanoplotter: no visible global function definition for ‘unit’
volcanoplotter: no visible global function definition for ‘gpar’
volcanoplotter: no visible global function definition for ‘grobWidth’
volcanoplotter: no visible global function definition for
  ‘convertHeight’
volcanoplotter: no visible global function definition for
  ‘dataViewport’
volcanoplotter: no visible global function definition for ‘grid.pretty’
volcanoplotter: no visible global function definition for
  ‘current.viewport’
volcanoplotter: no visible global function definition for ‘xaxisGrob’
volcanoplotter: no visible global function definition for ‘grid.yaxis’
volcanoplotter: no visible global function definition for ‘editGrob’
volcanoplotter: no visible global function definition for ‘gEditList’
volcanoplotter: no visible global function definition for ‘gEdit’
volcanoplotter: no visible global function definition for ‘grid.draw’
volcanoplotter: no visible global function definition for ‘densCols’
volcanoplotter: no visible global function definition for ‘grid.points’
volcanoplotter: no visible global function definition for ‘grid.text’
spectralMap,ExpressionSet-character: no visible global function
  definition for ‘na.omit’
spectralMap,ExpressionSet-character: no visible global function
  definition for ‘par’
spectralMap,ExpressionSet-character: no visible global function
  definition for ‘legend’
topTable,MArrayLM: no visible global function definition for
  ‘topTableF’
topTable,MArrayLM: no visible binding for global variable ‘number’
topTable,MArrayLM: no visible global function definition for ‘toptable’
topTable,fTest: no visible global function definition for ‘head’
topTable,limma: no visible global function definition for ‘topTableF’
topTable,limma: no visible binding for global variable ‘number’
topTable,limma: no visible global function definition for ‘toptable’
topTable,tTest: no visible global function definition for ‘head’
Undefined global functions or variables:
  CairoPNG IQR JavaGD aafSymbol abline addGeneInfo aggregate
  as.dendrogram axis barplot box boxplot browseURL col2rgb colorpanel
  colors convertHeight convertUnit cor cor.test current.viewport cutree
  dataViewport densCols dev.off dist editGrob filterfun fitted gEdit
  gEditList gList gPath gTree genefilter getText glm glmnet gpar
  grid.draw grid.garnish grid.hyperlink grid.layout grid.lines
  grid.newpage grid.points grid.pretty grid.rect grid.script
  grid.segments grid.text grid.xaxis grid.yaxis gridToSVG grobWidth hcl
  hclust head hist legend lines matplot model.matrix mt.rawp2adjp mtext
  na.omit number order.dendrogram pOverA pairs par pdf plotViewport png
  points popViewport pushViewport quantile rainbow rect rectGrob
  reorder rgb rowFtests rowttests strwidth symnum t.test text textGrob
  title topTableF toptable unit unit.c viewport x11 xaxisGrob
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "densCols", "dev.off",
             "hcl", "pdf", "png", "rainbow", "rgb", "x11")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "hist", "legend", "lines", "matplot", "mtext", "pairs",
             "par", "points", "rect", "strwidth", "text", "title")
  importFrom("stats", "IQR", "aggregate", "as.dendrogram", "cor",
             "cor.test", "cutree", "dist", "fitted", "glm", "hclust",
             "model.matrix", "na.omit", "order.dendrogram", "quantile",
             "reorder", "symnum", "t.test")
  importFrom("utils", "browseURL", "head")
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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
spectralMap     10.552  0.216  10.779
plotLogRatio     5.544  0.040   5.589
computeLogRatio  5.220  0.108   5.331
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Base.Rcheck/00check.log’
for details.



Installation output

a4Base.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL a4Base
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘a4Base’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (a4Base)

Tests output


Example timings

a4Base.Rcheck/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.0320.0000.035
addQuantilesColors2.0480.0682.118
boxPlot2.5480.0402.602
combineTwoExpressionSet000
computeLogRatio5.2200.1085.331
createExpressionSet0.0320.0000.033
filterVarInt2.1960.0402.240
heatmap.expressionSet0.0000.0000.001
histPvalue1.9480.0281.978
histpvalueplotter1.9400.0241.965
lassoReg1.9920.0322.024
logReg000
nlcvTT000
plot1gene1.9440.0321.979
plotComb2Samples2.5520.0442.603
plotCombMultSamples2.8480.0482.899
plotCombination2genes2.6080.0362.651
plotLogRatio5.5440.0405.589
probabilitiesPlot000
probe2gene1.6000.0161.617
profilesPlot2.0600.0202.079
propdegenescalculation2.2200.0522.284
replicates0.0040.0000.003
spectralMap10.552 0.21610.779
tTest2.2720.0402.313
volcanoPlot2.5600.0282.596