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BioC 3.4: CHECK report for a4Base on morelia

This page was generated on 2016-09-21 03:51:02 -0700 (Wed, 21 Sep 2016).

Package 2/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.21.0
Tobias Verbeke , Willem Ligtenberg
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Base
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Base
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings a4Base_1.21.0.tar.gz
StartedAt: 2016-09-20 02:48:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 02:51:04 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 158.1 seconds
RetCode: 0
Status:  OK 
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings a4Base_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/a4Base.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.21.0’
* 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 ... OK
* 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 ‘plot’
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 ‘plot’
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 ‘plot’
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 plot
  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", "plot", "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 or elapsed time > 5s
                 user system elapsed
spectralMap     8.796  0.605   9.501
computeLogRatio 7.113  0.174   7.823
plotLogRatio    6.859  0.116   7.020
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/a4Base.Rcheck/00check.log’
for details.

a4Base.Rcheck/00install.out:

* installing *source* package ‘a4Base’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (a4Base)

a4Base.Rcheck/a4Base-Ex.timings:

nameusersystemelapsed
a4palette0.0110.0000.010
addQuantilesColors2.0740.1362.210
boxPlot2.2850.0862.372
combineTwoExpressionSet0.0010.0000.001
computeLogRatio7.1130.1747.823
createExpressionSet0.0610.0010.061
filterVarInt2.2010.0872.289
heatmap.expressionSet0.0030.0010.004
histPvalue2.0660.0632.366
histpvalueplotter1.9740.0642.124
lassoReg1.7180.0451.776
logReg0.0010.0000.001
nlcvTT000
plot1gene1.9770.0662.200
plotComb2Samples2.2090.0632.370
plotCombMultSamples1.8460.0772.767
plotCombination2genes2.0070.0442.053
plotLogRatio6.8590.1167.020
probabilitiesPlot0.0010.0010.001
probe2gene2.0620.0542.117
profilesPlot1.8410.0551.907
propdegenescalculation1.8390.0631.905
replicates0.0010.0000.002
spectralMap8.7960.6059.501
tTest1.9920.0642.084
volcanoPlot2.1530.0962.274