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BioC 3.5: CHECK report for RNAither on toluca2

This page was generated on 2017-04-23 14:34:37 -0400 (Sun, 23 Apr 2017).

Package 1124/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAither 2.23.0
Lars Kaderali
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAither
Version: 2.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.23.0.tar.gz
StartedAt: 2017-04-23 09:14:02 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 09:19:21 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 318.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAither.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RNAither.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.23.0’
* 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 ‘RNAither’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RankProd’
  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
BScore: no visible global function definition for ‘medpolish’
BScore: no visible global function definition for ‘mad’
DRQualControl: no visible global function definition for ‘write.table’
DRQualControl: no visible global function definition for ‘axis’
DRQualControl: no visible global function definition for ‘pdf’
DRQualControl: no visible global function definition for ‘dev.off’
LiWongRank: no visible global function definition for ‘sd’
LiWongRank: no visible global function definition for ‘hist’
MannWhitney: no visible global function definition for ‘var’
MannWhitney: no visible global function definition for ‘wilcox.test’
PlotSpatialDistrib: no visible global function definition for ‘jpeg’
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
PlotSpatialDistrib: no visible global function definition for ‘dev.off’
RankProduct: no visible global function definition for ‘RP’
SNRQualControl: no visible global function definition for ‘read.table’
SNRQualControl: no visible global function definition for ‘hist’
SNRQualControl: no visible global function definition for ‘x11’
SNRQualControl: no visible global function definition for ‘par’
SNRQualControl: no visible global function definition for ‘pdf’
SNRQualControl: no visible global function definition for ‘dev.off’
Ttest: no visible global function definition for ‘var’
Ttest: no visible global function definition for ‘t.test’
ZPRIMEQualControl: no visible global function definition for
  ‘write.table’
ZPRIMEQualControl: no visible global function definition for ‘axis’
ZPRIMEQualControl: no visible global function definition for ‘pdf’
ZPRIMEQualControl: no visible global function definition for ‘dev.off’
ZPRIMEQualControl: no visible global function definition for ‘png’
ZPRIMEQualControl: no visible global function definition for
  ‘read.table’
ZPrime: no visible global function definition for ‘mad’
ZPrime: no visible global function definition for ‘median’
ZScore: no visible global function definition for ‘mad’
ZScore: no visible global function definition for ‘median’
ZScorePerScreen: no visible global function definition for ‘mad’
ZScorePerScreen: no visible global function definition for ‘median’
ZScorePlot: no visible global function definition for ‘sd’
ZScorePlot: no visible global function definition for ‘axis’
ZScorePlot: no visible global function definition for ‘abline’
ZScorePlot: no visible global function definition for ‘identify’
ZScorePlot: no visible global function definition for ‘pdf’
ZScorePlot: no visible global function definition for ‘dev.off’
ZScorePlot: no visible global function definition for ‘png’
ZScorePlotTwo: no visible global function definition for ‘sd’
ZScorePlotTwo: no visible global function definition for ‘median’
ZScorePlotTwo: no visible global function definition for ‘mad’
ZScorePlotTwo: no visible global function definition for ‘abline’
ZScorePlotTwo: no visible global function definition for ‘identify’
ZScorePlotTwo: no visible global function definition for ‘pdf’
ZScorePlotTwo: no visible global function definition for ‘dev.off’
ZScorePlotTwo: no visible global function definition for ‘png’
ZScorePlotTwo: no visible global function definition for ‘plot.new’
ZScorePlotTwo: no visible global function definition for ‘text’
channelPlot: no visible global function definition for ‘x11’
channelPlot: no visible global function definition for ‘lowess’
channelPlot: no visible global function definition for ‘pdf’
channelPlot: no visible global function definition for ‘dev.off’
channelPlot: no visible global function definition for ‘png’
compareReplicaPlates: no visible global function definition for ‘x11’
compareReplicaPlates: no visible global function definition for ‘par’
compareReplicaPlates: no visible global function definition for ‘mtext’
compareReplicaPlates: no visible global function definition for ‘pdf’
compareReplicaPlates: no visible global function definition for
  ‘dev.off’
compareReplicateSD: no visible global function definition for ‘sd’
compareReplicateSD: no visible global function definition for ‘x11’
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSD: no visible global function definition for ‘png’
compareReplicateSD: no visible global function definition for ‘dev.off’
compareReplicateSDPerScreen: no visible global function definition for
  ‘sd’
compareReplicateSDPerScreen: no visible global function definition for
  ‘x11’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘png’
compareReplicateSDPerScreen: no visible global function definition for
  ‘dev.off’
compareReplicates: no visible global function definition for ‘x11’
compareReplicates: no visible global function definition for ‘par’
compareReplicates: no visible global function definition for ‘points’
compareReplicates: no visible global function definition for ‘mtext’
compareReplicates: no visible global function definition for ‘identify’
compareReplicates: no visible global function definition for ‘pdf’
compareReplicates: no visible global function definition for ‘dev.off’
compareReplicates: no visible global function definition for ‘png’
controlDensity: no visible global function definition for ‘density’
controlDensity: no visible global function definition for ‘hist’
controlDensity: no visible global function definition for ‘par’
controlDensity: no visible global function definition for ‘axis’
controlDensity: no visible global function definition for ‘abline’
controlDensity: no visible global function definition for ‘legend’
controlDensity: no visible global function definition for ‘pdf’
controlDensity: no visible global function definition for ‘dev.off’
controlDensity: no visible global function definition for ‘png’
controlDensityPerPlate: no visible global function definition for ‘x11’
controlDensityPerPlate: no visible global function definition for ‘par’
controlDensityPerPlate: no visible global function definition for
  ‘density’
controlDensityPerPlate: no visible global function definition for
  ‘hist’
controlDensityPerPlate: no visible global function definition for
  ‘axis’
controlDensityPerPlate: no visible global function definition for
  ‘abline’
controlDensityPerPlate: no visible global function definition for
  ‘legend’
controlDensityPerPlate: no visible global function definition for ‘pdf’
controlDensityPerPlate: no visible global function definition for
  ‘plot.new’
controlDensityPerPlate: no visible global function definition for
  ‘text’
controlDensityPerPlate: no visible global function definition for
  ‘dev.off’
controlDensityPerPlate: no visible global function definition for ‘png’
controlDensityPerScreen: no visible global function definition for
  ‘par’
controlDensityPerScreen: no visible global function definition for
  ‘density’
controlDensityPerScreen: no visible global function definition for
  ‘hist’
controlDensityPerScreen: no visible global function definition for
  ‘axis’
controlDensityPerScreen: no visible global function definition for
  ‘abline’
controlDensityPerScreen: no visible global function definition for
  ‘legend’
controlDensityPerScreen: no visible global function definition for
  ‘pdf’
controlDensityPerScreen: no visible global function definition for
  ‘dev.off’
controlDensityPerScreen: no visible global function definition for
  ‘png’
controlNorm: no visible global function definition for ‘median’
doCtrlNorm: no visible global function definition for ‘median’
doCtrlNorm: no visible global function definition for ‘mad’
doPercNegNorm: no visible global function definition for ‘median’
doPocNorm: no visible global function definition for ‘median’
function1: no visible global function definition for ‘write.table’
function2: no visible global function definition for ‘write.table’
function2b: no visible global function definition for ‘write.table’
function2c: no visible global function definition for ‘write.table’
function3: no visible global function definition for ‘write.table’
function4a: no visible global function definition for ‘write.table’
function4b: no visible global function definition for ‘write.table’
function5: no visible global function definition for ‘write.table’
function6: no visible global function definition for ‘write.table’
function7: no visible global function definition for ‘write.table’
generateDatasetFile: no visible global function definition for
  ‘write.table’
gseaAnalysis: no visible global function definition for ‘new’
gseaAnalysisPt2: no visible global function definition for ‘new’
gseaTableFunc: no visible global function definition for ‘write.table’
hitselectionPval: no visible global function definition for ‘median’
hitselectionPval: no visible global function definition for
  ‘write.table’
hitselectionZscore: no visible global function definition for
  ‘write.table’
hitselectionZscorePval: no visible global function definition for
  ‘write.table’
joinDatasetFiles: no visible global function definition for
  ‘read.table’
joinDatasetFiles: no visible global function definition for
  ‘write.table’
lowessNorm: no visible global function definition for ‘lowess’
mainAnalysis: no visible global function definition for ‘write.table’
mainAnalysis: no visible global function definition for ‘read.table’
mainAnalysis: no visible binding for global variable ‘median’
makeBoxplot4PlateType: no visible global function definition for ‘x11’
makeBoxplot4PlateType: no visible global function definition for
  ‘boxplot’
makeBoxplot4PlateType: no visible global function definition for
  ‘plot.new’
makeBoxplot4PlateType: no visible global function definition for ‘text’
makeBoxplot4PlateType: no visible global function definition for ‘pdf’
makeBoxplot4PlateType: no visible global function definition for
  ‘dev.off’
makeBoxplot4PlateType: no visible global function definition for ‘png’
makeBoxplotControls: no visible global function definition for
  ‘boxplot’
makeBoxplotControls: no visible global function definition for ‘pdf’
makeBoxplotControls: no visible global function definition for
  ‘dev.off’
makeBoxplotControls: no visible global function definition for ‘png’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘par’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘boxplot’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘plot.new’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘text’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘pdf’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘dev.off’
makeBoxplotControlsPerPlate: no visible global function definition for
  ‘png’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘par’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘boxplot’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘pdf’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘dev.off’
makeBoxplotControlsPerScreen: no visible global function definition for
  ‘png’
makeBoxplotOverview: no visible global function definition for ‘jpeg’
makeBoxplotOverview: no visible global function definition for
  ‘boxplot’
makeBoxplotOverview: no visible global function definition for
  ‘dev.off’
makeBoxplotPerPlate: no visible global function definition for ‘par’
makeBoxplotPerPlate: no visible global function definition for
  ‘boxplot’
makeBoxplotPerPlate: no visible global function definition for ‘pdf’
makeBoxplotPerPlate: no visible global function definition for
  ‘dev.off’
makeBoxplotPerPlate: no visible global function definition for ‘png’
makeBoxplotPerScreen: no visible global function definition for
  ‘boxplot’
makeBoxplotPerScreen: no visible global function definition for ‘pdf’
makeBoxplotPerScreen: no visible global function definition for
  ‘dev.off’
makeBoxplotPerScreen: no visible global function definition for ‘png’
makeCorrPlots: no visible global function definition for ‘jpeg’
makeCorrPlots: no visible global function definition for ‘cor’
makeCorrPlots: no visible global function definition for ‘dev.off’
makeCtrlBoxPlot: no visible global function definition for ‘jpeg’
makeCtrlBoxPlot: no visible global function definition for ‘boxplot’
makeCtrlBoxPlot: no visible global function definition for ‘dev.off’
makeCtrlDensityPlot: no visible global function definition for ‘jpeg’
makeCtrlDensityPlot: no visible global function definition for
  ‘density’
makeCtrlDensityPlot: no visible global function definition for ‘hist’
makeCtrlDensityPlot: no visible global function definition for
  ‘dev.off’
makeQCPlots: no visible global function definition for ‘jpeg’
makeQCPlots: no visible global function definition for ‘boxplot’
makeQCPlots: no visible global function definition for ‘dev.off’
makeScreenOverview: no visible global function definition for ‘jpeg’
makeScreenOverview: no visible global function definition for ‘dev.off’
makefullbarplot: no visible global function definition for ‘jpeg’
makefullbarplot: no visible global function definition for ‘abline’
makefullbarplot: no visible global function definition for ‘dev.off’
makevolcanoplot: no visible global function definition for ‘jpeg’
makevolcanoplot: no visible global function definition for ‘abline’
makevolcanoplot: no visible global function definition for ‘dev.off’
multTestAdjust: no visible global function definition for ‘p.adjust’
numCellQualControl: no visible global function definition for
  ‘read.table’
numCellQualControl: no visible global function definition for ‘sd’
numCellQualControl: no visible global function definition for ‘hist’
numCellQualControl: no visible global function definition for
  ‘write.table’
numCellQualControl: no visible global function definition for ‘pdf’
numCellQualControl: no visible global function definition for ‘dev.off’
percCellQualControl: no visible global function definition for
  ‘read.table’
percCellQualControl: no visible global function definition for ‘sd’
percCellQualControl: no visible global function definition for ‘hist’
percCellQualControl: no visible global function definition for
  ‘write.table’
percCellQualControl: no visible global function definition for ‘pdf’
percCellQualControl: no visible global function definition for
  ‘dev.off’
plotBar: no visible global function definition for ‘boxplot’
plotBar: no visible global function definition for ‘abline’
plotBar: no visible global function definition for ‘pdf’
plotBar: no visible global function definition for ‘dev.off’
plotBar: no visible global function definition for ‘png’
plotBar: no visible global function definition for ‘x11’
plotBarGeruest: no visible global function definition for ‘median’
plotBarGeruest: no visible global function definition for ‘mad’
plotControlHisto: no visible global function definition for ‘hist’
plotControlHisto: no visible global function definition for ‘par’
plotControlHisto: no visible global function definition for ‘legend’
plotControlHisto: no visible global function definition for ‘pdf’
plotControlHisto: no visible global function definition for ‘dev.off’
plotControlHisto: no visible global function definition for ‘png’
plotControlHistoPerplate: no visible global function definition for
  ‘x11’
plotControlHistoPerplate: no visible global function definition for
  ‘par’
plotControlHistoPerplate: no visible global function definition for
  ‘plot.new’
plotControlHistoPerplate: no visible global function definition for
  ‘text’
plotControlHistoPerplate: no visible global function definition for
  ‘hist’
plotControlHistoPerplate: no visible global function definition for
  ‘legend’
plotControlHistoPerplate: no visible global function definition for
  ‘mtext’
plotControlHistoPerplate: no visible global function definition for
  ‘pdf’
plotControlHistoPerplate: no visible global function definition for
  ‘dev.off’
plotControlHistoPerplate: no visible global function definition for
  ‘png’
plotControlHistoPerscreen: no visible global function definition for
  ‘par’
plotControlHistoPerscreen: no visible global function definition for
  ‘hist’
plotControlHistoPerscreen: no visible global function definition for
  ‘legend’
plotControlHistoPerscreen: no visible global function definition for
  ‘pdf’
plotControlHistoPerscreen: no visible global function definition for
  ‘dev.off’
plotControlHistoPerscreen: no visible global function definition for
  ‘png’
plotHisto: no visible global function definition for ‘hist’
plotHisto: no visible global function definition for ‘pdf’
plotHisto: no visible global function definition for ‘dev.off’
plotHisto: no visible global function definition for ‘png’
plotHistoPerplate: no visible global function definition for ‘x11’
plotHistoPerplate: no visible global function definition for ‘par’
plotHistoPerplate: no visible global function definition for ‘hist’
plotHistoPerplate: no visible global function definition for ‘mtext’
plotHistoPerplate: no visible global function definition for ‘pdf’
plotHistoPerplate: no visible global function definition for ‘dev.off’
plotHistoPerplate: no visible global function definition for ‘png’
plotHistoPerscreen: no visible global function definition for ‘par’
plotHistoPerscreen: no visible global function definition for ‘hist’
plotHistoPerscreen: no visible global function definition for ‘pdf’
plotHistoPerscreen: no visible global function definition for ‘dev.off’
plotHistoPerscreen: no visible global function definition for ‘png’
plotQQ: no visible global function definition for ‘qqnorm’
plotQQ: no visible global function definition for ‘qqline’
plotQQ: no visible global function definition for ‘pdf’
plotQQ: no visible global function definition for ‘dev.off’
plotQQ: no visible global function definition for ‘png’
plotQQperplate: no visible global function definition for ‘x11’
plotQQperplate: no visible global function definition for ‘par’
plotQQperplate: no visible global function definition for ‘qqnorm’
plotQQperplate: no visible global function definition for ‘qqline’
plotQQperplate: no visible global function definition for ‘mtext’
plotQQperplate: no visible global function definition for ‘plot.new’
plotQQperplate: no visible global function definition for ‘text’
plotQQperplate: no visible global function definition for ‘pdf’
plotQQperplate: no visible global function definition for ‘dev.off’
plotQQperplate: no visible global function definition for ‘png’
plotQQperscreen: no visible global function definition for ‘par’
plotQQperscreen: no visible global function definition for ‘qqnorm’
plotQQperscreen: no visible global function definition for ‘qqline’
plotQQperscreen: no visible global function definition for ‘pdf’
plotQQperscreen: no visible global function definition for ‘dev.off’
plotQQperscreen: no visible global function definition for ‘png’
plothist: no visible global function definition for ‘jpeg’
plothist: no visible global function definition for ‘hist’
plothist: no visible global function definition for ‘dev.off’
plotmybar: no visible global function definition for ‘median’
plotmybar: no visible global function definition for ‘mad’
plotmybar: no visible global function definition for ‘jpeg’
plotmybar: no visible global function definition for ‘boxplot’
plotmybar: no visible global function definition for ‘abline’
plotmybar: no visible global function definition for ‘dev.off’
plotqq: no visible global function definition for ‘jpeg’
plotqq: no visible global function definition for ‘dev.off’
plotscatter: no visible global function definition for ‘jpeg’
plotscatter: no visible global function definition for ‘lowess’
plotscatter: no visible global function definition for ‘dev.off’
replicatesCV: no visible global function definition for ‘par’
replicatesCV: no visible global function definition for ‘sd’
replicatesCV: no visible global function definition for ‘points’
replicatesCV: no visible global function definition for ‘identify’
replicatesCV: no visible global function definition for ‘pdf’
replicatesCV: no visible global function definition for ‘dev.off’
replicatesCV: no visible global function definition for ‘png’
replicatesSpearmancor: no visible global function definition for
  ‘write.table’
replicatesSpearmancor: no visible global function definition for ‘cor’
replicatesSpearmancor: no visible global function definition for
  ‘read.table’
rnaither: no visible global function definition for ‘new’
rnaither: no visible global function definition for ‘quantile’
rnaither: no visible binding for global variable ‘median’
saveDataset: no visible global function definition for ‘write.table’
savepValVec: no visible global function definition for ‘write.table’
spatialDistrib: no visible global function definition for ‘x11’
spatialDistrib: no visible global function definition for ‘brewer.pal’
spatialDistrib: no visible global function definition for ‘png’
spatialDistrib: no visible global function definition for ‘dev.off’
spatialDistrib: no visible global function definition for ‘plot.new’
spatialDistrib: no visible global function definition for ‘text’
summarizeReplicates: no visible global function definition for ‘median’
summarizeReplicates: no visible global function definition for ‘mad’
summarizeReplicates: no visible global function definition for ‘sd’
summarizeReplicates: no visible global function definition for ‘t.test’
summarizeReplicates: no visible global function definition for
  ‘wilcox.test’
varAdjust: no visible global function definition for ‘mad’
vennDiag: no visible global function definition for ‘pdf’
vennDiag: no visible global function definition for ‘dev.off’
vennDiag: no visible global function definition for ‘png’
volcanoPlot: no visible global function definition for ‘abline’
volcanoPlot: no visible global function definition for ‘identify’
volcanoPlot: no visible global function definition for ‘pdf’
volcanoPlot: no visible global function definition for ‘dev.off’
volcanoPlot: no visible global function definition for ‘png’
writehitlist: no visible global function definition for ‘write.table’
writehitlist: no visible binding for global variable ‘median’
writehitlist: no visible global function definition for ‘median’
writehitlist: no visible global function definition for ‘mad’
writehitlist: no visible global function definition for ‘sd’
writehitlist: no visible global function definition for ‘t.test’
writehitlist: no visible global function definition for ‘wilcox.test’
ylabCompute: no visible global function definition for ‘sd’
ylabCompute: no visible global function definition for ‘median’
ylabCompute: no visible global function definition for ‘mad’
Undefined global functions or variables:
  RP abline axis boxplot brewer.pal cor density dev.off hist identify
  jpeg legend lowess mad median medpolish mtext new p.adjust par pdf
  plot.new png points qqline qqnorm quantile read.table sd t.test text
  var wilcox.test write.table x11
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "x11")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "identify",
             "legend", "mtext", "par", "plot.new", "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "cor", "density", "lowess", "mad", "median",
             "medpolish", "p.adjust", "qqline", "qqnorm", "quantile",
             "sd", "t.test", "var", "wilcox.test")
  importFrom("utils", "read.table", "write.table")
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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 32.106  1.582  35.648
rnaither     18.388  1.076  20.831
gseaAnalysis  7.188  0.083  13.757
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RNAither.Rcheck/00check.log’
for details.


RNAither.Rcheck/00install.out:

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

RNAither.Rcheck/RNAither-Ex.timings:

nameusersystemelapsed
BScore0.0760.0030.079
DRQualControl0.0220.0020.025
LiWongRank0.1660.0030.171
MannWhitney0.0360.0020.039
RankProduct0.5350.0050.544
SNRQualControl0.0250.0030.029
Ttest0.0310.0000.032
ZPRIMEQualControl0.0410.0070.049
ZScore0.0130.0010.015
ZScorePerScreen0.0090.0010.011
ZScorePlot0.1970.0120.227
ZScorePlotTwo0.0280.0030.033
channelPlot0.0350.0030.044
closestToZero0.0030.0000.003
compareHits0.1440.0020.146
compareReplicaPlates0.0190.0010.020
compareReplicateSD2.2370.0422.305
compareReplicateSDPerScreen0.3050.0120.328
compareReplicates0.2380.0170.274
controlDensity0.0630.0050.081
controlDensityPerPlate0.2120.0140.239
controlDensityPerScreen0.1090.0100.125
controlNorm0.0130.0000.013
createSubset0.0030.0000.003
discardLabtek0.0030.0000.004
discardWells0.0040.0000.005
divNorm0.0140.0010.015
divideChannels0.0030.0010.003
eraseDataSetColumn0.0120.0000.012
findReplicates0.0040.0010.005
furthestFromZero0.0030.0000.003
generateDatasetFile0.0150.0010.017
generateRepMatNoFilter0.0050.0000.006
generateReplicateMat0.0080.0010.009
gseaAnalysis 7.188 0.08313.757
hitselectionPval0.0210.0010.022
hitselectionZscore0.0250.0010.025
hitselectionZscorePval0.0250.0010.026
incorporatepValVec0.0170.0010.017
indexSubset0.0030.0010.003
joinDatasetFiles0.0180.0010.020
joinDatasets0.0030.0000.003
lowessNorm0.0110.0010.011
mainAnalysis32.106 1.58235.648
makeBoxplot4PlateType0.0570.0060.065
makeBoxplotControls0.0310.0030.035
makeBoxplotControlsPerPlate0.1100.0090.123
makeBoxplotControlsPerScreen0.0620.0040.069
makeBoxplotPerPlate0.0600.0040.066
makeBoxplotPerScreen0.0300.0030.033
multTestAdjust0.0020.0010.003
numCellQualControl0.0390.0030.048
orderGeneIDs0.0500.0010.052
percCellQualControl0.0270.0020.030
plotBar0.1420.0060.159
plotControlHisto0.0910.0040.099
plotControlHistoPerplate0.3920.0130.434
plotControlHistoPerscreen0.1840.0070.196
plotHisto0.0290.0040.033
plotHistoPerplate0.1100.0100.126
plotHistoPerscreen0.0550.0060.063
plotQQ0.0330.0030.039
plotQQperplate0.1070.0090.128
plotQQperscreen0.0480.0050.054
quantileNormalization0.1830.0010.184
replicatesCV0.0580.0050.067
replicatesSpearmancor0.0200.0020.021
rms0.0030.0000.003
rnaither18.388 1.07620.831
saveDataset0.1420.0010.144
saveOldIntensityColumns0.0030.0010.003
savepValVec0.0030.0000.003
spatialDistrib0.5720.0280.613
spatialDistribHits0.6050.0280.649
subtractBackground0.0050.0010.006
sumChannels0.0150.0010.016
summarizeReps0.0760.0010.077
summarizeRepsNoFiltering0.0880.0010.090
trim0.0040.0010.005
varAdjust0.0090.0010.009
vennDiag0.1970.0050.206
volcanoPlot0.0610.0040.068