Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.6: CHECK report for RNAither on veracruz1

This page was generated on 2017-08-16 13:40:20 -0400 (Wed, 16 Aug 2017).

Package 1147/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAither 2.25.0
Lars Kaderali
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAither
Version: 2.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.25.0.tar.gz
StartedAt: 2017-08-16 07:55:40 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 08:00:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 275.0 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_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/RNAither.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.25.0’
* 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 25.559  1.647  28.687
rnaither     13.342  1.061  15.658
gseaAnalysis  5.447  0.064  10.108
* 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-3.6-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
BScore0.0410.0000.042
DRQualControl0.0200.0020.023
LiWongRank0.1360.0020.142
MannWhitney0.0320.0010.034
RankProduct0.6450.0040.673
SNRQualControl0.0300.0040.034
Ttest0.0270.0010.028
ZPRIMEQualControl0.0380.0070.047
ZScore0.0120.0010.012
ZScorePerScreen0.0090.0010.010
ZScorePlot0.1330.0130.163
ZScorePlotTwo0.0250.0030.028
channelPlot0.0250.0030.030
closestToZero0.0030.0010.003
compareHits0.1030.0110.115
compareReplicaPlates0.0160.0020.019
compareReplicateSD1.3750.0261.442
compareReplicateSDPerScreen0.2830.0130.303
compareReplicates0.1820.0190.227
controlDensity0.0510.0050.060
controlDensityPerPlate0.1640.0140.199
controlDensityPerScreen0.0780.0100.095
controlNorm0.0070.0010.008
createSubset0.0020.0000.003
discardLabtek0.0020.0010.003
discardWells0.0030.0000.003
divNorm0.0090.0010.010
divideChannels0.0020.0000.002
eraseDataSetColumn0.0050.0000.005
findReplicates0.0030.0000.003
furthestFromZero0.0030.0000.003
generateDatasetFile0.0110.0000.012
generateRepMatNoFilter0.0040.0010.005
generateReplicateMat0.0080.0000.008
gseaAnalysis 5.447 0.06410.108
hitselectionPval0.0160.0010.017
hitselectionZscore0.0240.0010.025
hitselectionZscorePval0.0270.0010.029
incorporatepValVec0.0170.0010.017
indexSubset0.0030.0000.003
joinDatasetFiles0.0180.0020.020
joinDatasets0.0030.0000.004
lowessNorm0.0100.0010.010
mainAnalysis25.559 1.64728.687
makeBoxplot4PlateType0.0690.0060.079
makeBoxplotControls0.0300.0030.036
makeBoxplotControlsPerPlate0.1130.0090.127
makeBoxplotControlsPerScreen0.0590.0040.066
makeBoxplotPerPlate0.0570.0040.064
makeBoxplotPerScreen0.0290.0030.033
multTestAdjust0.0030.0000.003
numCellQualControl0.0300.0030.032
orderGeneIDs0.0430.0010.044
percCellQualControl0.0260.0030.028
plotBar0.1200.0070.136
plotControlHisto0.0760.0040.084
plotControlHistoPerplate0.3280.0140.363
plotControlHistoPerscreen0.1620.0070.183
plotHisto0.0250.0040.030
plotHistoPerplate0.0970.0110.117
plotHistoPerscreen0.0490.0060.059
plotQQ0.0260.0030.032
plotQQperplate0.1010.0100.121
plotQQperscreen0.0440.0050.053
quantileNormalization0.1900.0010.210
replicatesCV0.0580.0060.067
replicatesSpearmancor0.0200.0020.025
rms0.0030.0000.003
rnaither13.342 1.06115.658
saveDataset0.0960.0000.096
saveOldIntensityColumns0.0030.0000.004
savepValVec0.0020.0000.003
spatialDistrib0.4560.0290.506
spatialDistribHits0.3780.0270.428
subtractBackground0.0030.0000.003
sumChannels0.0080.0010.009
summarizeReps0.0410.0000.041
summarizeRepsNoFiltering0.0480.0010.048
trim0.0030.0010.003
varAdjust0.0050.0000.005
vennDiag0.1290.0050.140
volcanoPlot0.0480.0050.054