Package: PREDA

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PREDA_1.24.0.tar.gz

StartedAt: 2018-04-12 07:50:16 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 07:52:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 114.1 seconds

RetCode: 0

Status:  OK

CheckDir: PREDA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PREDA_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PREDA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDA/DESCRIPTION’ ... OK
* this is package ‘PREDA’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rsprng’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PREDA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘annotate’ ‘lokern’ ‘multtest’ ‘stats’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘affy’ ‘caTools’ ‘limma’ ‘quantsmooth’ ‘qvalue’ ‘rsprng’
  ‘samr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘annotate’ ‘lokern’ ‘methods’ ‘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 ... NOTE
Foreign function call to a different package:
  .Call("mpi_finalize", ..., PACKAGE = "Rmpi")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
GE_computeStatistic_onMatrix : <anonymous>: no visible global function
  definition for ‘t.test’
GE_computeStatistic_onMatrix : <anonymous>: no visible global function
  definition for ‘median’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘model.matrix’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘lmFit’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘makeContrasts’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘contrasts.fit’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘eBayes’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘topTable’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr.compute.delta.table’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr.compute.siggenes.table’
GenomicAnnotationsForPREDAFromfile: no visible global function
  definition for ‘read.table’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘annPkgName’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘keys’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘lookUp’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘slot’
GenomicAnnotationsFromdataframe: no visible global function definition
  for ‘new’
GenomicAnnotationsFromfile: no visible global function definition for
  ‘read.table’
GenomicRegions2dataframe: no visible global function definition for
  ‘slot’
GenomicRegionsFromdataframe: no visible global function definition for
  ‘new’
GenomicRegionsFromfile: no visible global function definition for
  ‘read.table’
MergeStatisticAnnotations2DataForPREDA: no visible global function
  definition for ‘slot’
MergeStatisticAnnotations2DataForPREDA: no visible global function
  definition for ‘new’
PREDA_main: no visible global function definition for ‘slot’
PREDA_main : .Last: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main : .Last: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main: no visible global function definition for ‘mpi.remote.exec’
PREDA_main: no visible global function definition for ‘init.sprng’
PREDA_main: no visible global function definition for ‘mpi.comm.size’
PREDA_main: no visible global function definition for ‘mpi.comm.rank’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.recv.Robj’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.any.tag’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.get.sourcetag’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.send.Robj’
PREDA_main: no visible global function definition for ‘txtProgressBar’
PREDA_main: no visible global function definition for
  ‘setTxtProgressBar’
PREDA_main: no visible global function definition for ‘mpi.isend.Robj’
PREDA_main: no visible global function definition for ‘mpi.bcast.cmd’
PREDA_main: no visible global function definition for ‘mpi.recv.Robj’
PREDA_main: no visible global function definition for ‘mpi.any.source’
PREDA_main: no visible global function definition for ‘mpi.any.tag’
PREDA_main: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main: no visible global function definition for ‘free.sprng’
PREDA_main: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main_permRows: no visible global function definition for ‘slot’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.remote.exec’
PREDA_main_permRows: no visible global function definition for
  ‘init.sprng’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.comm.rank’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.recv.Robj’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.any.tag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.get.sourcetag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.send.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘txtProgressBar’
PREDA_main_permRows: no visible global function definition for
  ‘setTxtProgressBar’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.isend.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.bcast.cmd’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.recv.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.any.source’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.any.tag’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main_permRows: no visible global function definition for
  ‘free.sprng’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main_permSamples: no visible global function definition for
  ‘slot’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.remote.exec’
PREDA_main_permSamples: no visible global function definition for
  ‘init.sprng’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.comm.rank’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.recv.Robj’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.any.tag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.get.sourcetag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.send.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘txtProgressBar’
PREDA_main_permSamples: no visible global function definition for
  ‘setTxtProgressBar’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.isend.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.bcast.cmd’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.recv.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.any.source’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.any.tag’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main_permSamples: no visible global function definition for
  ‘free.sprng’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_multTestCorrection: no visible global function definition for
  ‘qvalue’
PREDA_multTestCorrection: no visible global function definition for
  ‘mt.rawp2adjp’
PREDA_quantsmoothStat: no visible global function definition for
  ‘quantsmooth’
PREDA_quantsmoothStatPerm: no visible global function definition for
  ‘quantsmooth’
PREDA_smoothStat: no visible global function definition for ‘lokerns’
PREDA_smoothStatPerm: no visible global function definition for
  ‘lokerns’
PREDA_splineStat: no visible global function definition for
  ‘smooth.spline’
PREDA_splineStat: no visible global function definition for ‘predict’
PREDA_splineStatPerm: no visible global function definition for
  ‘smooth.spline’
PREDA_splineStatPerm: no visible global function definition for
  ‘predict’
RMAwithCDFfilter: no visible global function definition for
  ‘cleancdfname’
RMAwithCDFfilter: no visible global function definition for
  ‘multiassign’
RMAwithCDFfilter: no visible global function definition for
  ‘annotation<-’
RMAwithCDFfilter: no visible global function definition for ‘new’
RMAwithCDFfilter: no visible global function definition for ‘pData’
RMAwithCDFfilter: no visible global function definition for
  ‘sampleNames’
RMAwithCDFfilter: no visible global function definition for
  ‘phenoData<-’
RMAwithCDFfilter: no visible global function definition for ‘rma’
RMAwithCDFfilter: no visible global function definition for
  ‘read.table’
RMAwithCDFfilter: no visible global function definition for ‘justRMA’
StatisticsForPREDAFromdataframe: no visible global function definition
  for ‘new’
StatisticsForPREDAFromfile: no visible global function definition for
  ‘read.table’
datasetSignatureFromFlags : <anonymous>: no visible global function
  definition for ‘dbinom’
genomePlot_improved: no visible global function definition for
  ‘rainbow’
genomePlot_improved: no visible global function definition for ‘slot’
genomePlot_improved: no visible global function definition for ‘par’
genomePlot_improved: no visible global function definition for ‘plot’
genomePlot_improved : <anonymous>: no visible global function
  definition for ‘lines’
genomePlot_improved : <anonymous>: no visible global function
  definition for ‘slot’
genomePlot_improved: no visible global function definition for ‘lines’
genomePlot_improved: no visible global function definition for ‘axis’
genomePlot_improved: no visible global function definition for
  ‘polygon’
getExpectedSmoothFunction: no visible global function definition for
  ‘existsFunction’
getExpectedSmoothFunction_runmean : PREDA_runmeanStatPerm_fun: no
  visible global function definition for ‘runmean’
getObservedSmoothFunction: no visible global function definition for
  ‘existsFunction’
getObservedSmoothFunction_runmean : PREDA_runmeanStat_fun: no visible
  global function definition for ‘runmean’
getPermutationMatrix: no visible global function definition for ‘combn’
getStardadizeFunction : my_standardize: no visible global function
  definition for ‘sd’
getStardadizeFunction : my_standardize: no visible global function
  definition for ‘median’
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA: no visible global
  function definition for ‘new’
DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA: no visible global
  function definition for ‘slot’
DataForPREDA2StatisticsForPREDA,DataForPREDA: no visible global
  function definition for ‘new’
DataForPREDA2StatisticsForPREDA,DataForPREDA: no visible global
  function definition for ‘slot’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
  definition for ‘slot’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
  definition for ‘runif’
DataForPREDAAddEffect_single,DataForPREDA: no visible global function
  definition for ‘slot<-’
DataForPREDAAddEffects,DataForPREDA-GenomicRegions: no visible global
  function definition for ‘slot’
DataForPREDAMedianCenter,DataForPREDA: no visible global function
  definition for ‘slot’
DataForPREDAMedianCenter,DataForPREDA: no visible binding for global
  variable ‘median’
DataForPREDAMedianCenter,DataForPREDA: no visible global function
  definition for ‘slot<-’
DataForPREDARandomShuffle,DataForPREDA: no visible global function
  definition for ‘slot’
DataForPREDARandomShuffle,DataForPREDA: no visible global function
  definition for ‘slot<-’
DataForPREDASimulationGetExpectedFlags,DataForPREDA-GenomicRegions: no
  visible global function definition for ‘slot’
GE_computeStatistic,ExpressionSet: no visible global function
  definition for ‘pData’
GE_computeStatistic,ExpressionSet: no visible global function
  definition for ‘sampleNames’
GE_computeStatistic,ExpressionSet: no visible global function
  definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet: no visible global
  function definition for ‘pData’
GE_simulations_samplingColumns,ExpressionSet: no visible global
  function definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet: no visible global
  function definition for ‘exprs<-’
GE_standardize,ExpressionSet: no visible global function definition for
  ‘exprs’
GE_standardize,ExpressionSet: no visible global function definition for
  ‘exprs<-’
GE_standardize,StatisticsForPREDA: no visible global function
  definition for ‘slot’
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations: no
  visible global function definition for ‘new’
GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations: no
  visible global function definition for ‘slot’
GenomicAnnotations2dataframe,GenomicAnnotations: no visible global
  function definition for ‘slot’
GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA: no visible
  global function definition for ‘slot’
GenomicAnnotations2reference_positions,GenomicAnnotations: no visible
  global function definition for ‘slot’
GenomicAnnotationsExtract,GenomicAnnotations: no visible global
  function definition for ‘slot’
GenomicAnnotationsFilter_neg,GenomicAnnotations: no visible global
  function definition for ‘slot’
GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA: no visible
  global function definition for ‘slot’
GenomicAnnotationsFilter_pos,DataForPREDA: no visible global function
  definition for ‘slot’
GenomicAnnotationsFilter_pos,GenomicAnnotations: no visible global
  function definition for ‘slot’
GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA: no visible
  global function definition for ‘slot’
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA:
  no visible global function definition for ‘new’
GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA:
  no visible global function definition for ‘slot’
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA: no
  visible global function definition for ‘new’
GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA: no
  visible global function definition for ‘slot’
GenomicAnnotationsForPREDAGetExpectedFlags,GenomicAnnotationsForPREDA:
  no visible global function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,GenomicAnnotations: no visible global
  function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA: no visible
  global function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults: no visible global
  function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDADataAndResults: no visible global
  function definition for ‘new’
GenomicAnnotationsSortAndCleanNA,PREDAResults: no visible global
  function definition for ‘slot’
GenomicAnnotationsSortAndCleanNA,PREDAResults: no visible global
  function definition for ‘new’
GenomicRegionsAnnotate,GenomicRegions-GenomicAnnotations: no visible
  global function definition for ‘slot’
GenomicRegionsAnnotate,GenomicRegions-GenomicAnnotations: no visible
  global function definition for ‘new’
GenomicRegionsChrNumber,GenomicRegions: no visible global function
  definition for ‘slot’
GenomicRegionsCreateRegionsIds,GenomicRegions: no visible global
  function definition for ‘slot’
GenomicRegionsFilter_neg,GenomicRegions: no visible global function
  definition for ‘slot’
GenomicRegionsFilter_pos,GenomicRegions: no visible global function
  definition for ‘slot’
GenomicRegionsNumber,GenomicRegions: no visible global function
  definition for ‘slot’
GenomicRegionsSpan,GenomicRegions: no visible global function
  definition for ‘slot’
PREDADataAndResults2dataframe,PREDADataAndResults: no visible global
  function definition for ‘slot’
PREDAResults2GenomicRegions,PREDAResults: no visible global function
  definition for ‘slot’
PREDAResults2GenomicRegionsSingle,PREDAResults: no visible global
  function definition for ‘slot’
PREDAResults2PREDADataAndResults,PREDAResults: no visible global
  function definition for ‘slot’
PREDAResults2PREDADataAndResults,PREDAResults: no visible global
  function definition for ‘new’
PREDAResults2dataframe,PREDAResults: no visible global function
  definition for ‘slot’
PREDAResultsGetObservedFlags,PREDAResults: no visible global function
  definition for ‘slot’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
  definition for ‘pData’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
  definition for ‘exprs’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
  definition for ‘samr’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
  definition for ‘sampleNames’
SODEGIR_GEstatistics,ExpressionSet: no visible global function
  definition for ‘featureNames’
StatisticsForPREDA2dataframe,StatisticsForPREDA: no visible global
  function definition for ‘slot’
StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA: no visible
  global function definition for ‘slot’
StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA: no visible
  global function definition for ‘new’
StatisticsForPREDAFilterColumns_pos,DataForPREDA: no visible global
  function definition for ‘slot’
StatisticsForPREDAFilterColumns_pos,StatisticsForPREDA: no visible
  global function definition for ‘slot’
analysesNames,PREDAResults: no visible global function definition for
  ‘slot’
analysesNames,StatisticsForPREDA: no visible global function definition
  for ‘slot’
compareFunctionFromStatisticsForPREDA,StatisticsForPREDA: no visible
  global function definition for ‘slot’
computeDatasetSignature,GenomicAnnotationsForPREDA: no visible global
  function definition for ‘slot’
computeDatasetSignature,GenomicAnnotationsForPREDA: no visible global
  function definition for ‘new’
eset2GenomicAnnotations,ExpressionSet: no visible global function
  definition for ‘featureNames’
eset2GenomicAnnotations,ExpressionSet: no visible global function
  definition for ‘annotation’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘slot’
genomePlot,GenomicAnnotationsForPREDA : <anonymous>: no visible global
  function definition for ‘slot’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘rainbow’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘par’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘plot’
genomePlot,GenomicAnnotationsForPREDA : <anonymous>: no visible global
  function definition for ‘lines’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘lines’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘axis’
genomePlot,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘polygon’
getStatisticByName,StatisticsForPREDA: no visible global function
  definition for ‘slot’
initialize,DataForPREDA: no visible global function definition for
  ‘new’
initialize,DataForPREDA: no visible global function definition for
  ‘slot’
initialize,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘new’
initialize,GenomicAnnotationsForPREDA: no visible global function
  definition for ‘slot’
initialize,PREDADataAndResults: no visible global function definition
  for ‘new’
initialize,PREDADataAndResults: no visible global function definition
  for ‘slot’
initialize,PREDAResults: no visible global function definition for
  ‘new’
initialize,PREDAResults: no visible global function definition for
  ‘slot’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
  definition for ‘pData’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
  definition for ‘sampleNames’
statisticsForPREDAfromEset,ExpressionSet: no visible global function
  definition for ‘featureNames’
Undefined global functions or variables:
  annPkgName annotation annotation<- axis cleancdfname combn
  contrasts.fit dbinom eBayes existsFunction exprs exprs<- featureNames
  free.sprng init.sprng justRMA keys lines lmFit lokerns lookUp
  makeContrasts median model.matrix mpi.any.source mpi.any.tag
  mpi.bcast.Robj2slave mpi.bcast.cmd mpi.close.Rslaves mpi.comm.rank
  mpi.comm.size mpi.get.sourcetag mpi.isend.Robj mpi.recv.Robj
  mpi.remote.exec mpi.send.Robj mpi.spawn.Rslaves mt.rawp2adjp
  multiassign new pData par phenoData<- plot polygon predict
  quantsmooth qvalue rainbow read.table rma runif runmean sampleNames
  samr samr.compute.delta.table samr.compute.siggenes.table sd
  setTxtProgressBar slot slot<- smooth.spline t.test topTable
  txtProgressBar
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "par", "plot", "polygon")
  importFrom("methods", "existsFunction", "new", "slot", "slot<-")
  importFrom("stats", "dbinom", "median", "model.matrix", "predict",
             "runif", "sd", "smooth.spline", "t.test")
  importFrom("utils", "combn", "read.table", "setTxtProgressBar",
             "txtProgressBar")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/PREDA.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DataForPREDA-class	0.004	0.001	0.003
GenomicAnnotations-class	0.002	0.000	0.002
GenomicAnnotations2GenomicAnnotationsForPREDA	0.001	0.000	0.001
GenomicAnnotationsForPREDA-class	0.001	0.001	0.001
GenomicAnnotationsForPREDAFromfile	0.001	0.000	0.002
GenomicAnnotationsFromLibrary	0.001	0.001	0.001
GenomicAnnotationsFromfile	0.001	0.000	0.001
GenomicRegions-class	0.001	0.001	0.002
GenomicRegions2dataframe	0.001	0.000	0.001
GenomicRegionsFindOverlap	0.001	0.000	0.001
PREDADataAndResults-class	0.003	0.000	0.003
PREDAResults-class	0.002	0.000	0.003
PREDAResults2GenomicRegions	0.001	0.000	0.001
PREDA_main	0.001	0.000	0.001
SODEGIRpreprocessingGE	0.002	0.001	0.002
StatisticsForPREDA-class	0.002	0.000	0.002
StatisticsForPREDAFromdataframe	0.001	0.000	0.001
StatisticsForPREDAFromfile	0.001	0.000	0.001
analysesNames	0.837	0.040	1.203
computeDatasetSignature	0.000	0.000	0.001
eset2GenomicAnnotations	0.001	0.000	0.001
genomePlot	0.000	0.000	0.001
preprocessingGE	0.001	0.000	0.001
statisticsForPREDAfromEset	0.001	0.000	0.001