Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-01 12:02 -0400 (Fri, 01 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4503
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1588/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PREDA 1.52.0  (landing page)
Francesco Ferrari
Snapshot Date: 2024-10-31 13:40 -0400 (Thu, 31 Oct 2024)
git_url: https://git.bioconductor.org/packages/PREDA
git_branch: RELEASE_3_20
git_last_commit: f4bf445
git_last_commit_date: 2024-10-29 09:37:56 -0400 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for PREDA on teran2

To the developers/maintainers of the PREDA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PREDA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: PREDA
Version: 1.52.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PREDA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PREDA_1.52.0.tar.gz
StartedAt: 2024-11-01 06:01:06 -0400 (Fri, 01 Nov 2024)
EndedAt: 2024-11-01 06:03:56 -0400 (Fri, 01 Nov 2024)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PREDA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PREDA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PREDA_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/PREDA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PREDA/DESCRIPTION’ ... OK
* this is package ‘PREDA’ version ‘1.52.0’
* 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 ... OK
* 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 code 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
'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’
  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’
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 : <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 ‘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 : <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<- polygon predict quantsmooth
  qvalue rainbow read.table rma runif runmean sampleNames sd
  setTxtProgressBar slot slot<- smooth.spline t.test topTable
  txtProgressBar
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "par", "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 ... WARNING
Documented arguments not in \usage in Rd file 'StatisticsForPREDAFromdataframe.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'DataForPREDAMedianCenter.Rd':
  ‘\dots’
Argument items with no description in Rd file 'GenomicRegionsCreateRegionsIds.Rd':
  ‘\dots’
Argument items with no description in Rd file 'GenomicRegionsSpan.Rd':
  ‘\dots’
Argument items with no description in Rd file 'GenomicRegionsTotalSpan.Rd':
  ‘\dots’
* checking for unstated dependencies in examples ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/PREDA.Rcheck/00check.log’
for details.

Installation output

PREDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PREDA
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘PREDA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PREDA)

Tests output


Example timings

PREDA.Rcheck/PREDA-Ex.timings

nameusersystemelapsed
DataForPREDA-class0.0010.0000.001
GenomicAnnotations-class0.0000.0010.001
GenomicAnnotations2GenomicAnnotationsForPREDA000
GenomicAnnotationsForPREDA-class0.0010.0000.000
GenomicAnnotationsForPREDAFromfile000
GenomicAnnotationsFromLibrary000
GenomicAnnotationsFromfile0.0000.0010.000
GenomicRegions-class000
GenomicRegions2dataframe000
GenomicRegionsFindOverlap000
PREDADataAndResults-class0.0000.0000.001
PREDAResults-class0.0000.0000.001
PREDAResults2GenomicRegions000
PREDA_main000
SODEGIRpreprocessingGE000
StatisticsForPREDA-class000
StatisticsForPREDAFromdataframe000
StatisticsForPREDAFromfile000
analysesNames0.8510.0210.880
computeDatasetSignature000
eset2GenomicAnnotations000
genomePlot000
preprocessingGE000
statisticsForPREDAfromEset000