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CHECK report for affyPara on nebbiolo1

This page was generated on 2020-11-27 11:54:26 -0500 (Fri, 27 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affyPara PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 33/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPara 1.50.0
Markus Schmidberger
Snapshot Date: 2020-11-26 14:42:42 -0500 (Thu, 26 Nov 2020)
URL: https://git.bioconductor.org/packages/affyPara
Branch: RELEASE_3_12
Last Commit: 7c6df5a
Last Changed Date: 2020-10-27 10:33:03 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyPara
Version: 1.50.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:affyPara.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings affyPara_1.50.0.tar.gz
StartedAt: 2020-11-26 19:54:06 -0500 (Thu, 26 Nov 2020)
EndedAt: 2020-11-26 19:55:06 -0500 (Thu, 26 Nov 2020)
EllapsedTime: 60.3 seconds
RetCode: 0
Status:  OK 
CheckDir: affyPara.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:affyPara.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings affyPara_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/affyPara.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.50.0’
* 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 ‘affyPara’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’
A package should be listed in only one of these fields.
* 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:
  ‘affy’ ‘aplpack’ ‘snow’ ‘vsn’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘affyio’ ‘aplpack’ ‘methods’ ‘snow’ ‘vsn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘vsn:::isSmall’ ‘vsn:::optimparNames’ ‘vsn:::pstartHeuristic’
  ‘vsn:::vsnLTS’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.doSummarizationPara: no visible global function definition for
  ‘clusterCall’
.doSummarizationPara: no visible global function definition for ‘new’
.doSummarizationPara: no visible global function definition for
  ‘phenoData’
.doSummarizationPara: no visible global function definition for
  ‘experimentData’
.doSummarizationPara: no visible global function definition for
  ‘annotation’
.doSummarizationPara: no visible global function definition for
  ‘getMethod’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.permArrays: no visible global function definition for ‘clusterCall’
.permMatrix: no visible global function definition for ‘clusterCall’
.resetABSF: no visible global function definition for ‘sampleNames<-’
.rowMeansPara: no visible global function definition for ‘clusterCall’
.rowVPara: no visible global function definition for ‘clusterCall’
MAplotPara: no visible global function definition for ‘checkCluster’
MAplotPara: no visible global function definition for ‘clusterApply’
MAplotPara: no visible global function definition for ‘clusterCall’
bgCorrectPara: no visible global function definition for ‘new’
bgCorrectPara: no visible global function definition for ‘checkCluster’
bgCorrectPara: no visible global function definition for ‘clusterApply’
bgCorrectPara: no visible global function definition for ‘clusterCall’
bgCorrectPara: no visible global function definition for ‘pData’
boxplotPara: no visible global function definition for ‘checkCluster’
boxplotPara: no visible global function definition for ‘clusterApply’
boxplotPara: no visible global function definition for ‘clusterCall’
boxplotParagLimits: no visible global function definition for ‘par’
boxplotParagMdMnDef: no visible binding for global variable ‘median’
boxplotParagMdMnDef: no visible global function definition for ‘median’
boxplotParagMedIQR: no visible global function definition for ‘par’
boxplotParagMedIQR: no visible global function definition for ‘bxp’
boxplotParagMedIQR: no visible global function definition for ‘abline’
boxplotParagMedIQR: no visible global function definition for ‘bagplot’
boxplotParagMedIQR: no visible global function definition for ‘title’
boxplotParagMedIQR: no visible global function definition for ‘text’
computeExprSetPara: no visible global function definition for ‘new’
computeExprSetPara: no visible global function definition for
  ‘checkCluster’
computeExprSetPara: no visible global function definition for
  ‘clusterApply’
distributeFiles: no visible global function definition for
  ‘checkCluster’
distributeFiles: no visible global function definition for
  ‘clusterEvalQ’
distributeFiles: no visible global function definition for
  ‘clusterCall’
distributeFiles: no visible global function definition for
  ‘clusterSplit’
drawHistDiff: no visible global function definition for ‘abline’
drawHistDiff: no visible global function definition for ‘text’
drawMAplot: no visible global function definition for ‘frame’
drawMAplot: no visible global function definition for ‘par’
drawnBxp: no visible global function definition for ‘bxp’
drawnBxp: no visible global function definition for ‘abline’
drawnBxp: no visible global function definition for ‘legend’
getBoxplot: no visible global function definition for ‘par’
getBoxplot: no visible global function definition for ‘abline’
getValuesChips: no visible global function definition for ‘IQR’
getValuesChips: no visible global function definition for ‘median’
getValuesChips: no visible global function definition for ‘loess’
getValuesChips: no visible global function definition for ‘approx’
grad_loglikPara: no visible global function definition for
  ‘clusterCall’
justvsnPara: no visible global function definition for ‘clusterCall’
logikPara: no visible global function definition for ‘clusterCall’
mergeAffyBatches: no visible global function definition for ‘phenoData’
mergeAffyBatches: no visible global function definition for ‘new’
mergeAffyBatches: no visible global function definition for ‘notes<-’
mergeAffyBatches: no visible global function definition for ‘pData<-’
mergeAffyBatches: no visible global function definition for ‘pData’
mergeAffyBatches: no visible global function definition for
  ‘phenoData<-’
mergeAffyBatches: no visible global function definition for
  ‘experimentData<-’
normalizeAffyBatchConstantPara: no visible global function definition
  for ‘new’
normalizeAffyBatchConstantPara: no visible global function definition
  for ‘checkCluster’
normalizeAffyBatchConstantPara: no visible global function definition
  for ‘clusterApply’
normalizeAffyBatchConstantPara: no visible global function definition
  for ‘clusterCall’
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for ‘new’
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for ‘checkCluster’
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for ‘clusterApply’
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for ‘clusterCall’
normalizeAffyBatchLoessIterPara: no visible global function definition
  for ‘new’
normalizeAffyBatchLoessIterPara: no visible global function definition
  for ‘checkCluster’
normalizeAffyBatchLoessIterPara: no visible global function definition
  for ‘clusterApply’
normalizeAffyBatchLoessIterPara: no visible global function definition
  for ‘clusterCall’
normalizeAffyBatchLoessPara: no visible global function definition for
  ‘new’
normalizeAffyBatchLoessPara: no visible global function definition for
  ‘checkCluster’
normalizeAffyBatchLoessPara: no visible global function definition for
  ‘clusterApply’
normalizeAffyBatchLoessPara: no visible global function definition for
  ‘clusterCall’
normalizeAffyBatchQuantilesPara: no visible global function definition
  for ‘new’
normalizeAffyBatchQuantilesPara: no visible global function definition
  for ‘checkCluster’
normalizeAffyBatchQuantilesPara: no visible global function definition
  for ‘clusterApply’
normalizeAffyBatchQuantilesPara: no visible global function definition
  for ‘clusterCall’
normalizeConstantPara: no visible global function definition for
  ‘clusterCall’
normalizeInvariantsetPara: no visible global function definition for
  ‘clusterCall’
normalizeInvariantsetPara: no visible global function definition for
  ‘median’
normalizeInvariantsetPara: no visible binding for global variable
  ‘median’
normalizeInvariantsetPara: no visible global function definition for
  ‘rowMedians’
normalizeInvariantsetParaSF2: no visible global function definition for
  ‘approx’
normalizeLoessIterPara: no visible global function definition for
  ‘clusterCall’
normalizeLoessIterParaSFnodes: no visible global function definition
  for ‘loess’
normalizeLoessIterParaSFnodes: no visible global function definition
  for ‘predict’
normalizeLoessPara: no visible global function definition for
  ‘clusterCall’
normalizeLoessParaSFbetNodes: no visible global function definition for
  ‘loess’
normalizeLoessParaSFbetNodes: no visible global function definition for
  ‘predict’
normalizeLoessParaSFnodes: no visible global function definition for
  ‘loess’
normalizeLoessParaSFnodes: no visible global function definition for
  ‘predict’
normalizeQuantilesPara: no visible global function definition for
  ‘clusterCall’
preproPara: no visible global function definition for ‘new’
preproPara: no visible global function definition for ‘checkCluster’
preproPara: no visible global function definition for ‘clusterApply’
preproPara: no visible global function definition for ‘clusterCall’
read.affybatchPara: no visible global function definition for ‘new’
read.affybatchPara: no visible global function definition for
  ‘checkCluster’
read.affybatchPara: no visible global function definition for
  ‘clusterApply’
read.affybatchPara: no visible global function definition for
  ‘clusterCall’
read.affybatchPara: no visible global function definition for
  ‘phenoData<-’
read.affybatchPara: no visible global function definition for ‘notes<-’
removeDistributedFiles: no visible global function definition for
  ‘checkCluster’
removeDistributedFiles: no visible global function definition for
  ‘clusterEvalQ’
removeDistributedFiles: no visible global function definition for
  ‘clusterCall’
rmaPara: no visible global function definition for ‘new’
setupPara: no visible global function definition for ‘clusterCall’
splitAffyBatch: no visible global function definition for
  ‘splitIndices’
splitFileVector: no visible global function definition for
  ‘splitIndices’
splitMatrix: no visible global function definition for ‘splitCols’
stopCluster: no visible global function definition for ‘checkCluster’
vsn2Para: no visible global function definition for ‘new’
vsn2Para: no visible global function definition for ‘checkCluster’
vsn2Para: no visible global function definition for ‘clusterApply’
vsn2Para: no visible global function definition for ‘clusterCall’
vsn2_optimPara: no visible global function definition for ‘optim’
vsn2trsfPara: no visible global function definition for ‘clusterCall’
vsnColumnByColumnPara: no visible global function definition for
  ‘clusterCall’
vsnColumnByColumnPara: no visible global function definition for ‘new’
vsnColumnByColumnParaSF: no visible global function definition for
  ‘new’
vsnColumnByColumnParaSF: no visible global function definition for
  ‘coefficients’
vsnLTSPara: no visible global function definition for ‘clusterCall’
vsnLTSPara: no visible global function definition for ‘coefficients’
vsnLTSPara: no visible binding for global variable ‘quantile’
vsnMLPara: no visible global function definition for ‘new’
vsnMLPara: no visible global function definition for ‘coefficients’
vsnMatrixPara: no visible global function definition for ‘new’
vsnMatrixPara: no visible global function definition for ‘coefficients’
vsnMatrixPara: no visible global function definition for
  ‘scalingFactorTransformation’
vsnMatrixPara: no visible global function definition for ‘validObject’
vsnSamplePara: no visible global function definition for ‘clusterCall’
vsnrmaPara: no visible global function definition for ‘new’
vsnrmaPara: no visible global function definition for ‘checkCluster’
vsnrmaPara: no visible global function definition for ‘clusterApply’
vsnrmaPara: no visible global function definition for ‘clusterCall’
Undefined global functions or variables:
  IQR abline addVigs2WinMenu annotation approx bagplot bxp checkCluster
  clusterApply clusterCall clusterEvalQ clusterSplit coefficients
  experimentData experimentData<- frame getMethod legend loess median
  new notes<- optim pData pData<- par phenoData phenoData<- predict
  quantile rowMedians sampleNames<- scalingFactorTransformation
  splitCols splitIndices text title validObject
Consider adding
  importFrom("graphics", "abline", "bxp", "frame", "legend", "par",
             "text", "title")
  importFrom("methods", "getMethod", "new", "validObject")
  importFrom("stats", "IQR", "approx", "coefficients", "loess", "median",
             "optim", "predict", "quantile")
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 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/affyPara.Rcheck/00check.log’
for details.



Installation output

affyPara.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL affyPara
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘affyPara’ ...
** using staged installation
** R
** 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 (affyPara)

Tests output


Example timings

affyPara.Rcheck/affyPara-Ex.timings

nameusersystemelapsed
MAplotPara0.0000.0000.001
bgcPara000
boxplotPara0.0000.0000.001
computeExprSetPara0.0010.0000.000
distributeFiles0.0010.0000.000
mergeSplitObjects0.9460.0400.986
normalizeAffyBatchConstantPara0.0000.0000.001
normalizeAffyBatchInvariantsetPara0.0000.0000.001
normalizeAffyBatchLoessPara0.0000.0000.001
normalizeAffyBatchLoessParaIter0.0000.0000.001
normalizeAffyBatchQuantilesPara000
preproPara0.0000.0010.000
qa000
readAffybatchPara000
removeDistributedFiles000
rmaPara0.0000.0010.000
snowReplace000
split0.2580.0230.279
vsnPara000