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CHECK report for affyPara on malbec1

This page was generated on 2020-08-12 11:14:34 -0400 (Wed, 12 Aug 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 32/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPara 1.49.0
Markus Schmidberger
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/affyPara
Branch: master
Last Commit: 2af763a
Last Changed Date: 2020-04-27 14:16:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]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: 1.49.0
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_1.49.0.tar.gz
StartedAt: 2020-08-11 23:52:18 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 23:53:25 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 66.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affyPara.Rcheck
Warnings: 4

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_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/affyPara.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.49.0’
* 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
Maximum number of clients reachedMaximum number of clients reached'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 ... WARNING
Maximum number of clients reachedMaximum number of clients reached
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Maximum number of clients reachedMaximum number of clients reached
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Maximum number of clients reachedMaximum number of clients reachedForeign 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 ... WARNING
Maximum number of clients reachedMaximum number of clients reached
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Maximum number of clients reachedMaximum number of clients reached
Maximum number of clients reachedMaximum number of clients reached
Maximum number of clients reachedMaximum number of clients reached
* checking Rd \usage sections ... NOTE
Maximum number of clients reachedMaximum number of clients reached
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 WARNINGs, 5 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
Maximum number of clients reachedMaximum number of clients reachedWarning message:
In fun(libname, pkgname) : couldn't connect to display ":1.0"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Maximum number of clients reachedMaximum number of clients reachedWarning in fun(libname, pkgname) : couldn't connect to display ":1.0"
** testing if installed package can be loaded from final location
Maximum number of clients reachedMaximum number of clients reachedWarning in fun(libname, pkgname) : couldn't connect to display ":1.0"
** testing if installed package keeps a record of temporary installation path
* DONE (affyPara)

Tests output


Example timings

affyPara.Rcheck/affyPara-Ex.timings

nameusersystemelapsed
MAplotPara000
bgcPara0.0000.0000.001
boxplotPara000
computeExprSetPara000
distributeFiles000
mergeSplitObjects1.2800.0241.315
normalizeAffyBatchConstantPara000
normalizeAffyBatchInvariantsetPara000
normalizeAffyBatchLoessPara000
normalizeAffyBatchLoessParaIter000
normalizeAffyBatchQuantilesPara000
preproPara000
qa000
readAffybatchPara000
removeDistributedFiles000
rmaPara0.0000.0000.001
snowReplace0.0000.0000.001
split0.5000.0160.517
vsnPara0.0040.0000.000