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CHECK report for ArrayTools on machv2

This page was generated on 2020-10-17 11:58:03 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ArrayTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 83/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayTools 1.48.0
Arthur Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ArrayTools
Branch: RELEASE_3_11
Last Commit: e3575ed
Last Changed Date: 2020-04-27 14:18:01 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayTools
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayTools_1.48.0.tar.gz
StartedAt: 2020-10-16 22:42:45 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:44:07 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 82.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayTools_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ArrayTools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ version ‘1.48.0’
* 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 ‘ArrayTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘Biobase’ ‘methods’
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 in package code:
  ‘R2HTML’ ‘affyPLM’ ‘annaffy’ ‘gcrma’ ‘simpleaffy’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createIndex: no visible global function definition for ‘HTMLStart’
createIndex: no visible global function definition for ‘as.title’
createIndex: no visible global function definition for ‘HTML’
createIndex: no visible global function definition for ‘HTMLStop’
geneFilter: no visible global function definition for ‘getText’
geneFilter: no visible global function definition for ‘aafSymbol’
geneFilter: no visible global function definition for ‘aafDescription’
geneFilter: no visible global function definition for ‘aafChromosome’
geneFilter: no visible global function definition for ‘aafGenBank’
geneFilter: no visible global function definition for ‘aafCytoband’
geneFilter: no visible global function definition for ‘aafUniGene’
geneFilter: no visible global function definition for ‘aafPubMed’
geneFilter: no visible global function definition for ‘aafLocusLink’
output.ing: no visible global function definition for ‘getText’
output.ing: no visible global function definition for ‘aafSymbol’
output.ing: no visible global function definition for ‘aafDescription’
output.ing: no visible global function definition for ‘aafChromosome’
output.ing: no visible global function definition for ‘aafGenBank’
output.ing: no visible global function definition for ‘aafCytoband’
output.ing: no visible global function definition for ‘aafUniGene’
output.ing: no visible global function definition for ‘aafPubMed’
output.ing: no visible global function definition for ‘aafLocusLink’
preProcess3prime: no visible global function definition for ‘gcrma’
preProcess3prime: no visible global function definition for ‘getText’
preProcess3prime: no visible global function definition for ‘aafSymbol’
preProcess3prime: no visible global function definition for
  ‘aafDescription’
preProcess3prime: no visible global function definition for
  ‘aafChromosome’
preProcess3prime: no visible global function definition for
  ‘aafGenBank’
preProcess3prime: no visible global function definition for
  ‘aafCytoband’
preProcess3prime: no visible global function definition for
  ‘aafUniGene’
preProcess3prime: no visible global function definition for ‘aafPubMed’
preProcess3prime: no visible global function definition for
  ‘aafLocusLink’
preProcessGeneST: no visible binding for global variable
  ‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
  ‘mogene10stCONTROL’
preProcessGeneST: no visible global function definition for ‘getText’
preProcessGeneST: no visible global function definition for ‘aafSymbol’
preProcessGeneST: no visible global function definition for
  ‘aafDescription’
preProcessGeneST: no visible global function definition for
  ‘aafChromosome’
preProcessGeneST: no visible global function definition for
  ‘aafGenBank’
preProcessGeneST: no visible global function definition for
  ‘aafCytoband’
preProcessGeneST: no visible global function definition for
  ‘aafUniGene’
preProcessGeneST: no visible global function definition for ‘aafPubMed’
preProcessGeneST: no visible global function definition for
  ‘aafLocusLink’
qa3prime: no visible global function definition for ‘setQCEnvironment’
qa3prime: no visible global function definition for ‘qc.get.alpha1’
qa3prime: no visible global function definition for ‘HTMLStart’
qa3prime: no visible global function definition for ‘as.title’
qa3prime: no visible global function definition for ‘HTML’
qa3prime: no visible global function definition for ‘HTMLInsertGraph’
qa3prime: no visible global function definition for ‘call.exprs’
qa3prime: no visible global function definition for ‘avbg’
qa3prime: no visible global function definition for ‘percent.present’
qa3prime: no visible global function definition for ‘sfs’
qa3prime: no visible global function definition for ‘spikeInProbes’
qa3prime: no visible global function definition for ‘ratios’
qa3prime: no visible global function definition for ‘fitPLM’
qa3prime: no visible global function definition for ‘HTMLStop’
qaGeneST: no visible global function definition for ‘HTMLStart’
qaGeneST: no visible global function definition for ‘as.title’
qaGeneST: no visible global function definition for ‘HTML’
qaGeneST: no visible global function definition for ‘HTMLInsertGraph’
qaGeneST: no visible global function definition for ‘HTMLStop’
regress: no visible global function definition for ‘permute.1’
regress: no visible binding for global variable ‘design’
Output2HTML,interactionResult: no visible global function definition
  for ‘aaf.handler’
Output2HTML,interactionResult: no visible global function definition
  for ‘aafTableAnn’
Output2HTML,interactionResult: no visible global function definition
  for ‘aafTable’
Output2HTML,interactionResult: no visible global function definition
  for ‘saveHTML’
Output2HTML,regressResult: no visible global function definition for
  ‘aaf.handler’
Output2HTML,regressResult: no visible global function definition for
  ‘aafTableAnn’
Output2HTML,regressResult: no visible global function definition for
  ‘aafTable’
Output2HTML,regressResult: no visible global function definition for
  ‘saveHTML’
Undefined global functions or variables:
  HTML HTMLInsertGraph HTMLStart HTMLStop aaf.handler aafChromosome
  aafCytoband aafDescription aafGenBank aafLocusLink aafPubMed
  aafSymbol aafTable aafTableAnn aafUniGene as.title avbg call.exprs
  design fitPLM gcrma getText hugene10stCONTROL mogene10stCONTROL
  percent.present permute.1 qc.get.alpha1 ratios saveHTML
  setQCEnvironment sfs spikeInProbes
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
geneFilter 5.981   0.21   6.195
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.



Installation output

ArrayTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ArrayTools’ ...
** using staged installation
** R
** data
** 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 (ArrayTools)

Tests output


Example timings

ArrayTools.Rcheck/ArrayTools-Ex.timings

nameusersystemelapsed
Output2HTML0.1620.0080.171
QC0.0020.0020.004
Sort0.1020.0040.105
contrastMatrix-class0.0300.0050.035
createExpressionSet0.0810.0040.086
createGSEAFiles0.0050.0020.006
createIndex0.0910.0030.094
createIngenuityFile0.0150.0020.016
designMatrix-class0.0190.0060.024
eSetExample0.0040.0020.006
exprsExample0.0030.0020.004
geneFilter5.9810.2106.195
interactionResult-class0.1100.0050.115
pDataExample0.0020.0020.004
postInteraction0.1070.0110.118
preProcess3prime2.6610.0632.727
preProcessGeneST0.0210.0040.025
qa3prime000
qaGeneST0.0200.0050.024
regress0.0470.0070.054
regressResult-class0.0200.0020.023
selectSigGene0.0270.0020.029
selectSigGeneInt0.1090.0030.113