BioC 3.5: CHECK report for ArrayTools on veracruz2

Package: ArrayTools

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayTools_1.36.0.tar.gz

StartedAt: 2017-10-18 00:34:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:35:18 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 67.2 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayTools_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayTools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.36.0’
* 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 loading without being on the library search path ... 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Output2HTML	0.245	0.010	0.262
QC	0.002	0.001	0.003
Sort	0.859	0.006	0.885
contrastMatrix-class	0.025	0.002	0.030
createExpressionSet	0.111	0.009	0.120
createGSEAFiles	0.004	0.001	0.005
createIndex	0.291	0.004	0.303
createIngenuityFile	0.043	0.002	0.047
designMatrix-class	0.014	0.002	0.017
eSetExample	0.003	0.001	0.005
exprsExample	0.003	0.001	0.004
geneFilter	4.175	0.120	4.412
interactionResult-class	0.173	0.017	0.193
pDataExample	0.002	0.001	0.003
postInteraction	0.118	0.007	0.126
preProcess3prime	2.469	0.046	2.620
preProcessGeneST	0.021	0.003	0.025
qa3prime	0.000	0.000	0.001
qaGeneST	0.098	0.015	0.115
regress	0.045	0.006	0.051
regressResult-class	0.037	0.005	0.042
selectSigGene	0.043	0.007	0.049
selectSigGeneInt	0.138	0.006	0.146