Package: HELP

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HELP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HELP_1.40.0.tar.gz

StartedAt: 2019-04-16 00:31:45 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:32:26 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 41.3 seconds

RetCode: 0

Status:  OK

CheckDir: HELP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HELP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HELP_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/HELP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HELP/DESCRIPTION’ ... OK
* this is package ‘HELP’ version ‘1.40.0’
* 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 ‘HELP’ 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 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
Package in Depends field not imported from: ‘methods’
  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 ... OK
* checking R code for possible problems ... NOTE
calcTm: no visible global function definition for ‘data’
calcTm: no visible binding for global variable
  ‘base.stacking.thermodynamics’
readSampleKey: no visible global function definition for ‘read.table’
calcGC,ExpressionSet: no visible global function definition for
  ‘validObject’
calcGC,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcGC,ExpressionSet: no visible global function definition for ‘new’
calcPrototype,ExpressionSet: no visible global function definition for
  ‘validObject’
calcPrototype,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcPrototype,vector: no visible global function definition for
  ‘callGeneric’
calcTm,ExpressionSet: no visible global function definition for
  ‘validObject’
calcTm,ExpressionSet: no visible global function definition for
  ‘callGeneric’
calcTm,ExpressionSet: no visible global function definition for ‘new’
calcTm,character: no visible binding for global variable
  ‘base.stacking.thermodynamics’
combineData,ExpressionSet-missing-missing: no visible global function
  definition for ‘validObject’
combineData,ExpressionSet-missing-missing: no visible global function
  definition for ‘callGeneric’
combineData,ExpressionSet-vector-missing: no visible global function
  definition for ‘validObject’
combineData,ExpressionSet-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,matrix-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-missing-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-missing-vector: no visible global function
  definition for ‘callGeneric’
combineData,vector-vector-missing: no visible global function
  definition for ‘callGeneric’
combineData,vector-vector-vector: no visible global function definition
  for ‘callGeneric’
createWiggle,ExpressionSet-matrix: no visible global function
  definition for ‘validObject’
createWiggle,ExpressionSet-matrix: no visible global function
  definition for ‘callGeneric’
createWiggle,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
createWiggle,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
createWiggle,matrix-matrix: no visible global function definition for
  ‘rainbow’
createWiggle,matrix-matrix: no visible global function definition for
  ‘col2rgb’
createWiggle,vector-matrix: no visible global function definition for
  ‘callGeneric’
getFeatures,AnnotatedDataFrame-NULL: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-missing: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for ‘validObject’
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for ‘callGeneric’
getFeatures,ExpressionSet-NULL: no visible global function definition
  for ‘validObject’
getFeatures,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
getFeatures,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
getFeatures,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
getFeatures,vector-vector: no visible global function definition for
  ‘callGeneric’
getSamples,ExpressionSet-NULL: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-missing: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
getSamples,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
getSamples,vector-vector: no visible global function definition for
  ‘callGeneric’
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘validObject’
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for ‘callGeneric’
plotBins,ExpressionSet-missing: no visible global function definition
  for ‘validObject’
plotBins,ExpressionSet-missing: no visible global function definition
  for ‘callGeneric’
plotBins,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
plotBins,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
plotBins,matrix-missing: no visible global function definition for
  ‘callGeneric’
plotBins,vector-ExpressionSet: no visible global function definition
  for ‘validObject’
plotBins,vector-ExpressionSet: no visible global function definition
  for ‘callGeneric’
plotBins,vector-vector: no visible global function definition for
  ‘rainbow’
plotBins,vector-vector: no visible global function definition for
  ‘quantile’
plotBins,vector-vector: no visible global function definition for
  ‘layout’
plotBins,vector-vector: no visible global function definition for
  ‘plot’
plotBins,vector-vector: no visible global function definition for
  ‘axis’
plotBins,vector-vector: no visible global function definition for
  ‘rect’
plotBins,vector-vector: no visible global function definition for
  ‘density’
plotBins,vector-vector: no visible global function definition for
  ‘lines’
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for ‘validObject’
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for ‘callGeneric’
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for ‘validObject’
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for ‘callGeneric’
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for ‘validObject’
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for ‘callGeneric’
plotChip,matrix-missing-missing: no visible global function definition
  for ‘callGeneric’
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for ‘validObject’
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for ‘callGeneric’
plotChip,vector-vector-vector: no visible global function definition
  for ‘rainbow’
plotChip,vector-vector-vector: no visible global function definition
  for ‘quantile’
plotChip,vector-vector-vector: no visible global function definition
  for ‘plot’
plotChip,vector-vector-vector: no visible global function definition
  for ‘rect’
plotFeature,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
plotFeature,ExpressionSet-vector: no visible global function definition
  for ‘validObject’
plotFeature,ExpressionSet-vector: no visible global function definition
  for ‘callGeneric’
plotFeature,matrix-vector: no visible global function definition for
  ‘par’
plotFeature,matrix-vector: no visible global function definition for
  ‘median’
plotFeature,matrix-vector: no visible global function definition for
  ‘mad’
plotFeature,matrix-vector: no visible global function definition for
  ‘layout’
plotFeature,matrix-vector: no visible global function definition for
  ‘density’
plotFeature,matrix-vector: no visible global function definition for
  ‘plot’
plotFeature,matrix-vector: no visible global function definition for
  ‘points’
plotFeature,matrix-vector: no visible global function definition for
  ‘abline’
plotPairs,ExpressionSet: no visible global function definition for
  ‘validObject’
plotPairs,ExpressionSet: no visible global function definition for
  ‘callGeneric’
plotPairs,matrix: no visible global function definition for ‘par’
plotPairs,matrix: no visible global function definition for ‘hclust’
plotPairs,matrix: no visible global function definition for ‘dist’
plotPairs,matrix: no visible global function definition for ‘cutree’
plotPairs,matrix: no visible global function definition for ‘rainbow’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘par’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘points’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘cor’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘lowess’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘lines’
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for ‘text’
plotPairs,matrix: no visible global function definition for ‘layout’
plotPairs,matrix: no visible global function definition for ‘pairs’
plotPairs,matrix: no visible global function definition for ‘plot’
plotPairs,matrix: no visible global function definition for ‘points’
plotPairs,matrix: no visible global function definition for ‘abline’
plotPairs,matrix: no visible global function definition for ‘text’
plotPairs,matrix : draw.tree: no visible global function definition for
  ‘points’
plotPairs,matrix: no visible global function definition for
  ‘as.dendrogram’
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for ‘validObject’
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for ‘callGeneric’
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for ‘validObject’
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for ‘callGeneric’
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for ‘validObject’
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for ‘callGeneric’
quantileNormalize,matrix-missing: no visible global function definition
  for ‘callGeneric’
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for ‘validObject’
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for ‘callGeneric’
quantileNormalize,vector-vector: no visible global function definition
  for ‘quantile’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘validObject’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘read.table’
readDesign,character-character-ExpressionSet: no visible global
  function definition for ‘new’
readDesign,vector-missing-missing: no visible global function
  definition for ‘callGeneric’
readDesign,vector-missing-missing: no visible global function
  definition for ‘new’
readDesign,vector-vector-missing: no visible global function definition
  for ‘callGeneric’
readDesign,vector-vector-missing: no visible global function definition
  for ‘new’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘validObject’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘read.table’
readPairs,character-character-ExpressionSet: no visible global function
  definition for ‘new’
readPairs,vector-missing-missing: no visible global function definition
  for ‘callGeneric’
readPairs,vector-missing-missing: no visible global function definition
  for ‘new’
readPairs,vector-vector-missing: no visible global function definition
  for ‘callGeneric’
readPairs,vector-vector-missing: no visible global function definition
  for ‘new’
Undefined global functions or variables:
  abline as.dendrogram axis base.stacking.thermodynamics callGeneric
  col2rgb cor cutree data density dist hclust layout lines lowess mad
  median new pairs par plot points quantile rainbow read.table rect
  text validObject
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("graphics", "abline", "axis", "layout", "lines", "pairs",
             "par", "plot", "points", "rect", "text")
  importFrom("methods", "callGeneric", "new", "validObject")
  importFrom("stats", "as.dendrogram", "cor", "cutree", "density",
             "dist", "hclust", "lowess", "mad", "median", "quantile")
  importFrom("utils", "data", "read.table")
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 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
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/HELP.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HELP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘HELP’ ...
** R
** data
** demo
** 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
* DONE (HELP)

name	user	system	elapsed
base.stacking.thermodynamics	0.015	0.005	0.019
calcGC	0.000	0.000	0.001
calcPrototype	0.082	0.002	0.085
calcTm	0.057	0.004	0.063
combineData	0.096	0.001	0.097
createWiggle	0.004	0.001	0.005
exprs2	0.001	0.000	0.000
fuzzyMatches	0.107	0.001	0.109
getFeatures	0.067	0.007	0.075
getSamples	0.029	0.009	0.039
plotBins	0.076	0.005	0.081
plotChip	0.199	0.011	0.210
plotFeature	0.059	0.004	0.063
plotPairs	0.482	0.018	0.504
quantileNormalize	0.047	0.002	0.050
readDesign	0.086	0.002	0.090
readPairs	0.138	0.003	0.143
readSampleKey	0.004	0.001	0.004