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CHECK report for HELP on merida2

This page was generated on 2019-04-09 13:24:19 -0400 (Tue, 09 Apr 2019).

Package 737/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HELP 1.41.0
Reid F. Thompson
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/HELP
Branch: master
Last Commit: d06d2ac
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: HELP
Version: 1.41.0
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_1.41.0.tar.gz
StartedAt: 2019-04-09 01:27:57 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:28:41 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 44.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HELP.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HELP.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.41.0’
* 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-3.9-bioc/meat/HELP.Rcheck/00check.log’
for details.



Installation output

HELP.Rcheck/00install.out

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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/3.6/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)

Tests output


Example timings

HELP.Rcheck/HELP-Ex.timings

nameusersystemelapsed
base.stacking.thermodynamics0.0210.0060.027
calcGC0.0010.0000.000
calcPrototype0.0770.0020.079
calcTm0.0670.0030.071
combineData0.1060.0010.109
createWiggle0.0040.0010.005
exprs20.0010.0000.000
fuzzyMatches0.0860.0010.088
getFeatures0.0610.0050.067
getSamples0.0360.0060.041
plotBins0.0960.0040.101
plotChip0.1690.0080.178
plotFeature0.0620.0030.066
plotPairs0.4320.0150.449
quantileNormalize0.0380.0020.039
readDesign0.0890.0020.092
readPairs0.1200.0010.123
readSampleKey0.0020.0010.003