BioC 3.5: CHECK report for motifStack on veracruz2

Package: motifStack

Version: 1.20.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.20.1.tar.gz

StartedAt: 2017-10-18 06:24:20 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:28:51 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 271.1 seconds

RetCode: 0

Status:  OK

CheckDir: motifStack.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/motifStack.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 ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.20.1’
* 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 ‘motifStack’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
browseMotifs : <anonymous>: no visible binding for global variable
  ‘pfm’
browseMotifs : <anonymous>: no visible binding for global variable
  ‘nodeName’
getoffsetPosByIC_old: no visible global function definition for ‘sd’
getoffsetPosByIC_old: no visible global function definition for ‘cor’
hex2psrgb: no visible global function definition for ‘col2rgb’
highlightCol: no visible global function definition for ‘col2rgb’
highlightCol : <anonymous>: no visible global function definition for
  ‘rgb’
isHomoDimer: no visible global function definition for ‘loess’
isHomoDimer: no visible global function definition for ‘predict’
mergeMotifs : rdirichlet: no visible global function definition for
  ‘rgamma’
motifCircos: no visible global function definition for ‘par’
motifCircos: no visible global function definition for ‘dev.size’
motifCircos: no visible global function definition for ‘plot.default’
motifCircos: no visible binding for global variable ‘strwidth’
motifCircos : plotBgArc: no visible global function definition for
  ‘polygon’
motifCircos: no visible global function definition for ‘text’
motifCircos: no visible global function definition for ‘segments’
motifCircos: no visible global function definition for ‘grey’
motifCircos : drawPFMcir: no visible global function definition for
  ‘median’
motifCircos: no visible global function definition for ‘points’
motifCircos: no visible global function definition for ‘lines’
motifCircos: no visible global function definition for ‘symbols’
motifCircos: no visible global function definition for ‘strwidth’
motifCircos: no visible global function definition for ‘box’
motifCloud: no visible global function definition for ‘par’
motifCloud: no visible global function definition for ‘plot.new’
motifCloud: no visible global function definition for ‘strheight’
motifCloud: no visible global function definition for ‘plot.window’
motifCloud: no visible global function definition for ‘runif’
motifCloud: no visible global function definition for ‘plot.default’
motifCloud : plotUnrootedTree: no visible global function definition
  for ‘segments’
motifCloud : plotUnrootedTree: no visible global function definition
  for ‘strheight’
motifCloud: no visible global function definition for ‘segments’
motifCloud: no visible global function definition for ‘legend’
motifPiles: no visible global function definition for ‘par’
motifPiles: no visible global function definition for ‘dev.size’
motifPiles: no visible global function definition for ‘plot.default’
motifPiles: no visible binding for global variable ‘strwidth’
motifPiles: no visible global function definition for ‘strwidth’
motifPiles: no visible global function definition for ‘points’
motifPiles: no visible global function definition for ‘col2rgb’
motifPiles: no visible global function definition for ‘rgb’
motifPiles: no visible global function definition for ‘segments’
motifPiles: no visible global function definition for ‘abline’
motifPiles: no visible global function definition for ‘rect’
motifPiles: no visible global function definition for ‘text’
motifPiles: no visible global function definition for ‘grey’
motifStack: no visible global function definition for ‘plot’
plotMotifLogo: no visible global function definition for ‘plot.new’
plotMotifLogo: no visible global function definition for ‘text’
plotMotifLogo: no visible global function definition for ‘mtext’
plotMotifLogoStack: no visible global function definition for ‘par’
plotMotifLogoStack: no visible global function definition for ‘plot’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘par’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘layout’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘plot.new’
plotMotifLogoStackWithTree: no visible global function definition for
  ‘plot’
plotMotifOverMotif : rdirichlet: no visible global function definition
  for ‘rgamma’
plotMotifOverMotif: no visible global function definition for
  ‘plot.new’
plotMotifOverMotif: no visible global function definition for
  ‘dev.size’
plotMotifStackWithPhylog: no visible global function definition for
  ‘par’
plotMotifStackWithPhylog: no visible global function definition for
  ‘plot.default’
plotMotifStackWithPhylog: no visible binding for global variable
  ‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
  ‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
  ‘text’
plotMotifStackWithPhylog: no visible global function definition for
  ‘segments’
plotMotifStackWithPhylog: no visible global function definition for
  ‘grey’
plotMotifStackWithPhylog: no visible global function definition for
  ‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘par’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘plot.default’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘dev.size’
plotMotifStackWithRadialPhylog: no visible binding for global variable
  ‘strwidth’
plotMotifStackWithRadialPhylog : plotBgArc: no visible global function
  definition for ‘polygon’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘text’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘segments’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘grey’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘median’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘lines’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘symbols’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘strwidth’
plotMotifStackWithRadialPhylog: no visible global function definition
  for ‘box’
plotXaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘par’
readPCM : <anonymous>: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  abline axis box col2rgb cor dev.size grey layout legend lines loess
  median mtext nodeName par pfm plot plot.default plot.new plot.window
  points polygon predict read.table rect rgamma rgb runif sd segments
  strheight strwidth symbols text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.size", "grey", "rgb")
  importFrom("graphics", "abline", "axis", "box", "layout", "legend",
             "lines", "mtext", "par", "plot", "plot.default", "plot.new",
             "plot.window", "points", "polygon", "rect", "segments",
             "strheight", "strwidth", "symbols", "text")
  importFrom("stats", "cor", "loess", "median", "predict", "rgamma",
             "runif", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/motifStack.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DNAmotifAlignment	0.351	0.038	0.399
browseMotifs	2.032	0.038	2.145
colorset	0.000	0.000	0.001
getRankedUniqueMotifs	0.002	0.000	0.003
highlightCol	0.001	0.000	0.001
mergeMotifs	0.223	0.003	0.241
motifCircos	0.008	0.000	0.011
motifCloud	0.005	0.001	0.006
motifPiles	0.008	0.000	0.008
motifSignature	0.005	0.001	0.005
motifStack	0.003	0.000	0.002
ouNode-class	0.007	0.001	0.008
pcm-class	1.012	0.129	1.191
pcm-methods	0.008	0.001	0.009
pfm-class	0.716	0.118	0.876
pfm-methods	0.008	0.002	0.011
pfm2pwm	0.118	0.001	0.125
plotMotifLogo	0.551	0.115	0.701
plotMotifLogoA	0.759	0.114	0.911
plotMotifLogoStack	0.576	0.107	0.727
plotMotifLogoStackWithTree	1.713	0.231	2.032
plotMotifOverMotif	0.673	0.113	0.824
plotMotifStackWithPhylog	0.004	0.000	0.004
plotMotifStackWithRadialPhylog	0.005	0.000	0.006
readPCM	0.009	0.001	0.010
reorderUPGMAtree	0.003	0.000	0.004