BioC 3.4: CHECK report for motifStack on morelia

Package: motifStack

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.18.0.tar.gz

StartedAt: 2017-04-15 05:18:56 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:22:59 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 242.8 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/motifStack.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.18.0’
* 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 ‘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 ... NOTE
Warning: no function found corresponding to methods exports from ‘motifStack’ for: ‘plot’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
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 par 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 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 ‘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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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	0.181	0.008	0.190
colorset	0.001	0.000	0.000
getRankedUniqueMotifs	0.002	0.000	0.002
highlightCol	0.001	0.000	0.001
mergeMotifs	0.231	0.004	0.235
motifCircos	0.010	0.001	0.010
motifCloud	0.003	0.000	0.003
motifPiles	0.011	0.001	0.012
motifSignature	0.005	0.000	0.005
motifStack	0.003	0.000	0.003
ouNode-class	0.004	0.000	0.004
pcm-class	0.588	0.098	0.992
pcm-methods	0.009	0.001	0.009
pfm-class	0.593	0.101	0.978
pfm-methods	0.009	0.001	0.010
pfm2pwm	1.374	0.038	1.413
plotMotifLogo	0.638	0.106	0.916
plotMotifLogoA	0.878	0.102	1.002
plotMotifLogoStack	0.659	0.103	0.829
plotMotifLogoStackWithTree	2.074	0.221	2.437
plotMotifOverMotif	0.820	0.096	1.047
plotMotifStackWithPhylog	0.007	0.000	0.007
plotMotifStackWithRadialPhylog	0.009	0.001	0.009
readPCM	0.017	0.001	0.018
reorderUPGMAtree	0.003	0.000	0.003