BioC 3.4: CHECK report for seqPattern on morelia

Package: seqPattern

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqPattern_1.6.0.tar.gz

StartedAt: 2017-04-15 07:58:49 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:02:11 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 201.4 seconds

RetCode: 0

Status:  OK

CheckDir: seqPattern.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 seqPattern_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqPattern.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 ‘seqPattern/DESCRIPTION’ ... OK
* this is package ‘seqPattern’ version ‘1.6.0’
* 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 ‘seqPattern’ 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
'library' or 'require' call to ‘parallel’ in package code.
  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
.pattern.smoothscatter: no visible global function definition for
  ‘mclapply’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘png’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘par’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘colorRampPalette’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘axis’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘box’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘lines’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘text’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘abline’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘dev.off’
.pattern.smoothscatter: no visible global function definition for ‘png’
.pattern.smoothscatter: no visible global function definition for ‘par’
.pattern.smoothscatter: no visible global function definition for
  ‘colorRampPalette’
.pattern.smoothscatter: no visible global function definition for
  ‘axis’
.pattern.smoothscatter: no visible global function definition for ‘box’
.pattern.smoothscatter: no visible global function definition for
  ‘lines’
.pattern.smoothscatter: no visible global function definition for
  ‘text’
.pattern.smoothscatter: no visible global function definition for
  ‘abline’
.pattern.smoothscatter: no visible global function definition for
  ‘dev.off’
.pattern.smoothscatter: no visible global function definition for
  ‘plot’
.plot.motif.heatmap: no visible global function definition for ‘par’
.plot.motif.heatmap: no visible global function definition for ‘image’
.plot.motif.heatmap: no visible global function definition for ‘axis’
.plot.motif.heatmap: no visible global function definition for ‘box’
.plot.motif.heatmap: no visible global function definition for ‘lines’
.plot.motif.heatmap: no visible global function definition for ‘text’
.plot.motif.heatmap: no visible global function definition for ‘abline’
.plot.windowed.average: no visible global function definition for
  ‘rainbow’
.plot.windowed.average: no visible global function definition for
  ‘plot’
.plot.windowed.average : <anonymous>: no visible global function
  definition for ‘lines’
.plot.windowed.average: no visible global function definition for
  ‘legend’
.plot.windowed.average: no visible global function definition for
  ‘abline’
.smoothScatter: no visible global function definition for
  ‘colorRampPalette’
.smoothScatter: no visible binding for global variable ‘blues9’
.smoothScatter: no visible binding for global variable ‘box’
.smoothScatter: no visible global function definition for ‘par’
.smoothScatter: no visible global function definition for ‘xy.coords’
.smoothScatter: no visible global function definition for ‘image’
.smoothScatter: no visible global function definition for ‘points’
plotPatternOccurrenceAverage: no visible global function definition for
  ‘rainbow’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘installed.packages’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘detectCores’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘mclapply’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘png’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘colorRampPalette’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘layout’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘par’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘plot’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘box’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘dev.off’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘installed.packages’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘detectCores’
plotPatternOccurrenceAverage,DNAStringSet: no visible global function
  definition for ‘rainbow’
Undefined global functions or variables:
  abline axis blues9 box colorRampPalette detectCores dev.off image
  installed.packages layout legend lines mclapply par plot png points
  rainbow text xy.coords
Consider adding
  importFrom("grDevices", "blues9", "colorRampPalette", "dev.off", "png",
             "rainbow", "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "legend", "lines", "par", "plot", "points", "text")
  importFrom("utils", "installed.packages")
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 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
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotPatternDensityMap        52.064  1.190  53.256
plotMotifDensityMap          20.890  0.177  21.076
plotMotifScanScores          13.563  0.069  13.626
plotPatternOccurrenceAverage  3.861  1.305   5.170
* 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/seqPattern.Rcheck/00check.log’
for details.

* installing *source* package ‘seqPattern’ ...
** 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 (seqPattern)

name	user	system	elapsed
getPatternOccurrenceList	2.974	0.527	3.504
motifScanHits	2.617	0.016	2.636
motifScanScores	2.361	0.024	2.385
plotMotifDensityMap	20.890	0.177	21.076
plotMotifOccurrenceAverage	3.035	0.024	3.071
plotMotifScanScores	13.563	0.069	13.626
plotPatternDensityMap	52.064	1.190	53.256
plotPatternOccurrenceAverage	3.861	1.305	5.170