Package: wavClusteR

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings wavClusteR_2.14.0.tar.gz

StartedAt: 2018-10-17 00:38:15 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:42:48 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 273.1 seconds

RetCode: 0

Status:  OK

CheckDir: wavClusteR.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:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings wavClusteR_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/wavClusteR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wavClusteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wavClusteR’ version ‘2.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘wavClusteR’ 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 ‘doMC’ 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
annotateClusters: no visible binding for global variable ‘Percentage’
annotateClusters: no visible binding for global variable ‘Compartment’
estimateFDR: no visible global function definition for ‘DNAString’
estimateFDR: no visible global function definition for ‘lines’
estimateFDR: no visible global function definition for ‘legend’
estimateFDR: no visible global function definition for ‘axis’
exportGR: no visible global function definition for ‘write.table’
filterClustersCWT: no visible global function definition for
  ‘DNAString’
filterClustersMRN: no visible global function definition for
  ‘txtProgressBar’
filterClustersMRN: no visible global function definition for
  ‘setTxtProgressBar’
getClustersCWT: no visible global function definition for
  ‘registerDoMC’
getClustersCWT: no visible global function definition for ‘seqlevels’
getClustersMRN: no visible global function definition for
  ‘registerDoMC’
getComplSubst: no visible global function definition for ‘DNAStringSet’
getExpInterval: no visible global function definition for ‘par’
getExpInterval: no visible global function definition for ‘lines’
getExpInterval: no visible global function definition for ‘legend’
getExpInterval: no visible global function definition for ‘polygon’
getExpInterval: no visible global function definition for ‘rect’
getExpInterval: no visible global function definition for ‘text’
getLogOdd: no visible global function definition for ‘dbinom’
getMetaCoverage: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘grid’
getMetaGene: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘abline’
getMetaTSS: no visible global function definition for ‘grid’
getMetaTSS: no visible global function definition for ‘axis’
plotSizeDistribution: no visible global function definition for ‘hist’
plotStatistics: no visible binding for global variable ‘panel.smooth’
plotStatistics : panelCor: no visible global function definition for
  ‘par’
plotStatistics : panelCor: no visible global function definition for
  ‘strwidth’
plotStatistics : panelCor: no visible global function definition for
  ‘text’
plotStatistics: no visible global function definition for ‘pairs’
plotSubstitutions: no visible global function definition for ‘par’
plotSubstitutions: no visible global function definition for ‘barplot’
processChunk: no visible global function definition for ‘extractAt’
processMD: no visible global function definition for ‘registerDoMC’
readSortedBam: no visible global function definition for ‘scanBamFlag’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘rname’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘qwidth’
Undefined global functions or variables:
  Compartment DNAString DNAStringSet Percentage abline axis barplot
  dbinom extractAt grid hist legend lines pairs panel.smooth par
  polygon qwidth rect registerDoMC rname scanBamFlag seqlevels
  setTxtProgressBar strwidth text txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "grid", "hist",
             "legend", "lines", "pairs", "panel.smooth", "par",
             "polygon", "rect", "strwidth", "text")
  importFrom("stats", "dbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
annotateClusters 5.357  0.238   5.644
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
FitMixtureModel	0.060	0.003	0.063
annotateClusters	5.357	0.238	5.644
filterClusters	3.348	0.032	3.403
getAllSub	1.908	0.020	1.936
getClusters	2.586	0.022	2.631
getExpInterval	0.040	0.009	0.048
getHighConfSub	1.915	0.083	2.028
getMetaCoverage	2.871	0.041	2.926
getMetaGene	2.936	0.026	2.993
getMetaTSS	0.157	0.008	0.166
plotSizeDistribution	3.024	0.021	3.067
plotStatistics	3.008	0.030	3.063
plotSubstitutions	1.912	0.015	1.951
readSortedBam	0.101	0.007	0.111