BioC 3.4: CHECK report for CAGEr on morelia

Package: CAGEr

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.16.0.tar.gz

StartedAt: 2017-04-13 23:21:14 -0700 (Thu, 13 Apr 2017)

EndedAt: 2017-04-13 23:25:53 -0700 (Thu, 13 Apr 2017)

EllapsedTime: 279.0 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.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 CAGEr_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CAGEr.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 ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.16.0’
* 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 ‘CAGEr’ 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.
Unexported object imported by a ':::' call: ‘grDevices:::.smoothScatterCalcDensity’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cluster.ctss.strand: no visible binding for global variable ‘tpm’
.cluster.ctss.strand: no visible global function definition for ‘Rle’
.cluster.ctss.strand: no visible global function definition for
  ‘queryHits’
.cluster.ctss.strand.predef: no visible global function definition for
  ‘subjectHits’
.cluster.ctss.strand.predef: no visible global function definition for
  ‘queryHits’
.clusterExpression: no visible global function definition for ‘kmeans’
.ctss2clusters: no visible global function definition for ‘detectCores’
.ctss2clusters: no visible global function definition for ‘mclapply’
.ctss2clusters : <anonymous>: no visible binding for global variable
  ‘chr’
.ctss2clusters.predef: no visible global function definition for
  ‘detectCores’
.ctss2clusters.predef: no visible global function definition for
  ‘mclapply’
.ctss2clusters.predef : <anonymous>: no visible binding for global
  variable ‘chr’
.distclu: no visible binding for global variable ‘tpm’
.distclu: no visible global function definition for ‘mclapply’
.estimate.G.addition.and.correct: no visible binding for global
  variable ‘removedG’
.estimate.G.addition.and.correct: no visible binding for global
  variable ‘V1’
.estimate.G.addition.and.correct: no visible binding for global
  variable ‘V2’
.estimate.G.addition.and.correct: no visible binding for global
  variable ‘nr_tags’
.export.bw.all : <anonymous> : <anonymous>: no visible global function
  definition for ‘seqlengths’
.export.bw.all : <anonymous> : <anonymous>: no visible global function
  definition for ‘seqlengths<-’
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable ‘num’
.fit.power.law.to.reverse.cumulative: no visible binding for global
  variable ‘nr_tags’
.fit.power.law.to.reverse.cumulative: no visible global function
  definition for ‘lm’
.fit.power.law.to.reverse.cumulative: no visible global function
  definition for ‘coefficients’
.get.quant.pos: no visible global function definition for ‘detectCores’
.get.quant.pos: no visible global function definition for ‘mclapply’
.getCumsum: no visible global function definition for ‘detectCores’
.getCumsum: no visible global function definition for ‘mclapply’
.getCumsum : <anonymous>: no visible binding for global variable ‘chr’
.getCumsumChr: no visible global function definition for ‘Rle’
.getCumsumChr2: no visible binding for global variable ‘chr’
.getTotalTagCount: no visible global function definition for
  ‘subjectHits’
.getTotalTagCount: no visible global function definition for
  ‘queryHits’
.getTotalTagCount: no visible binding for global variable ‘tpm’
.getTotalTagCount: no visible binding for global variable
  ‘consensus.cluster’
.make.consensus.clusters: no visible binding for global variable ‘tpm’
.make.consensus.clusters: no visible global function definition for
  ‘queryHits’
.make.consensus.clusters: no visible global function definition for
  ‘subjectHits’
.myColorRamp: no visible global function definition for ‘colorRamp’
.myColorRamp : <anonymous>: no visible global function definition for
  ‘rgb’
.mySmoothScatter: no visible global function definition for
  ‘colorRampPalette’
.mySmoothScatter: no visible binding for global variable ‘blues9’
.mySmoothScatter: no visible binding for global variable ‘box’
.mySmoothScatter: no visible global function definition for ‘par’
.mySmoothScatter: no visible global function definition for ‘xy.coords’
.mySmoothScatter: no visible global function definition for ‘image’
.mySmoothScatter: no visible global function definition for ‘points’
.paraclu: no visible binding for global variable ‘tpm’
.paraclu3: no visible global function definition for ‘detectCores’
.paraclu3 : <anonymous>: no visible binding for global variable ‘chr’
.paraclu3: no visible global function definition for ‘mclapply’
.paraclu3: no visible binding for global variable ‘chr’
.paraclu3: no visible binding for global variable ‘max_d’
.paraclu3: no visible binding for global variable ‘min_d’
.paraclu3: no visible binding for global variable ‘tpm’
.paraclu3: no visible global function definition for ‘queryHits’
.plot.clusters.beanplots: no visible global function definition for
  ‘rgb’
.plotReverseCumulative: no visible binding for global variable ‘num’
.plotReverseCumulative: no visible binding for global variable
  ‘nr_tags’
.plotReverseCumulative: no visible global function definition for
  ‘lines’
.plotReverseCumulative: no visible global function definition for
  ‘plot’
.plotReverseCumulative: no visible global function definition for
  ‘axis’
.predefined.clusters: no visible binding for global variable ‘tpm’
.predefined.clusters: no visible global function definition for
  ‘mclapply’
.remove.added.G : <anonymous>: no visible binding for global variable
  ‘chr’
.remove.added.G: no visible binding for global variable ‘removedG’
.remove.added.G: no visible binding for global variable ‘chr’
.remove.added.G: no visible binding for global variable ‘nr_tags’
.remove.added.G: no visible binding for global variable ‘tag_count’
.reverse.cumsum: no visible global function definition for
  ‘detectCores’
.reverse.cumsum: no visible global function definition for ‘mclapply’
.score.promoter.shifting: no visible global function definition for
  ‘detectCores’
.score.promoter.shifting: no visible global function definition for
  ‘mclapply’
.summarize.clusters: no visible binding for global variable ‘chr’
.summarize.clusters: no visible binding for global variable ‘tpm’
.summarize.clusters: no visible binding for global variable ‘cluster’
.summarize.clusters: no visible binding for global variable ‘nr_ctss’
.summarize.clusters.predef: no visible binding for global variable
  ‘chr’
.summarize.clusters.predef: no visible binding for global variable
  ‘tpm’
.summarize.clusters.predef: no visible binding for global variable
  ‘cluster’
aggregateTagClusters,CAGEset: no visible binding for global variable
  ‘consensus.cluster’
aggregateTagClusters,CAGEset: no visible binding for global variable
  ‘chr’
aggregateTagClusters,CAGEset: no visible binding for global variable
  ‘tpm’
consensusClusters,CAGEset: no visible binding for global variable ‘tpm’
cumulativeCTSSdistribution,CAGEset: no visible binding for global
  variable ‘tpm’
exportToBed,CAGEset : <anonymous>: no visible global function
  definition for ‘col2rgb’
extractExpressionClass,CAGEset: no visible binding for global variable
  ‘expression_class’
getCTSS,CAGEset: no visible global function definition for ‘rainbow’
getCTSS,CAGEset: no visible global function definition for ‘seqlengths’
getCTSS,CAGEset: no visible binding for global variable ‘tag_count’
getCTSS,CAGEset: no visible binding for global variable ‘chr’
getShiftingPromoters,CAGEset: no visible binding for global variable
  ‘groupX.tpm’
getShiftingPromoters,CAGEset: no visible binding for global variable
  ‘groupY.tpm’
getShiftingPromoters,CAGEset: no visible binding for global variable
  ‘shifting.score’
getShiftingPromoters,CAGEset: no visible binding for global variable
  ‘fdr.KS’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘ENCODEtissueCAGEfly’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘ENCODEhumanCellLinesSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘FANTOMhumanSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘FANTOMmouseSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘FANTOM5humanSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘FANTOM5mouseSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘ZebrafishSamples’
importPublicData,character-character-ANY-character: no visible binding
  for global variable ‘ZebrafishCAGE’
importPublicData,character-character-ANY-character: no visible global
  function definition for ‘rainbow’
mergeCAGEsets,CAGEset-CAGEset: no visible global function definition
  for ‘rainbow’
mergeSamples,CAGEset-numeric: no visible global function definition for
  ‘rainbow’
plotCorrelation,CAGEset: no visible global function definition for
  ‘png’
plotCorrelation,CAGEset: no visible global function definition for
  ‘par’
plotCorrelation,CAGEset: no visible global function definition for
  ‘plot’
plotCorrelation,CAGEset: no visible global function definition for
  ‘text’
plotCorrelation,CAGEset: no visible binding for global variable
  ‘strwidth’
plotCorrelation,CAGEset: no visible global function definition for
  ‘box’
plotCorrelation,CAGEset: no visible global function definition for
  ‘strwidth’
plotCorrelation,CAGEset: no visible global function definition for
  ‘axis’
plotCorrelation,CAGEset: no visible global function definition for
  ‘dev.off’
plotExpressionProfiles,CAGEset: no visible global function definition
  for ‘pdf’
plotExpressionProfiles,CAGEset: no visible global function definition
  for ‘par’
plotExpressionProfiles,CAGEset: no visible global function definition
  for ‘dev.off’
plotInterquantileWidth,CAGEset: no visible global function definition
  for ‘pdf’
plotInterquantileWidth,CAGEset: no visible global function definition
  for ‘par’
plotInterquantileWidth,CAGEset : <anonymous>: no visible global
  function definition for ‘hist’
plotInterquantileWidth,CAGEset : <anonymous>: no visible global
  function definition for ‘col2rgb’
plotInterquantileWidth,CAGEset : <anonymous>: no visible global
  function definition for ‘plot’
plotInterquantileWidth,CAGEset : <anonymous>: no visible global
  function definition for ‘rgb’
plotInterquantileWidth,CAGEset: no visible global function definition
  for ‘dev.off’
plotReverseCumulatives,CAGEset: no visible global function definition
  for ‘pdf’
plotReverseCumulatives,CAGEset: no visible global function definition
  for ‘par’
plotReverseCumulatives,CAGEset: no visible global function definition
  for ‘abline’
plotReverseCumulatives,CAGEset: no visible global function definition
  for ‘legend’
plotReverseCumulatives,CAGEset : <anonymous>: no visible global
  function definition for ‘abline’
plotReverseCumulatives,CAGEset : <anonymous>: no visible global
  function definition for ‘text’
plotReverseCumulatives,CAGEset : <anonymous>: no visible global
  function definition for ‘legend’
plotReverseCumulatives,CAGEset: no visible global function definition
  for ‘dev.off’
scoreShift,CAGEset-character-character: no visible global function
  definition for ‘detectCores’
scoreShift,CAGEset-character-character: no visible global function
  definition for ‘mclapply’
scoreShift,CAGEset-character-character : <anonymous>: no visible
  binding for global variable ‘consensus.cluster’
scoreShift,CAGEset-character-character : <anonymous> : <anonymous>: no
  visible global function definition for ‘Rle’
scoreShift,CAGEset-character-character: no visible binding for global
  variable ‘tagcount’
scoreShift,CAGEset-character-character: no visible global function
  definition for ‘p.adjust’
setColors,CAGEset: no visible global function definition for ‘rainbow’
setColors,CAGEset: no visible global function definition for ‘col2rgb’
setColors,CAGEset : <anonymous>: no visible global function definition
  for ‘rgb’
Undefined global functions or variables:
  ENCODEhumanCellLinesSamples ENCODEtissueCAGEfly FANTOM5humanSamples
  FANTOM5mouseSamples FANTOMhumanSamples FANTOMmouseSamples Rle V1 V2
  ZebrafishCAGE ZebrafishSamples abline axis blues9 box chr cluster
  coefficients col2rgb colorRamp colorRampPalette consensus.cluster
  detectCores dev.off expression_class fdr.KS groupX.tpm groupY.tpm
  hist image kmeans legend lines lm max_d mclapply min_d nr_ctss
  nr_tags num p.adjust par pdf plot png points queryHits rainbow
  removedG rgb seqlengths seqlengths<- shifting.score strwidth
  subjectHits tag_count tagcount text tpm xy.coords
Consider adding
  importFrom("grDevices", "blues9", "col2rgb", "colorRamp",
             "colorRampPalette", "dev.off", "pdf", "png", "rainbow",
             "rgb", "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "hist", "image",
             "legend", "lines", "par", "plot", "points", "strwidth",
             "text")
  importFrom("stats", "coefficients", "kmeans", "lm", "p.adjust")
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
importPublicData 34.865  1.513  39.842
plotCorrelation  33.545  0.301  33.837
* 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/CAGEr.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CAGEset-class	0.002	0.000	0.003
CTSSclusteringMethod	0.020	0.004	0.023
CTSScoordinates	0.022	0.003	0.025
CTSSnormalizedTpm	0.024	0.004	0.027
CTSStagCount	0.023	0.003	0.027
aggregateTagClusters	0.362	0.013	0.421
clusterCTSS	2.749	0.081	2.831
consensusClusters	0.025	0.019	0.044
consensusClustersTpm	0.020	0.015	0.034
cumulativeCTSSdistribution	4.010	0.233	4.242
exportCTSStoBedGraph	0.297	0.030	0.326
exportToBed	0.507	0.038	0.547
expressionClasses	0.021	0.015	0.036
extractExpressionClass	0.024	0.016	0.039
genomeName	0.019	0.015	0.035
getCTSS	0.120	0.008	0.481
getExpressionProfiles	0.370	0.021	0.405
getShiftingPromoters	0.024	0.016	0.039
importPublicData	34.865	1.513	39.842
inputFiles	0.019	0.016	0.034
inputFilesType	0.018	0.015	0.034
librarySizes	0.019	0.015	0.035
mergeCAGEsets	0.176	0.012	0.188
mergeSamples	0.031	0.019	0.051
normalizeTagCount	0.041	0.021	0.061
plotCorrelation	33.545	0.301	33.837
plotExpressionProfiles	0.188	0.009	0.199
plotInterquantileWidth	0.039	0.006	0.045
plotReverseCumulatives	0.053	0.006	0.059
quantilePositions	3.971	0.033	4.006
sampleLabels	0.020	0.006	0.025
scoreShift	2.656	0.131	2.787
setColors	0.019	0.004	0.023
tagClusters	0.026	0.003	0.029