Package: CAGEr

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.20.0.tar.gz

StartedAt: 2018-04-12 01:13:22 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:18:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 282.8 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CAGEr.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.20.0’
* 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           35.567  2.478  39.709
plotCorrelation            33.317  0.336  34.708
cumulativeCTSSdistribution  4.705  0.324   5.004
* 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-3.6-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	0.003	0.000	0.004
CTSSclusteringMethod	0.017	0.002	0.019
CTSScoordinates	0.020	0.002	0.021
CTSSnormalizedTpm	0.021	0.003	0.025
CTSStagCount	0.043	0.003	0.046
aggregateTagClusters	1.422	0.159	1.095
clusterCTSS	3.427	0.158	3.447
consensusClusters	0.127	0.063	0.066
consensusClustersTpm	0.097	0.054	0.052
cumulativeCTSSdistribution	4.705	0.324	5.004
exportCTSStoBedGraph	0.831	0.064	0.898
exportToBed	1.165	0.035	1.215
expressionClasses	0.030	0.027	0.057
extractExpressionClass	0.025	0.027	0.053
genomeName	0.020	0.023	0.044
getCTSS	0.209	0.033	0.157
getExpressionProfiles	0.806	0.160	0.566
getShiftingPromoters	0.030	0.022	0.055
importPublicData	35.567	2.478	39.709
inputFiles	0.129	0.062	0.050
inputFilesType	0.023	0.021	0.046
librarySizes	0.019	0.021	0.041
mergeCAGEsets	0.677	0.125	0.395
mergeSamples	0.135	0.060	0.062
normalizeTagCount	0.229	0.038	0.185
plotCorrelation	33.317	0.336	34.708
plotExpressionProfiles	0.618	0.007	0.628
plotInterquantileWidth	0.063	0.004	0.069
plotReverseCumulatives	0.240	0.021	0.153
quantilePositions	4.089	0.036	3.981
sampleLabels	0.023	0.002	0.025
scoreShift	2.625	0.092	2.754
setColors	0.026	0.002	0.027
tagClusters	0.029	0.003	0.032