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BioC 3.4: CHECK report for CAGEr on malbec1

This page was generated on 2017-04-14 16:08:05 -0400 (Fri, 14 Apr 2017).

Package 153/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.16.0
Vanja Haberle
Snapshot Date: 2017-04-12 17:17:05 -0400 (Wed, 12 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CAGEr
Last Changed Rev: 122710 / Revision: 128622
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.16.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.16.0.tar.gz
StartedAt: 2017-04-12 21:17:16 -0400 (Wed, 12 Apr 2017)
EndedAt: 2017-04-12 21:20:55 -0400 (Wed, 12 Apr 2017)
EllapsedTime: 219.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CAGEr.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 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           29.140  0.272  33.235
cumulativeCTSSdistribution  5.108  0.112   5.227
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CAGEr.Rcheck/00check.log’
for details.

CAGEr.Rcheck/00install.out:

* 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)

CAGEr.Rcheck/CAGEr-Ex.timings:

nameusersystemelapsed
CAGEset-class0.0000.0000.002
CTSSclusteringMethod0.0200.0000.022
CTSScoordinates0.0240.0000.024
CTSSnormalizedTpm0.0280.0000.027
CTSStagCount0.0280.0000.027
aggregateTagClusters0.3720.0120.365
clusterCTSS3.9520.0483.978
consensusClusters0.0560.0000.055
consensusClustersTpm0.0240.0000.027
cumulativeCTSSdistribution5.1080.1125.227
exportCTSStoBedGraph0.3000.0040.307
exportToBed0.5040.0280.534
expressionClasses0.0240.0000.023
extractExpressionClass0.0160.0080.026
genomeName0.0160.0040.022
getCTSS0.1760.0000.697
getExpressionProfiles0.4120.0040.419
getShiftingPromoters0.0320.0000.033
importPublicData29.140 0.27233.235
inputFiles0.0200.0000.021
inputFilesType0.0200.0000.021
librarySizes0.0200.0000.021
mergeCAGEsets0.1680.0000.159
mergeSamples0.0320.0000.032
normalizeTagCount0.0560.0000.045
plotCorrelation3.7560.0363.793
plotExpressionProfiles0.1920.0000.193
plotInterquantileWidth0.0320.0000.032
plotReverseCumulatives0.0560.0000.044
quantilePositions3.8480.0003.852
sampleLabels0.0160.0040.022
scoreShift2.6640.0002.668
setColors0.0200.0000.021
tagClusters0.0240.0000.026