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BioC 3.5: CHECK report for CAGEr on veracruz2

This page was generated on 2017-08-16 13:30:50 -0400 (Wed, 16 Aug 2017).

Package 163/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.18.1
Vanja Haberle , Charles Plessy
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CAGEr
Last Changed Rev: 131771 / Revision: 131943
Last Changed Date: 2017-08-07 04:04:05 -0400 (Mon, 07 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.18.1.tar.gz
StartedAt: 2017-08-16 00:31:01 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:35:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 282.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CAGEr.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.18.1’
* 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           31.146  2.294  34.240
plotCorrelation            31.783  0.371  33.140
cumulativeCTSSdistribution  4.934  0.291   5.039
* 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-3.5-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-class0.0040.0010.005
CTSSclusteringMethod0.0250.0040.029
CTSScoordinates0.0220.0040.026
CTSSnormalizedTpm0.0220.0040.026
CTSStagCount0.0320.0060.039
aggregateTagClusters1.2730.1630.989
clusterCTSS3.1430.1412.947
consensusClusters0.1700.0300.052
consensusClustersTpm0.1640.0270.049
cumulativeCTSSdistribution4.9340.2915.039
exportCTSStoBedGraph1.0340.0651.107
exportToBed0.8320.0340.866
expressionClasses0.0220.0240.046
extractExpressionClass0.0290.0270.056
genomeName0.0170.0270.044
getCTSS0.2260.0430.139
getExpressionProfiles0.7950.1880.497
getShiftingPromoters0.0290.0260.057
importPublicData31.146 2.29434.240
inputFiles0.0180.0010.019
inputFilesType0.0230.0030.032
librarySizes0.0210.0030.023
mergeCAGEsets0.6760.1270.372
mergeSamples0.1290.0370.044
normalizeTagCount0.2420.0060.152
plotCorrelation31.783 0.37133.140
plotExpressionProfiles0.8090.0080.856
plotInterquantileWidth0.0790.0060.090
plotReverseCumulatives0.8260.1761.068
quantilePositions3.8630.0123.985
sampleLabels0.0160.0010.018
scoreShift2.5920.0092.623
setColors0.0240.0020.028
tagClusters0.0270.0020.029