BioC 3.2: CHECK report for CAGEr on linux1.bioconductor.org

Package: CAGEr

Version: 1.12.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.12.0.tar.gz

StartedAt: 2015-10-27 01:38:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:42:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 214.7 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CAGEr.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.12.0’
* 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 ... [16s/16s] 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.
* 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’
.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 ‘pos’
.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’
.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’
.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 binding for global variable ‘tpm’
.getTotalTagCount: no visible binding for global variable
  ‘consensus.cluster’
.make.consensus.clusters: no visible binding for global variable ‘tpm’
.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’
.plotReverseCumulative: no visible binding for global variable ‘num’
.plotReverseCumulative: no visible binding for global variable
  ‘nr_tags’
.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 ‘pos’
.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 ‘pos’
.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
  ‘pos’
.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’
cumulativeCTSSdistribution,CAGEset: no visible binding for global
  variable ‘tpm’
extractExpressionClass,CAGEset: no visible binding for global variable
  ‘expression_class’
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’
getCTSS,CAGEset: no visible binding for global variable ‘pos’
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’
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’
* 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 ... [69s/74s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
importPublicData 41.548   0.62  47.269
* 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-3.2-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	0.002
CTSSclusteringMethod	0.017	0.004	0.020
CTSScoordinates	0.023	0.000	0.023
CTSSnormalizedTpm	0.023	0.004	0.027
CTSStagCount	0.027	0.000	0.027
aggregateTagClusters	0.639	0.000	0.640
clusterCTSS	2.515	0.072	2.588
consensusClusters	0.022	0.000	0.022
consensusClustersTpm	0.021	0.000	0.020
cumulativeCTSSdistribution	4.411	0.240	4.658
exportCTSStoBedGraph	0.34	0.00	0.34
exportToBed	0.367	0.004	0.371
expressionClasses	0.022	0.000	0.022
extractExpressionClass	0.028	0.000	0.027
genomeName	0.016	0.004	0.020
getCTSS	0.076	0.008	0.084
getExpressionProfiles	0.195	0.004	0.199
getShiftingPromoters	0.024	0.000	0.024
importPublicData	41.548	0.620	47.269
inputFiles	0.036	0.000	0.036
inputFilesType	0.036	0.000	0.036
librarySizes	0.031	0.004	0.036
mergeCAGEsets	0.289	0.000	0.288
mergeSamples	0.048	0.000	0.048
normalizeTagCount	0.075	0.000	0.075
plotCorrelation	4.645	0.112	4.772
plotExpressionProfiles	0.183	0.004	0.188
plotInterquantileWidth	0.031	0.000	0.031
plotReverseCumulatives	0.048	0.000	0.048
quantilePositions	2.322	0.000	2.326
sampleLabels	0.032	0.000	0.033
scoreShift	3.799	0.000	3.803
setColors	0.015	0.004	0.020
tagClusters	0.022	0.000	0.022