BioC 3.2: CHECK report for CAGEr on oaxaca

Package: CAGEr

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAGEr_1.12.0.tar.gz

StartedAt: 2016-04-22 22:20:45 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:41:15 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 1230.5 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CAGEr.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.12.0’
* 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 ... [18s/18s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1m/17m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotCorrelation            46.092  0.378  46.501
importPublicData            9.299  0.550 967.500
cumulativeCTSSdistribution  5.112  0.311   5.425
scoreShift                  4.980  0.034   5.016
* 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-3.2-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	0.004	0.000	0.005
CTSSclusteringMethod	0.027	0.008	0.034
CTSScoordinates	0.035	0.005	0.041
CTSSnormalizedTpm	0.041	0.007	0.049
CTSStagCount	0.046	0.008	0.054
aggregateTagClusters	0.855	0.011	0.866
clusterCTSS	2.784	0.112	2.896
consensusClusters	0.036	0.026	0.061
consensusClustersTpm	0.034	0.024	0.057
cumulativeCTSSdistribution	5.112	0.311	5.425
exportCTSStoBedGraph	0.477	0.029	0.505
exportToBed	0.408	0.027	0.436
expressionClasses	0.030	0.017	0.047
extractExpressionClass	0.04	0.02	0.06
genomeName	0.025	0.020	0.045
getCTSS	0.171	0.009	0.539
getExpressionProfiles	0.546	0.024	0.583
getShiftingPromoters	0.036	0.022	0.058
importPublicData	9.299	0.550	967.500
inputFiles	0.031	0.008	0.039
inputFilesType	0.032	0.009	0.042
librarySizes	0.031	0.009	0.039
mergeCAGEsets	0.664	0.066	0.730
mergeSamples	0.051	0.003	0.053
normalizeTagCount	0.071	0.002	0.072
plotCorrelation	46.092	0.378	46.501
plotExpressionProfiles	0.286	0.011	0.299
plotInterquantileWidth	0.050	0.009	0.063
plotReverseCumulatives	0.082	0.010	0.092
quantilePositions	3.756	0.053	3.814
sampleLabels	0.026	0.005	0.031
scoreShift	4.980	0.034	5.016
setColors	0.032	0.006	0.039
tagClusters	0.033	0.007	0.040