BioC 3.1: CHECK report for CAGEr on moscato2

Package: CAGEr

Version: 1.10.1

Command: rm -rf CAGEr.buildbin-libdir CAGEr.Rcheck && mkdir CAGEr.buildbin-libdir CAGEr.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.10.1.tar.gz >CAGEr.Rcheck\00install.out 2>&1 && cp CAGEr.Rcheck\00install.out CAGEr-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.10.1.tar.gz

StartedAt: 2015-10-08 23:56:16 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:03:10 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 413.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CAGEr.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf CAGEr.buildbin-libdir CAGEr.Rcheck && mkdir CAGEr.buildbin-libdir CAGEr.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.10.1.tar.gz >CAGEr.Rcheck\00install.out 2>&1 && cp CAGEr.Rcheck\00install.out CAGEr-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.10.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CAGEr.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.10.1'
* 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 whether package 'CAGEr' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'data.table::shift' when loading 'CAGEr'
See 'E:/biocbld/bbs-3.1-bioc/meat/CAGEr.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [87s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
importPublicData 46.74   0.84   53.56
plotCorrelation   5.87   2.03    7.97
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           44.13   1.00   51.71
plotCorrelation             4.97   1.88    6.85
cumulativeCTSSdistribution  6.10   0.34    6.44
scoreShift                  5.03   0.05    5.07
* 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: 1 WARNING, 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CAGEr' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'data.table::shift' when loading 'CAGEr'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'data.table::shift' when loading 'CAGEr'

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'data.table::shift' when loading 'CAGEr'
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.10.1.zip
* DONE (CAGEr)

name	user	system	elapsed
CAGEset-class	0	0	0
CTSSclusteringMethod	0.04	0.00	0.03
CTSScoordinates	0.03	0.00	0.03
CTSSnormalizedTpm	0.03	0.00	0.03
CTSStagCount	0.05	0.00	0.04
aggregateTagClusters	0.42	0.00	0.97
clusterCTSS	2.31	0.07	2.37
consensusClusters	0.03	0.00	0.03
consensusClustersTpm	0.03	0.00	0.03
cumulativeCTSSdistribution	4.50	0.31	4.81
exportCTSStoBedGraph	0.43	0.03	0.64
exportToBed	0.69	0.00	0.68
expressionClasses	0.03	0.00	0.04
extractExpressionClass	0.03	0.00	0.03
genomeName	0.03	0.00	0.03
getCTSS	0.15	0.00	0.16
getExpressionProfiles	0.77	0.00	0.78
getShiftingPromoters	0.03	0.00	0.03
importPublicData	46.74	0.84	53.56
inputFiles	0.01	0.02	0.03
inputFilesType	0.03	0.00	0.03
librarySizes	0.04	0.00	0.03
mergeCAGEsets	0.29	0.00	0.30
mergeSamples	0.05	0.00	0.04
normalizeTagCount	0.06	0.01	0.08
plotCorrelation	5.87	2.03	7.97
plotExpressionProfiles	0.37	0.00	0.42
plotInterquantileWidth	0.05	0.00	0.05
plotReverseCumulatives	0.08	0.00	0.08
quantilePositions	2.67	0.05	2.72
sampleLabels	0.05	0.00	0.05
scoreShift	4.19	0.03	4.22
setColors	0.03	0.00	0.03
tagClusters	0.03	0.00	0.04

name	user	system	elapsed
CAGEset-class	0	0	0
CTSSclusteringMethod	0.03	0.00	0.03
CTSScoordinates	0.03	0.00	0.03
CTSSnormalizedTpm	0.05	0.00	0.04
CTSStagCount	0.03	0.00	0.04
aggregateTagClusters	0.50	0.00	0.49
clusterCTSS	2.81	0.09	2.91
consensusClusters	0.02	0.00	0.02
consensusClustersTpm	0.03	0.00	0.03
cumulativeCTSSdistribution	6.10	0.34	6.44
exportCTSStoBedGraph	0.53	0.00	0.53
exportToBed	0.61	0.00	0.61
expressionClasses	0.03	0.00	0.03
extractExpressionClass	0.05	0.00	0.05
genomeName	0.01	0.00	0.01
getCTSS	0.11	0.03	0.14
getExpressionProfiles	0.62	0.00	0.66
getShiftingPromoters	0.04	0.00	0.03
importPublicData	44.13	1.00	51.71
inputFiles	0.03	0.00	0.03
inputFilesType	0.01	0.00	0.02
librarySizes	0.02	0.00	0.02
mergeCAGEsets	0.28	0.00	0.28
mergeSamples	0.04	0.00	0.05
normalizeTagCount	0.07	0.01	0.07
plotCorrelation	4.97	1.88	6.85
plotExpressionProfiles	0.38	0.00	0.38
plotInterquantileWidth	0.04	0.00	0.04
plotReverseCumulatives	0.07	0.00	0.07
quantilePositions	3.02	0.01	3.04
sampleLabels	0.03	0.00	0.03
scoreShift	5.03	0.05	5.07
setColors	0.03	0.00	0.03
tagClusters	0.03	0.00	0.03