BioC 2.14: CHECK report for CAGEr on moscato2

Package: CAGEr

Version: 1.6.1

Command: rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.6.1.tar.gz >CAGEr-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.6.1.tar.gz

StartedAt: 2014-10-07 23:22:00 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:30:06 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 485.7 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAGEr.buildbin-libdir CAGEr_1.6.1.tar.gz >CAGEr-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CAGEr.buildbin-libdir --install="check:CAGEr-install.out" --force-multiarch --no-vignettes --timings CAGEr_1.6.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/CAGEr.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.6.1'
* 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 ... 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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'
.ctss2clusters : <anonymous>: no visible binding for global variable
  'chr'
.ctss2clusters.predef : <anonymous>: no visible binding for global
  variable 'chr'
.distclu: no visible binding for global variable 'tpm'
.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'
.getCumsum : <anonymous>: no visible binding for global variable 'chr'
.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 : <anonymous>: no visible binding for global variable 'chr'
.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'
.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'
.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 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 : <anonymous>: no visible
  binding for global variable 'consensus.cluster'
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' ... [93s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           36.98   0.66   50.23
plotCorrelation             6.29   1.73    8.02
quantilePositions           6.16   0.03    6.19
scoreShift                  6.05   0.00    6.05
cumulativeCTSSdistribution  5.57   0.25    5.82
** running examples for arch 'x64' ... [103s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           41.81   1.09   54.23
plotCorrelation             7.16   2.13   10.18
cumulativeCTSSdistribution  7.05   0.19    7.24
scoreShift                  6.18   0.00    6.18
quantilePositions           5.65   0.03    5.69
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.6.1.zip
* DONE (CAGEr)

name	user	system	elapsed
CAGEset-class	0	0	0
CTSSclusteringMethod	0.02	0.01	0.03
CTSScoordinates	0.04	0.00	0.05
CTSSnormalizedTpm	0.03	0.02	0.04
CTSStagCount	0.04	0.00	0.04
aggregateTagClusters	1.06	0.01	1.09
clusterCTSS	2.02	0.13	2.15
consensusClusters	0.04	0.00	0.03
consensusClustersTpm	0.03	0.00	0.03
cumulativeCTSSdistribution	5.57	0.25	5.82
exportCTSStoBedGraph	0.65	0.01	0.87
exportToBed	0.77	0.00	0.77
expressionClasses	0.03	0.00	0.03
extractExpressionClass	0.04	0.00	0.05
genomeName	0.03	0.00	0.03
getCTSS	0.18	0.00	0.17
getExpressionProfiles	0.60	0.00	0.61
getShiftingPromoters	0.04	0.02	0.05
importPublicData	36.98	0.66	50.23
inputFiles	0.03	0.00	0.03
inputFilesType	0.04	0.00	0.03
librarySizes	0.03	0.00	0.03
mergeSamples	0.06	0.00	0.06
normalizeTagCount	0.06	0.01	0.08
plotCorrelation	6.29	1.73	8.02
plotExpressionProfiles	0.39	0.02	0.42
plotInterquantileWidth	0.06	0.00	0.06
plotReverseCumulatives	0.08	0.00	0.08
quantilePositions	6.16	0.03	6.19
sampleLabels	0.05	0.00	0.05
scoreShift	6.05	0.00	6.05
setColors	0.03	0.00	0.04
tagClusters	0.03	0.00	0.03

name	user	system	elapsed
CAGEset-class	0	0	0
CTSSclusteringMethod	0.02	0.00	0.01
CTSScoordinates	0.03	0.00	0.03
CTSSnormalizedTpm	0.04	0.00	0.03
CTSStagCount	0.04	0.00	0.05
aggregateTagClusters	1.28	0.02	1.31
clusterCTSS	2.75	0.07	2.82
consensusClusters	0.03	0.00	0.03
consensusClustersTpm	0.03	0.00	0.03
cumulativeCTSSdistribution	7.05	0.19	7.24
exportCTSStoBedGraph	0.81	0.02	0.85
exportToBed	0.91	0.00	0.90
expressionClasses	0.03	0.01	0.03
extractExpressionClass	0.03	0.00	0.03
genomeName	0.03	0.00	0.03
getCTSS	0.16	0.02	0.17
getExpressionProfiles	0.48	0.00	0.48
getShiftingPromoters	0.05	0.00	0.05
importPublicData	41.81	1.09	54.23
inputFiles	0.03	0.00	0.03
inputFilesType	0.01	0.00	0.01
librarySizes	0.01	0.00	0.02
mergeSamples	0.07	0.00	0.06
normalizeTagCount	0.06	0.02	0.08
plotCorrelation	7.16	2.13	10.18
plotExpressionProfiles	0.59	0.02	0.63
plotInterquantileWidth	0.08	0.00	0.07
plotReverseCumulatives	0.12	0.00	0.13
quantilePositions	5.65	0.03	5.69
sampleLabels	0.03	0.00	0.03
scoreShift	6.18	0.00	6.18
setColors	0.03	0.00	0.03
tagClusters	0.03	0.00	0.03