BioC 2.12: CHECK report for CAGEr on petty

Package: CAGEr

Version: 1.2.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CAGEr_1.2.9.tar.gz

StartedAt: 2013-10-08 21:47:48 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:55:26 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 458.6 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.2.9'
* 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 ... [30s/32s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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'
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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'images'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [140s/141s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotCorrelation            55.608  0.965  57.064
importPublicData           28.665  1.380  30.403
quantilePositions          10.161  0.065  10.341
cumulativeCTSSdistribution  7.727  0.592   8.415
scoreShift                  4.976  0.058   5.056
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

* installing *source* package 'CAGEr' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'last' when loading 'data.table'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'last' when loading 'data.table'
* DONE (CAGEr)

name	user	system	elapsed
CAGEset-class	0.006	0.003	0.009
CTSSclusteringMethod	0.033	0.004	0.037
CTSScoordinates	0.051	0.005	0.056
CTSSnormalizedTpm	0.060	0.003	0.064
CTSStagCount	0.056	0.006	0.062
aggregateTagClusters	1.437	0.030	1.487
clusterCTSS	4.225	0.294	4.826
consensusClusters	0.043	0.030	0.075
consensusClustersTpm	0.036	0.008	0.043
cumulativeCTSSdistribution	7.727	0.592	8.415
exportCTSStoBedGraph	2.711	0.074	2.800
exportToBed	1.480	0.018	1.508
expressionClasses	0.045	0.007	0.053
extractExpressionClass	0.053	0.012	0.064
genomeName	0.036	0.006	0.042
getCTSS	1.317	0.166	1.549
getExpressionProfiles	1.015	0.030	1.075
getShiftingPromoters	0.048	0.007	0.062
importPublicData	28.665	1.380	30.403
inputFiles	0.038	0.007	0.044
inputFilesType	0.037	0.007	0.045
librarySizes	0.034	0.006	0.041
mergeSamples	0.093	0.013	0.106
normalizeTagCount	0.103	0.006	0.108
plotCorrelation	55.608	0.965	57.064
plotExpressionProfiles	0.452	0.012	0.486
plotInterquantileWidth	0.077	0.103	0.190
plotReverseCumulatives	0.108	0.008	0.116
quantilePositions	10.161	0.065	10.341
sampleLabels	0.036	0.005	0.042
scoreShift	4.976	0.058	5.056
setColors	0.037	0.007	0.044
tagClusters	0.043	0.008	0.051