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BioC 2.13: CHECK report for CAGEr on zin1

This page was generated on 2014-04-05 09:48:34 -0700 (Sat, 05 Apr 2014).

Package 106/750HostnameOS / ArchBUILDCHECKBUILD BIN
CAGEr 1.4.1
Vanja Haberle
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CAGEr
Last Changed Rev: 83252 / Revision: 88450
Last Changed Date: 2013-11-13 06:43:25 -0800 (Wed, 13 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CAGEr
Version: 1.4.1
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CAGEr_1.4.1.tar.gz
StartedAt: 2014-04-05 00:01:00 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:04:38 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 218.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CAGEr.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.4.1’
* 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 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
Package in Depends field not imported from: ‘BSgenome.Mmusculus.UCSC.mm9’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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’
.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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘CAGEr.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
importPublicData           14.749  0.152  14.998
cumulativeCTSSdistribution  6.133  0.344   6.500
scoreShift                  5.377  0.000   5.382
* 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 were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/CAGEr.Rcheck/00check.log’
for details.

CAGEr.Rcheck/00install.out:

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

CAGEr.Rcheck/CAGEr-Ex.timings:

nameusersystemelapsed
CAGEset-class0.2120.0000.212
CTSSclusteringMethod0.0200.0000.019
CTSScoordinates0.0240.0000.022
CTSSnormalizedTpm0.0280.0000.026
CTSStagCount0.2240.0000.225
aggregateTagClusters0.7400.0040.825
clusterCTSS2.3400.1402.488
consensusClusters0.0200.0040.024
consensusClustersTpm0.0200.0000.021
cumulativeCTSSdistribution6.1330.3446.500
exportCTSStoBedGraph1.6640.0081.675
exportToBed0.7640.0000.763
expressionClasses0.020.000.02
extractExpressionClass0.0280.0000.029
genomeName0.0160.0000.019
getCTSS0.6880.0760.765
getExpressionProfiles0.2840.0000.283
getShiftingPromoters0.0240.0000.026
importPublicData14.749 0.15214.998
inputFiles0.0160.0000.019
inputFilesType0.2560.0200.283
librarySizes0.0160.0000.019
mergeSamples0.0520.0000.054
normalizeTagCount0.0560.0040.061
plotCorrelation4.7320.0724.831
plotExpressionProfiles0.260.000.26
plotInterquantileWidth0.0320.0000.031
plotReverseCumulatives0.0720.0000.073
quantilePositions4.9640.0084.982
sampleLabels0.0200.0000.018
scoreShift5.3770.0005.382
setColors0.0200.0000.018
tagClusters0.0160.0040.020