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BioC 3.2: CHECK report for ChIPQC on oaxaca

This page was generated on 2016-04-23 10:27:42 -0700 (Sat, 23 Apr 2016).

Package 166/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.6.1
Tom Carroll , Rory Stark
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChIPQC
Last Changed Rev: 109652 / Revision: 116712
Last Changed Date: 2015-10-15 08:14:18 -0700 (Thu, 15 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPQC
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.6.1.tar.gz
StartedAt: 2016-04-22 22:37:45 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:45:16 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 451.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPQC.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPQC_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPQC.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 ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPQC’ can be installed ... [33s/34s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
'library' or 'require' calls in package code:
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
  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 ... NOTE
Foreign function call to a different package:
  .Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
GetGRanges: warning in read.delim(LoadFile, sep = sepr, header = TRUE,
  comment = "#"): partial argument match of 'comment' to 'comment.char'
GetGRanges: no visible global function definition for ‘seqlevels<-’
findCovMaxPos: no visible global function definition for ‘seqlengths’
findCovMaxPos: no visible global function definition for ‘seqlengths<-’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg18.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Celegans.UCSC.ce6.ensGene’
getAnnotation: no visible binding for global variable
  ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
getAnnotation: no visible global function definition for
  ‘fiveUTRsByTranscript’
getAnnotation: no visible global function definition for
  ‘threeUTRsByTranscript’
getAnnotation: no visible global function definition for ‘cdsBy’
getAnnotation: no visible global function definition for
  ‘intronsByTranscript’
getAnnotation: no visible global function definition for ‘transcripts’
getAnnotation: no visible global function definition for ‘seqlengths’
makeCCplot: no visible binding for global variable ‘Shift_Size’
makeCCplot: no visible binding for global variable ‘CC_Score’
makeCoveragePlot: no visible binding for global variable ‘Depth’
makeCoveragePlot: no visible binding for global variable ‘log10_bp’
makeCoveragePlot: no visible binding for global variable ‘Sample’
makeFriblPlot: no visible binding for global variable ‘Sample’
makeFriblPlot: no visible binding for global variable ‘FRIBL’
makeFriblPlot: no visible binding for global variable ‘Reads’
makeFripPlot: no visible binding for global variable ‘Sample’
makeFripPlot: no visible binding for global variable ‘FRIP’
makeFripPlot: no visible binding for global variable ‘Reads’
makePeakProfilePlot: no visible binding for global variable ‘Distance’
makePeakProfilePlot: no visible binding for global variable ‘Signal’
makeRapPlot: no visible binding for global variable ‘Sample’
makeRapPlot: no visible binding for global variable ‘CountsInPeaks’
makeRegiPlot: no visible binding for global variable ‘Sample’
makeRegiPlot: no visible binding for global variable ‘GenomicIntervals’
makeRegiPlot: no visible binding for global variable ‘log2_Enrichment’
makeSSDPlot: no visible binding for global variable ‘Sample’
makeSSDPlot: no visible global function definition for ‘geom_point’
sampleQC: no visible global function definition for ‘index’
sampleQC: no visible global function definition for ‘BamFile’
sampleQC: no visible global function definition for ‘indexBam’
sampleQC: no visible global function definition for ‘seqlevels<-’
plotCC,ChIPQCexperiment: no visible binding for global variable
  ‘Sample’
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable ‘Sample’
plotRap,ChIPQCexperiment: no visible global function definition for
  ‘coord_cartesian’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotCC-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotCoverageHist-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotFribl-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotFrip-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotPeakProfile-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotRap-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotRegi-methods.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotSSD-methods.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... [96s/97s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ChIPQCreport 54.36  1.759  56.555
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.


ChIPQC.Rcheck/00install.out:

* installing *source* package ‘ChIPQC’ ...
** 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 (ChIPQC)

ChIPQC.Rcheck/ChIPQC-Ex.timings:

nameusersystemelapsed
ChIPQC-data1.7180.0381.757
ChIPQC1.0510.0231.075
ChIPQCexperiment-class0.5810.0240.606
ChIPQCreport54.360 1.75956.555
ChIPQCsample-class0.9840.0261.036
FragmentLengthCrossCoverage-methods0.0940.0040.100
Normalisedaveragepeaksignal-methods0.0250.0050.030
QCannotation-methods0.0140.0050.018
QCcontrol-methods0.2460.0090.256
QCdba-methods0.1180.0060.125
QCmetadata-methods0.1290.0080.137
QCmetrics-methods0.6120.0130.625
QCsample-methods0.0700.0060.075
ReadLengthCrossCoverage-methods0.0140.0050.019
RelativeCrossCoverage-methods0.0780.0060.085
averagepeaksignal-methods0.0230.0060.030
coveragehistogram-methods0.0240.0060.030
crosscoverage-methods0.0220.0060.029
duplicateRate-methods0.0140.0050.020
duplicates-methods0.0160.0060.021
flagtagcounts-methods0.0150.0060.021
fragmentlength-methods0.0740.0050.080
frip-methods0.0150.0060.020
mapped-methods0.0150.0060.020
peaks-methods0.0880.0060.095
plotCC-methods0.9500.0100.961
plotCorHeatmap-methods2.6300.0772.710
plotCoverageHist-methods0.8190.0090.830
plotFribl-methods0.8790.0050.885
plotFrip-methods0.9370.0070.944
plotPeakProfile-methods1.9880.0472.038
plotPrincomp-methods3.1080.0803.192
plotRap-methods1.1480.0091.159
plotRegi-methods1.7300.0161.748
plotSSD-methods1.6560.0151.673
readlength-methods0.0130.0050.017
reads-methods0.0120.0060.018
regi-methods0.0650.0060.071
ribl-methods0.0150.0060.021
rip-methods0.0120.0050.018
ssd-methods0.0130.0040.017