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CHECK report for ChIPQC on celaya2

This page was generated on 2019-04-09 13:10:16 -0400 (Tue, 09 Apr 2019).

Package 256/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.19.2
Tom Carroll , Rory Stark
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ChIPQC
Branch: master
Last Commit: 4a26e5c
Last Changed Date: 2019-02-28 21:36:10 -0400 (Thu, 28 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ChIPQC
Version: 1.19.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.19.2.tar.gz
StartedAt: 2019-04-09 00:36:52 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:46:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 576.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.19.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.19.2’
* 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 ... 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
Unexported object imported by a ':::' call: ‘S4Vectors:::tabulate2’
  See the note in ?`:::` about the use of this operator.
* 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: 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.hg38.knownGene’
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 binding for global variable ‘SSD’
makeSSDPlot: no visible global function definition for ‘geom_point’
sampleQC: no visible global function definition for ‘seqlevels<-’
plotCC,ChIPQCexperiment: no visible binding for global variable
  ‘Sample’
plotCC,list: no visible binding for global variable ‘Sample’
plotPeakProfile,ChIPQCexperiment: no visible binding for global
  variable ‘Sample’
plotPeakProfile,list: no visible binding for global variable ‘Sample’
Undefined global functions or variables:
  CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals
  Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene
  geom_point log10_bp log2_Enrichment seqlengths seqlengths<-
  seqlevels<-
Consider adding
  importFrom("stats", "SSD")
to your NAMESPACE file.
* 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 ... NOTE
Output for data("tamoxifen_QC", package = "ChIPQC"):
  
* checking data for non-ASCII characters ... WARNING
  Error loading dataset 'exampleExp':
   Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  
  Error loading dataset 'tamoxifen':
   Error in .requirePackage(package) : 
    unable to find required package 'ChIPQC'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ChIPQCreport 55.061   5.56  61.944
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.



Installation output

ChIPQC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPQC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ChIPQC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ChIPQC.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPQC)

Tests output


Example timings

ChIPQC.Rcheck/ChIPQC-Ex.timings

nameusersystemelapsed
ChIPQC-data2.0130.0752.088
ChIPQC0.7730.0520.824
ChIPQCexperiment-class1.4100.0361.446
ChIPQCreport55.061 5.56061.944
ChIPQCsample-class2.0820.0662.151
FragmentLengthCrossCoverage-methods0.1280.0060.134
Normalisedaveragepeaksignal-methods0.0400.0110.051
QCannotation-methods0.0240.0090.033
QCcontrol-methods0.3070.0250.332
QCdba-methods0.1880.0180.205
QCmetadata-methods0.2050.0220.228
QCmetrics-methods0.8430.0320.876
QCsample-methods0.0950.0150.112
ReadLengthCrossCoverage-methods0.0230.0150.038
RelativeCrossCoverage-methods0.1310.0140.145
averagepeaksignal-methods0.0430.0160.059
coveragehistogram-methods0.0460.0150.060
crosscoverage-methods0.0390.0150.055
duplicateRate-methods0.0220.0150.037
duplicates-methods0.0220.0100.033
flagtagcounts-methods0.0210.0130.033
fragmentlength-methods0.1330.0160.152
frip-methods0.0250.0130.044
mapped-methods0.0260.0140.039
peaks-methods0.2710.0160.298
plotCC-methods2.6250.0242.653
plotCorHeatmap-methods0.3720.0390.409
plotCoverageHist-methods1.1400.0221.159
plotFribl-methods1.3470.0251.372
plotFrip-methods1.3200.0171.337
plotPeakProfile-methods2.3830.0762.461
plotPrincomp-methods0.4360.0270.464
plotRap-methods1.4880.0441.542
plotRegi-methods1.8510.0401.892
plotSSD-methods2.7360.0322.770
readlength-methods0.0170.0100.027
reads-methods0.0160.0090.025
regi-methods0.0590.0120.072
ribl-methods0.0160.0090.024
rip-methods0.0200.0130.034
ssd-methods0.0220.0120.034