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CHECK report for ChIPQC on malbec1

This page was generated on 2020-08-10 11:38:37 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChIPQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 275/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.25.2
Tom Carroll , Rory Stark
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/ChIPQC
Branch: master
Last Commit: bd13ca8
Last Changed Date: 2020-07-18 12:34:52 -0400 (Sat, 18 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPQC
Version: 1.25.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChIPQC_1.25.2.tar.gz
StartedAt: 2020-08-10 00:36:49 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 00:44:45 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 475.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChIPQC_1.25.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/ChIPQC.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.25.2’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ChIPQCreport 31.376  0.204  31.706
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.



Installation output

ChIPQC.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ChIPQC
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-data1.4920.0281.521
ChIPQC0.6640.0040.671
ChIPQCexperiment-class0.6160.0080.624
ChIPQCreport31.376 0.20431.706
ChIPQCsample-class1.6640.0121.688
FragmentLengthCrossCoverage-methods0.0880.0000.086
Normalisedaveragepeaksignal-methods0.040.000.04
QCannotation-methods0.0240.0000.025
QCcontrol-methods0.3200.0120.333
QCdba-methods0.20.00.2
QCmetadata-methods0.2040.0040.210
QCmetrics-methods0.6120.0000.611
QCsample-methods0.0560.0000.055
ReadLengthCrossCoverage-methods0.0120.0040.016
RelativeCrossCoverage-methods0.0560.0000.055
averagepeaksignal-methods0.0360.0000.034
coveragehistogram-methods0.040.000.04
crosscoverage-methods0.0400.0000.038
duplicateRate-methods0.0240.0000.024
duplicates-methods0.0120.0040.015
flagtagcounts-methods0.0200.0000.021
fragmentlength-methods0.0760.0000.074
frip-methods0.020.000.02
mapped-methods0.0120.0040.014
peaks-methods0.1800.0040.184
plotCC-methods1.5600.0041.565
plotCorHeatmap-methods0.3320.0080.339
plotCoverageHist-methods0.6680.0040.670
plotFribl-methods0.6960.0000.703
plotFrip-methods0.5360.0000.536
plotPeakProfile-methods1.8640.0001.868
plotPrincomp-methods0.2520.0040.255
plotRap-methods1.1200.0081.230
plotRegi-methods1.1040.0041.112
plotSSD-methods1.7360.0121.768
readlength-methods0.0200.0000.017
reads-methods0.0240.0000.025
regi-methods0.0680.0000.071
ribl-methods0.0160.0080.024
rip-methods0.0240.0000.024
ssd-methods0.0200.0040.025