Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-04 11:04:46 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ChIPQC on nebbiolo1


To the developers/maintainers of the ChIPQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPQC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 309/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.35.1  (landing page)
Tom Carroll , Rory Stark
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/ChIPQC
git_branch: master
git_last_commit: 0aa2fcd
git_last_commit_date: 2023-01-10 08:07:36 -0500 (Tue, 10 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ChIPQC
Version: 1.35.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPQC_1.35.1.tar.gz
StartedAt: 2023-02-03 19:41:44 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 19:49:07 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 443.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ChIPQC_1.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.35.1’
* 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 ... 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: ‘BiocParallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
ChIPQC: no visible global function definition for ‘is’
ChIPQC: no visible global function definition for ‘multicoreWorkers’
ChIPQC: no visible global function definition for ‘snowWorkers’
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 is log10_bp log2_Enrichment multicoreWorkers seqlengths
  seqlengths<- seqlevels<- snowWorkers
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "SSD")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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 20.068  0.792  20.809
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ChIPQC.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.



Installation output

ChIPQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChIPQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
** 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-data2.0370.1922.229
ChIPQC0.3900.0470.437
ChIPQCexperiment-class0.3380.0410.379
ChIPQCreport20.068 0.79220.809
ChIPQCsample-class0.9230.0841.007
FragmentLengthCrossCoverage-methods0.0430.0040.047
Normalisedaveragepeaksignal-methods0.0240.0000.024
QCannotation-methods0.0150.0000.015
QCcontrol-methods0.1710.0080.179
QCdba-methods0.0950.0120.107
QCmetadata-methods0.1100.0030.113
QCmetrics-methods0.3560.0080.364
QCsample-methods0.0500.0040.053
ReadLengthCrossCoverage-methods0.0130.0040.016
RelativeCrossCoverage-methods0.0520.0000.053
averagepeaksignal-methods0.0270.0000.026
coveragehistogram-methods0.0350.0000.035
crosscoverage-methods0.0240.0000.024
duplicateRate-methods0.0120.0040.015
duplicates-methods0.0150.0000.015
flagtagcounts-methods0.0150.0000.015
fragmentlength-methods0.0650.0000.066
frip-methods0.0150.0000.015
mapped-methods0.0140.0000.015
peaks-methods0.1310.0000.131
plotCC-methods0.9640.0080.973
plotCorHeatmap-methods0.1760.0000.176
plotCoverageHist-methods0.4330.0040.437
plotFribl-methods0.5040.0160.520
plotFrip-methods0.4670.0040.472
plotPeakProfile-methods1.2260.0121.239
plotPrincomp-methods0.1890.0080.197
plotRap-methods0.6780.0160.694
plotRegi-methods0.9170.0080.925
plotSSD-methods1.1660.0201.186
readlength-methods0.0140.0000.015
reads-methods0.0150.0000.015
regi-methods0.0390.0000.039
ribl-methods0.0150.0000.015
rip-methods0.0110.0040.014
ssd-methods0.0070.0080.015