Multiple platform build/check report for BioC 3.19 - CHECK results for ChIPQC on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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 kjohnson3

To the developers/maintainers of the ChIPQC package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ChIPQC

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPQC_1.40.0.tar.gz

StartedAt: 2024-06-10 10:19:39 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 10:32:37 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 778.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: ChIPQC.Rcheck

Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPQC_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPQC.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.40.0’
* 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 code 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 ... NOTE
checkRd: (-1) ChIPQC.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQC.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:29-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:62-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChIPQCsample-class.Rd:68-70: Lost braces in \itemize; meant \describe ?
* 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 Depends/Imports.
* 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 (user + system) or elapsed time > 5s
               user system elapsed
ChIPQCreport 24.407  0.627  37.937
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

Installation output

ChIPQC.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPQC
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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
** 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

name	user	system	elapsed
ChIPQC-data	1.186	0.046	1.864
ChIPQC	0.330	0.012	0.523
ChIPQCexperiment-class	0.493	0.022	0.811
ChIPQCreport	24.407	0.627	37.937
ChIPQCsample-class	1.122	0.065	1.761
FragmentLengthCrossCoverage-methods	0.048	0.004	0.077
Normalisedaveragepeaksignal-methods	0.023	0.005	0.035
QCannotation-methods	0.013	0.004	0.022
QCcontrol-methods	0.178	0.008	0.274
QCdba-methods	0.100	0.005	0.167
QCmetadata-methods	0.104	0.006	0.157
QCmetrics-methods	0.347	0.011	0.536
QCsample-methods	0.054	0.005	0.099
ReadLengthCrossCoverage-methods	0.014	0.002	0.022
RelativeCrossCoverage-methods	0.049	0.004	0.080
averagepeaksignal-methods	0.025	0.005	0.053
coveragehistogram-methods	0.023	0.005	0.040
crosscoverage-methods	0.021	0.005	0.045
duplicateRate-methods	0.014	0.003	0.026
duplicates-methods	0.013	0.003	0.024
flagtagcounts-methods	0.014	0.003	0.026
fragmentlength-methods	0.047	0.004	0.072
frip-methods	0.013	0.003	0.022
mapped-methods	0.013	0.003	0.025
peaks-methods	0.158	0.005	0.241
plotCC-methods	1.089	0.026	1.735
plotCorHeatmap-methods	0.186	0.010	0.312
plotCoverageHist-methods	0.492	0.012	0.756
plotFribl-methods	0.536	0.012	0.870
plotFrip-methods	0.584	0.011	0.906
plotPeakProfile-methods	1.199	0.026	1.866
plotPrincomp-methods	0.214	0.010	0.333
plotRap-methods	0.841	0.018	1.318
plotRegi-methods	0.993	0.020	1.458
plotSSD-methods	1.282	0.026	2.033
readlength-methods	0.014	0.003	0.021
reads-methods	0.014	0.003	0.026
regi-methods	0.042	0.005	0.068
ribl-methods	0.013	0.003	0.016
rip-methods	0.012	0.003	0.025
ssd-methods	0.013	0.003	0.016