Multiple platform build/check report for BioC 3.21 - CHECK results for ChIPQC on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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:
- 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: 1.43.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChIPQC_1.43.0.tar.gz

StartedAt: 2024-12-23 20:35:19 -0500 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 20:42:22 -0500 (Mon, 23 Dec 2024)

EllapsedTime: 423.6 seconds

RetCode: 0

Status: OK

CheckDir: ChIPQC.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChIPQC_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPQC.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChIPQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPQC’ version ‘1.43.0’
* 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ChIPQC-data.Rd: GRanges, DiffBind
  ChIPQC-package.Rd: DiffBind
  ChIPQC.Rd: DBA-object, DiffBind, dba.peakset, dba, GRanges,
    dba.count, bplapply, BiocParallel, register
  ChIPQCexperiment-class.Rd: DBA-object, DiffBind
  ChIPQCsample-class.Rd: GRanges, GRanges-class
  QCdba-methods.Rd: DBA-object, DiffBind, dba
  peaks-methods.Rd: GRangesList, GRanges
  plotCorHeatmap-methods.Rd: dba.plotHeatmap
  plotPrincomp-methods.Rd: dba.plotPCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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 19.653  0.591  20.185
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.

Installation output

ChIPQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ChIPQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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	1.014	0.118	1.133
ChIPQC	0.349	0.006	0.355
ChIPQCexperiment-class	0.321	0.017	0.338
ChIPQCreport	19.653	0.591	20.185
ChIPQCsample-class	0.920	0.032	0.953
FragmentLengthCrossCoverage-methods	0.049	0.001	0.049
Normalisedaveragepeaksignal-methods	0.025	0.000	0.025
QCannotation-methods	0.014	0.001	0.015
QCcontrol-methods	0.170	0.008	0.178
QCdba-methods	0.101	0.005	0.106
QCmetadata-methods	0.103	0.005	0.109
QCmetrics-methods	0.341	0.007	0.348
QCsample-methods	0.046	0.001	0.046
ReadLengthCrossCoverage-methods	0.016	0.000	0.015
RelativeCrossCoverage-methods	0.046	0.001	0.047
averagepeaksignal-methods	0.025	0.001	0.026
coveragehistogram-methods	0.024	0.000	0.025
crosscoverage-methods	0.021	0.001	0.023
duplicateRate-methods	0.014	0.001	0.016
duplicates-methods	0.013	0.002	0.015
flagtagcounts-methods	0.013	0.001	0.015
fragmentlength-methods	0.047	0.001	0.048
frip-methods	0.015	0.000	0.015
mapped-methods	0.014	0.001	0.015
peaks-methods	0.131	0.000	0.131
plotCC-methods	0.929	0.003	0.932
plotCorHeatmap-methods	0.170	0.009	0.179
plotCoverageHist-methods	0.425	0.001	0.426
plotFribl-methods	0.436	0.003	0.439
plotFrip-methods	0.466	0.003	0.469
plotPeakProfile-methods	1.035	0.008	1.044
plotPrincomp-methods	0.200	0.005	0.204
plotRap-methods	0.686	0.001	0.687
plotRegi-methods	0.907	0.006	0.913
plotSSD-methods	1.059	0.005	1.064
readlength-methods	0.015	0.000	0.015
reads-methods	0.015	0.000	0.015
regi-methods	0.038	0.001	0.039
ribl-methods	0.014	0.001	0.015
rip-methods	0.015	0.000	0.015
ssd-methods	0.015	0.000	0.015