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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 338/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPQC 1.40.0  (landing page)
Tom Carroll , Rory Stark
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/ChIPQC
git_branch: RELEASE_3_19
git_last_commit: b105a43
git_last_commit_date: 2024-04-30 10:35:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPQC_1.40.0.tar.gz
StartedAt: 2024-06-19 21:33:59 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:41:08 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 429.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChIPQC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChIPQC_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ChIPQC.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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 ... 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 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 19.197  0.482  19.582
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ChIPQC.Rcheck/00check.log’
for details.


Installation output

ChIPQC.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChIPQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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

nameusersystemelapsed
ChIPQC-data1.0230.0801.102
ChIPQC0.3530.0130.364
ChIPQCexperiment-class0.3440.0120.355
ChIPQCreport19.197 0.48219.582
ChIPQCsample-class0.8960.0200.917
FragmentLengthCrossCoverage-methods0.0470.0000.047
Normalisedaveragepeaksignal-methods0.0210.0040.025
QCannotation-methods0.0140.0000.014
QCcontrol-methods0.1630.0120.175
QCdba-methods0.1060.0000.106
QCmetadata-methods0.1050.0040.109
QCmetrics-methods0.3390.0080.347
QCsample-methods0.0470.0000.047
ReadLengthCrossCoverage-methods0.0150.0000.015
RelativeCrossCoverage-methods0.0470.0000.047
averagepeaksignal-methods0.0230.0040.026
coveragehistogram-methods0.0260.0000.025
crosscoverage-methods0.0230.0000.023
duplicateRate-methods0.0150.0000.015
duplicates-methods0.0150.0000.015
flagtagcounts-methods0.0110.0040.015
fragmentlength-methods0.0420.0040.046
frip-methods0.0110.0040.014
mapped-methods0.0150.0000.015
peaks-methods0.1220.0000.122
plotCC-methods0.8560.0280.884
plotCorHeatmap-methods0.1780.0040.181
plotCoverageHist-methods0.4140.0200.434
plotFribl-methods0.4270.0000.427
plotFrip-methods0.4490.0000.449
plotPeakProfile-methods1.1160.0041.120
plotPrincomp-methods0.2040.0040.208
plotRap-methods0.6780.0040.682
plotRegi-methods0.8370.0000.837
plotSSD-methods1.0200.0081.028
readlength-methods0.0150.0000.015
reads-methods0.0150.0000.015
regi-methods0.0400.0040.044
ribl-methods0.0150.0000.015
rip-methods0.0150.0000.015
ssd-methods0.0150.0000.015