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This page was generated on 2021-10-15 15:06:31 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 295/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPQC 1.28.0 (landing page) Tom Carroll
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ChIPQC |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.28.0.tar.gz |
StartedAt: 2021-10-14 17:19:24 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:28:21 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 537.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChIPQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPQC_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPQC.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.28.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... 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 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 22.757 0.531 23.441 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChIPQC.Rcheck/00check.log’ for details.
ChIPQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 ‘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)
ChIPQC.Rcheck/ChIPQC-Ex.timings
name | user | system | elapsed | |
ChIPQC-data | 1.191 | 0.040 | 1.231 | |
ChIPQC | 0.462 | 0.014 | 0.475 | |
ChIPQCexperiment-class | 0.432 | 0.008 | 0.440 | |
ChIPQCreport | 22.757 | 0.531 | 23.441 | |
ChIPQCsample-class | 1.264 | 0.045 | 1.311 | |
FragmentLengthCrossCoverage-methods | 0.062 | 0.006 | 0.069 | |
Normalisedaveragepeaksignal-methods | 0.025 | 0.007 | 0.032 | |
QCannotation-methods | 0.015 | 0.006 | 0.022 | |
QCcontrol-methods | 0.256 | 0.010 | 0.266 | |
QCdba-methods | 0.122 | 0.009 | 0.131 | |
QCmetadata-methods | 0.221 | 0.047 | 0.268 | |
QCmetrics-methods | 0.444 | 0.014 | 0.457 | |
QCsample-methods | 0.076 | 0.007 | 0.083 | |
ReadLengthCrossCoverage-methods | 0.015 | 0.006 | 0.021 | |
RelativeCrossCoverage-methods | 0.061 | 0.006 | 0.068 | |
averagepeaksignal-methods | 0.026 | 0.007 | 0.033 | |
coveragehistogram-methods | 0.025 | 0.007 | 0.032 | |
crosscoverage-methods | 0.023 | 0.006 | 0.030 | |
duplicateRate-methods | 0.015 | 0.005 | 0.021 | |
duplicates-methods | 0.015 | 0.006 | 0.022 | |
flagtagcounts-methods | 0.015 | 0.006 | 0.021 | |
fragmentlength-methods | 0.061 | 0.006 | 0.068 | |
frip-methods | 0.015 | 0.006 | 0.021 | |
mapped-methods | 0.015 | 0.006 | 0.021 | |
peaks-methods | 0.244 | 0.007 | 0.251 | |
plotCC-methods | 1.042 | 0.016 | 1.060 | |
plotCorHeatmap-methods | 0.237 | 0.008 | 0.245 | |
plotCoverageHist-methods | 0.483 | 0.009 | 0.490 | |
plotFribl-methods | 0.494 | 0.007 | 0.501 | |
plotFrip-methods | 0.503 | 0.007 | 0.511 | |
plotPeakProfile-methods | 1.328 | 0.026 | 1.357 | |
plotPrincomp-methods | 0.240 | 0.011 | 0.252 | |
plotRap-methods | 0.811 | 0.009 | 0.823 | |
plotRegi-methods | 0.902 | 0.017 | 0.920 | |
plotSSD-methods | 1.205 | 0.021 | 1.229 | |
readlength-methods | 0.015 | 0.006 | 0.022 | |
reads-methods | 0.015 | 0.007 | 0.022 | |
regi-methods | 0.049 | 0.007 | 0.057 | |
ribl-methods | 0.015 | 0.007 | 0.022 | |
rip-methods | 0.015 | 0.006 | 0.022 | |
ssd-methods | 0.015 | 0.007 | 0.022 | |