Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:38:59 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 334/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPQC 1.39.0 (landing page) Tom Carroll
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: ChIPQC |
Version: 1.39.0 |
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_1.39.0.tar.gz |
StartedAt: 2024-03-02 01:36:43 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 01:51:35 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 892.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChIPQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPQC.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPQC’ version ‘1.39.0’ * 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 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 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 41.995 1.032 50.348 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPQC.Rcheck/00check.log’ for details.
ChIPQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
ChIPQC.Rcheck/ChIPQC-Ex.timings
name | user | system | elapsed | |
ChIPQC-data | 2.521 | 0.088 | 2.909 | |
ChIPQC | 0.886 | 0.027 | 1.026 | |
ChIPQCexperiment-class | 0.884 | 0.032 | 1.067 | |
ChIPQCreport | 41.995 | 1.032 | 50.348 | |
ChIPQCsample-class | 2.300 | 0.145 | 3.011 | |
FragmentLengthCrossCoverage-methods | 0.122 | 0.013 | 0.158 | |
Normalisedaveragepeaksignal-methods | 0.040 | 0.015 | 0.233 | |
QCannotation-methods | 0.023 | 0.013 | 0.038 | |
QCcontrol-methods | 0.367 | 0.020 | 0.427 | |
QCdba-methods | 0.188 | 0.016 | 0.254 | |
QCmetadata-methods | 0.195 | 0.019 | 0.250 | |
QCmetrics-methods | 0.904 | 0.038 | 1.128 | |
QCsample-methods | 0.106 | 0.015 | 0.147 | |
ReadLengthCrossCoverage-methods | 0.024 | 0.013 | 0.044 | |
RelativeCrossCoverage-methods | 0.123 | 0.013 | 0.161 | |
averagepeaksignal-methods | 0.042 | 0.014 | 0.061 | |
coveragehistogram-methods | 0.042 | 0.014 | 0.067 | |
crosscoverage-methods | 0.039 | 0.014 | 0.060 | |
duplicateRate-methods | 0.024 | 0.012 | 0.044 | |
duplicates-methods | 0.024 | 0.011 | 0.044 | |
flagtagcounts-methods | 0.024 | 0.013 | 0.042 | |
fragmentlength-methods | 0.124 | 0.013 | 0.164 | |
frip-methods | 0.024 | 0.013 | 0.045 | |
mapped-methods | 0.024 | 0.012 | 0.041 | |
peaks-methods | 0.318 | 0.016 | 0.400 | |
plotCC-methods | 2.140 | 0.039 | 2.649 | |
plotCorHeatmap-methods | 0.370 | 0.022 | 0.462 | |
plotCoverageHist-methods | 1.076 | 0.030 | 1.282 | |
plotFribl-methods | 1.072 | 0.023 | 1.274 | |
plotFrip-methods | 1.113 | 0.022 | 1.333 | |
plotPeakProfile-methods | 2.469 | 0.057 | 2.983 | |
plotPrincomp-methods | 0.421 | 0.020 | 0.579 | |
plotRap-methods | 1.585 | 0.036 | 1.961 | |
plotRegi-methods | 2.040 | 0.051 | 2.479 | |
plotSSD-methods | 2.545 | 0.057 | 3.028 | |
readlength-methods | 0.025 | 0.013 | 0.044 | |
reads-methods | 0.024 | 0.014 | 0.043 | |
regi-methods | 0.088 | 0.015 | 0.124 | |
ribl-methods | 0.024 | 0.014 | 0.046 | |
rip-methods | 0.024 | 0.013 | 0.041 | |
ssd-methods | 0.025 | 0.013 | 0.042 | |