############################################################################## ############################################################################## ### ### 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_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPQC.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPQC’ version ‘1.42.0’ * 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 ... OK * 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 44.711 0.837 48.163 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPQC.Rcheck/00check.log’ for details.