############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChIPQC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChIPQC_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ChIPQC.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’ * 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 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 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 19.727 0.469 20.195 * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/ChIPQC.Rcheck/00check.log’ for details.