############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:chipseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings chipseq_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/chipseq.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘chipseq/DESCRIPTION’ ... OK * this is package ‘chipseq’ version ‘1.56.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘chipseq’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘ShortRead’ A package should be listed in only one of these fields. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .genomicContext: no visible global function definition for ‘transcripts’ .genomicContext: no visible global function definition for ‘cdsBy’ .genomicContext: no visible global function definition for ‘threeUTRsByTranscript’ .genomicContext: no visible global function definition for ‘fiveUTRsByTranscript’ .genomicContext: no visible global function definition for ‘intronsByTranscript’ .nearestTss: no visible global function definition for ‘transcripts’ .nearestTss: no visible global function definition for ‘seqlevels<-’ .nearestTss: no visible global function definition for ‘seqlevels’ applyPosByChrAndStrand: no visible global function definition for ‘seqnames’ correlation.estimate: no visible binding for global variable ‘mu’ correlation.estimate: no visible binding for global variable ‘corr’ correlationProfile : : no visible global function definition for ‘subseq’ coverage.estimate: no visible binding for global variable ‘mu’ coverage.estimate: no visible binding for global variable ‘covered’ islandDepthPlot: no visible binding for global variable ‘depth’ islandDepthPlot : : no visible global function definition for ‘panel.lines’ islandDepthPlot : : no visible global function definition for ‘panel.xyplot’ laneSubsample: no visible global function definition for ‘seqnames’ laneSubsample: no visible global function definition for ‘GRangesList’ subsetSummary: no visible global function definition for ‘seqlengths’ subsetSummary: no visible global function definition for ‘GRanges’ subsetSummary: no visible global function definition for ‘seqnames’ subsetSummary: no visible global function definition for ‘seqlengths<-’ diffPeakSummary,RleViewsList-RleViewsList: no visible global function definition for ‘GRanges’ estimate.mean.fraglen,GRanges: no visible global function definition for ‘seqnames’ peakSummary,RleViewsList: no visible global function definition for ‘GRanges’ Undefined global functions or variables: GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript intronsByTranscript mu panel.lines panel.xyplot seqlengths seqlengths<- seqlevels seqlevels<- seqnames subseq threeUTRsByTranscript transcripts * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'densityCorr' and siglist 'GenomicRanges' generic 'densityCorr' and siglist 'list' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'estimate.mean.fraglen.Rd': densityCorr Code: function(x, ...) Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width = seqLen * 2L, seqLen = 100L, maxDist = 500L, ...) Argument names in docs not in code: shift center width seqLen maxDist Mismatches in argument names: Position: 2 Code: ... Docs: shift * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed diffPeakSummary 5.12 0.083 5.203 * 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: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/chipseq.Rcheck/00check.log’ for details.