############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BBCAnalyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BBCAnalyzer_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BBCAnalyzer.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘BBCAnalyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BBCAnalyzer’ version ‘1.36.0’ * 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 ‘BBCAnalyzer’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE analyzeBases: no visible global function definition for ‘read.table’ analyzeBasesPlotOnly: no visible global function definition for ‘read.table’ analyzeReads: no visible global function definition for ‘path’ analyzeReads: no visible global function definition for ‘write.table’ checkBamInput: no visible global function definition for ‘path’ checkVcfInput: no visible global function definition for ‘path’ frequencyAnalysis: no visible global function definition for ‘write.table’ frequencyAnalysisVcf: no visible global function definition for ‘read.table’ frequencyAnalysisVcf: no visible global function definition for ‘path’ frequencyAnalysisVcf: no visible global function definition for ‘write.table’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘par’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘rect’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘lines’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘text’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘par’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘rect’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘lines’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘text’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘par’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘rect’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘lines’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘text’ plotCountsPerSample_plot: no visible global function definition for ‘par’ plotCountsPerSample_plot: no visible global function definition for ‘barplot’ plotCountsPerSample_plot: no visible global function definition for ‘rect’ plotCountsPerSample_plot: no visible global function definition for ‘lines’ plotCountsPerSample_plot: no visible global function definition for ‘text’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘par’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘rect’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘lines’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘text’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘par’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘rect’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘lines’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘text’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘par’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘rect’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘lines’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘text’ plotCountsPerTarget_plot: no visible global function definition for ‘par’ plotCountsPerTarget_plot: no visible global function definition for ‘barplot’ plotCountsPerTarget_plot: no visible global function definition for ‘rect’ plotCountsPerTarget_plot: no visible global function definition for ‘lines’ plotCountsPerTarget_plot: no visible global function definition for ‘text’ processVcfFile: no visible global function definition for ‘read.table’ reportVariants: no visible global function definition for ‘write.table’ reportVariantsVcf: no visible global function definition for ‘write.table’ Undefined global functions or variables: barplot lines par path read.table rect text write.table Consider adding importFrom("graphics", "barplot", "lines", "par", "rect", "text") importFrom("utils", "read.table", "write.table") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyzeBasesPlotOnly 16.416 0.378 16.853 * 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 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BBCAnalyzer.Rcheck/00check.log’ for details.