############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IdeoViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IdeoViz_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/IdeoViz.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * 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 ‘IdeoViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IdeoViz’ version ‘1.40.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'IRanges', 'GenomicRanges', 'RColorBrewer', 'rtracklayer', 'GenomeInfoDb' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘IdeoViz’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 Packages in Depends field not imported from: ‘Biobase’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘IRanges’ ‘RColorBrewer’ ‘rtracklayer’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .plotChromosome: no visible global function definition for ‘modifyList’ .plotChromosome: no visible global function definition for ‘axTicks’ .plotChromosome: no visible global function definition for ‘axis’ .plotChromosome: no visible global function definition for ‘polygon’ .plotChromosome: no visible global function definition for ‘rect’ .plotChromosome: no visible global function definition for ‘mtext’ .plot_values: no visible global function definition for ‘start’ .plot_values: no visible global function definition for ‘ranges’ .plot_values: no visible global function definition for ‘end’ .plot_values: no visible global function definition for ‘seqnames’ .plot_values: no visible global function definition for ‘mcols’ .plot_values: no visible global function definition for ‘modifyList’ .plot_values: no visible global function definition for ‘loess’ .plot_values: no visible binding for global variable ‘span’ .plot_values: no visible global function definition for ‘predict’ .plot_values: no visible global function definition for ‘axis’ .plot_values: no visible global function definition for ‘mtext’ .plot_values: no visible global function definition for ‘rect’ .plot_values: no visible global function definition for ‘lines’ .plot_values: no visible global function definition for ‘abline’ .printMargins: no visible global function definition for ‘par’ avgByBin: no visible global function definition for ‘GRanges’ avgByBin: no visible global function definition for ‘IRanges’ avgByBin: no visible global function definition for ‘seqnames’ avgByBin: no visible global function definition for ‘seqlevels’ avgByBin: no visible global function definition for ‘seqlevels<-’ avgByBin: no visible global function definition for ‘findOverlaps’ avgByBin: no visible global function definition for ‘ave’ avgByBin : corFunc: no visible global function definition for ‘cor’ avgByBin: no visible global function definition for ‘mcols<-’ getBins: no visible global function definition for ‘GRanges’ getBins: no visible global function definition for ‘IRanges’ getIdeo: no visible global function definition for ‘browserSession’ getIdeo: no visible global function definition for ‘genome<-’ getIdeo: no visible global function definition for ‘getTable’ getIdeo: no visible global function definition for ‘ucscTableQuery’ plotChromValuePair : : no visible global function definition for ‘seqnames’ plotChromValuePair: no visible global function definition for ‘seqnames’ plotChromValuePair: no visible global function definition for ‘par’ plotChromValuePair: no visible global function definition for ‘modifyList’ plotOnIdeo: no visible global function definition for ‘par’ plotOnIdeo: no visible global function definition for ‘layout’ plotOnIdeo: no visible global function definition for ‘mtext’ Undefined global functions or variables: GRanges IRanges abline ave axTicks axis browserSession cor end findOverlaps genome<- getTable layout lines loess mcols mcols<- modifyList mtext par polygon predict ranges rect seqlevels seqlevels<- seqnames span start ucscTableQuery Consider adding importFrom("graphics", "abline", "axTicks", "axis", "layout", "lines", "mtext", "par", "polygon", "rect") importFrom("stats", "ave", "cor", "end", "loess", "predict", "start") importFrom("utils", "modifyList") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: GSM733664_broadPeaks.Rd:11-12: Dropping empty section \format prepare_Rd: GSM733664_broadPeaks.Rd:16-18: Dropping empty section \source prepare_Rd: binned_fullGenome.Rd:12-13: Dropping empty section \format prepare_Rd: binned_fullGenome.Rd:14-16: Dropping empty section \details prepare_Rd: binned_fullGenome.Rd:20-22: Dropping empty section \references prepare_Rd: binned_multiSeries.Rd:12-13: Dropping empty section \format prepare_Rd: binned_multiSeries.Rd:14-15: Dropping empty section \details prepare_Rd: binned_multiSeries.Rd:19-20: Dropping empty section \references prepare_Rd: binned_singleSeries.Rd:11-12: Dropping empty section \format prepare_Rd: binned_singleSeries.Rd:13-15: Dropping empty section \details prepare_Rd: binned_singleSeries.Rd:19-21: Dropping empty section \references checkRd: (-1) getBins.Rd:16: Lost braces 16 | \item{binLim}{(numeric, }{length 2) [start, end] of genomic range to generate bins for. A value of NULL results in binning of entire chromosome} | ^ prepare_Rd: hg18_ideo.Rd:11-12: Dropping empty section \format prepare_Rd: hg18_ideo.Rd:13-14: Dropping empty section \details prepare_Rd: hg18_ideo.Rd:18-19: Dropping empty section \references prepare_Rd: wins.Rd:12-13: Dropping empty section \format prepare_Rd: wins.Rd:14-15: Dropping empty section \details prepare_Rd: wins.Rd:19-20: Dropping empty section \references prepare_Rd: wins_discrete.Rd:11-12: Dropping empty section \format prepare_Rd: wins_discrete.Rd:13-15: Dropping empty section \details prepare_Rd: wins_discrete.Rd:19-21: Dropping empty section \references prepare_Rd: wins_entiregenome.Rd:11-12: Dropping empty section \format prepare_Rd: wins_entiregenome.Rd:13-15: Dropping empty section \details prepare_Rd: wins_entiregenome.Rd:19-21: Dropping empty section \references * 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 ... WARNING Undocumented arguments in Rd file 'plotChromValuePair.Rd' ‘chrom’ ‘cytoTable’ ‘bpLim’ ‘vertical’ ‘values_GR’ ‘val_range’ ‘col’ ‘value_cols’ ‘default_margins’ ‘addScale’ ‘ablines_y’ ‘smoothVals’ ‘span’ ‘verbose’ Documented arguments not in \usage in Rd file 'plotChromValuePair.Rd': ‘chrom(character)’ ‘cytoTable(data.frame)’ ‘bpLim(numeric)’ ‘vertical(logical)’ ‘values_GR(list’ ‘val_range(numeric)’ ‘col(character)’ ‘value_cols(character)’ ‘default_margins(numeric)’ ‘addScale(logical)’ ‘ablines_y(numeric)’ ‘smoothVals(logical)’ ‘span(numeric)’ ‘verbose(logical)’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘IdeoViz.Rmd’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed avgByBin 3.522 0.244 14.374 getBins 2.739 0.150 13.609 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/IdeoViz.Rcheck/00check.log’ for details.