############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:tilingArray.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings tilingArray_1.85.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tilingArray.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘tilingArray/DESCRIPTION’ ... OK * this is package ‘tilingArray’ version ‘1.85.0’ * 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 ‘tilingArray’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘pixmap’ 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 .onAttach: no visible global function definition for ‘addVigs2WinMenu’ comparisonPlot : myColors: no visible global function definition for ‘quantile’ grid.image: no visible global function definition for ‘colorRamp’ grid.image: no visible global function definition for ‘rgb’ interpolateZ: no visible global function definition for ‘approx’ matDensities : densXY: no visible global function definition for ‘density’ myPixmap: no visible global function definition for ‘pixmapGrey’ myWrite: no visible global function definition for ‘write.pnm’ normalizeByReference: no visible global function definition for ‘exprs’ normalizeByReference: no visible global function definition for ‘quantile’ normalizeByReference: no visible global function definition for ‘approxfun’ normalizeByReference: no visible global function definition for ‘pdf’ normalizeByReference: no visible global function definition for ‘smoothScatter’ normalizeByReference: no visible global function definition for ‘lines’ normalizeByReference: no visible global function definition for ‘dev.off’ normalizeByReference: no visible global function definition for ‘exprs<-’ plotAlongChrom: no visible global function definition for ‘colorRamp’ plotAlongChrom: no visible global function definition for ‘quantile’ plotFeatures: no visible global function definition for ‘listLen’ plotPenLL: no visible binding for global variable ‘quantile’ plotPenLL: no visible global function definition for ‘matplot’ plotPenLL: no visible global function definition for ‘segments’ plotPenLL: no visible global function definition for ‘legend’ plotSegmentationDots: no visible global function definition for ‘quantile’ plotSegmentationHeatmap: no visible global function definition for ‘colorRamp’ plotSegmentationHeatmap: no visible global function definition for ‘quantile’ qcPlots: no visible global function definition for ‘pData’ qcPlots: no visible global function definition for ‘exprs’ qcPlots: no visible global function definition for ‘png’ qcPlots: no visible global function definition for ‘boxplot’ qcPlots: no visible global function definition for ‘dev.off’ qcPlots: no visible global function definition for ‘matplot’ qcPlots: no visible global function definition for ‘jpeg’ raster.image: no visible global function definition for ‘colorRamp’ raster.image: no visible global function definition for ‘rgb’ readCel2eSet: no visible global function definition for ‘varLabels’ segChrom: no visible global function definition for ‘exprs’ plot,segmentation-ANY: no visible global function definition for ‘note’ plot,segmentation-ANY: no visible global function definition for ‘plot.default’ plot,segmentation-ANY: no visible global function definition for ‘abline’ plot,segmentation-ANY: no visible global function definition for ‘mtext’ Undefined global functions or variables: abline addVigs2WinMenu approx approxfun boxplot colorRamp density dev.off exprs exprs<- jpeg legend lines listLen matplot mtext note pData pdf pixmapGrey plot.default png quantile rgb segments smoothScatter varLabels write.pnm Consider adding importFrom("grDevices", "colorRamp", "dev.off", "jpeg", "pdf", "png", "rgb") importFrom("graphics", "abline", "boxplot", "legend", "lines", "matplot", "mtext", "plot.default", "segments", "smoothScatter") importFrom("stats", "approx", "approxfun", "density", "quantile") 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 ... NOTE S3 methods shown with full name in Rd file 'breakpointsPretend.Rd': ‘breakpoints.breakpointsPretend’ The \usage entries for S3 methods should use the \method markup and not their full name. 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/tilingArray.Rcheck/00check.log’ for details.