* using log directory 'd:/Rcompile/CRANpkg/local/3.1/LDheatmap.Rcheck' * using R version 3.1.3 (2015-03-09) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'LDheatmap/DESCRIPTION' ... OK * this is package 'LDheatmap' version '0.99-1' * 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 whether package 'LDheatmap' 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'GenomicRanges' 'chopsticks' 'rtracklayer' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: 'grid' 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 LDheatmap : makeImageRect: no visible global function definition for 'rectGrob' LDheatmap : makeImageRect: no visible global function definition for 'gpar' LDheatmap : makeImageText: no visible global function definition for 'textGrob' LDheatmap : makeImageText: no visible global function definition for 'gpar' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'viewport' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'textGrob' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'gpar' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'segmentsGrob' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'linesGrob' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'gTree' LDheatmap : LDheatmap.Legend.add: no visible global function definition for 'gList' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'linesGrob' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'gpar' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'segmentsGrob' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'textGrob' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'gTree' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'gList' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'pointsGrob' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'convertWidth' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'grobWidth' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'editGrob' LDheatmap : LDheatmap.Map.add: no visible global function definition for 'unit' LDheatmap: no visible global function definition for 'ld.snp' LDheatmap: no visible global function definition for 'viewport' LDheatmap: no visible global function definition for 'unit' LDheatmap: no visible global function definition for 'grid.newpage' LDheatmap: no visible global function definition for 'textGrob' LDheatmap: no visible global function definition for 'gpar' LDheatmap: no visible global function definition for 'editGrob' LDheatmap: no visible global function definition for 'gTree' LDheatmap: no visible global function definition for 'gList' LDheatmap: no visible global function definition for 'grid.draw' LDheatmap: no visible global function definition for 'downViewport' LDheatmap: no visible global function definition for 'popViewport' LDheatmap.addGenes: no visible global function definition for 'pushViewport' LDheatmap.addGenes: no visible global function definition for 'vpStack' LDheatmap.addGenes: no visible global function definition for 'editGrob' LDheatmap.addGenes: no visible global function definition for 'addGrob' LDheatmap.addGrob: no visible global function definition for 'unit' LDheatmap.addGrob: no visible global function definition for 'vpStack' LDheatmap.addGrob: no visible global function definition for 'gTree' LDheatmap.addGrob: no visible global function definition for 'gList' LDheatmap.addGrob: no visible global function definition for 'addGrob' LDheatmap.addRecombRate: no visible global function definition for 'unit' LDheatmap.addRecombRate: no visible global function definition for 'pushViewport' LDheatmap.addRecombRate: no visible global function definition for 'vpStack' LDheatmap.addRecombRate: no visible global function definition for 'editGrob' LDheatmap.addRecombRate: no visible global function definition for 'addGrob' LDheatmap.addScatterplot: no visible global function definition for 'unit' LDheatmap.addScatterplot: no visible global function definition for 'linesGrob' LDheatmap.addScatterplot: no visible global function definition for 'yaxisGrob' LDheatmap.addScatterplot: no visible global function definition for 'gpar' LDheatmap.addScatterplot: no visible global function definition for 'textGrob' LDheatmap.addScatterplot: no visible global function definition for 'vpStack' LDheatmap.addScatterplot: no visible global function definition for 'gTree' LDheatmap.addScatterplot: no visible global function definition for 'gList' LDheatmap.addScatterplot: no visible global function definition for 'pointsGrob' LDheatmap.addScatterplot: no visible global function definition for 'addGrob' LDheatmap.highlight: no visible global function definition for 'current.vpTree' LDheatmap.highlight: no visible global function definition for 'seekViewport' LDheatmap.highlight: no visible global function definition for 'pushViewport' LDheatmap.highlight: no visible global function definition for 'polygonGrob' LDheatmap.highlight: no visible global function definition for 'gpar' LDheatmap.highlight: no visible global function definition for 'grid.draw' LDheatmap.highlight: no visible global function definition for 'upViewport' LDheatmap.highlight: no visible global function definition for 'popViewport' LDheatmap.marks: no visible global function definition for 'gpar' LDheatmap.marks: no visible global function definition for 'current.vpTree' LDheatmap.marks: no visible global function definition for 'seekViewport' LDheatmap.marks: no visible global function definition for 'pushViewport' LDheatmap.marks: no visible global function definition for 'pointsGrob' LDheatmap.marks: no visible global function definition for 'gTree' LDheatmap.marks: no visible global function definition for 'gList' LDheatmap.marks: no visible global function definition for 'grid.draw' LDheatmap.marks: no visible global function definition for 'upViewport' LDheatmap.marks: no visible global function definition for 'popViewport' constructVP: no visible global function definition for 'convertX' constructVP: no visible global function definition for 'getGrob' constructVP: no visible global function definition for 'viewport' drawLDheatmapGrob: no visible global function definition for 'convertY' drawLDheatmapGrob: no visible global function definition for 'getGrob' drawLDheatmapGrob: no visible global function definition for 'viewport' drawLDheatmapGrob: no visible global function definition for 'gpar' drawLDheatmapGrob: no visible global function definition for 'grid.newpage' drawLDheatmapGrob: no visible global function definition for 'pushViewport' drawLDheatmapGrob: no visible global function definition for 'grid.draw' drawLDheatmapGrob: no visible global function definition for 'popViewport' moveTitles: no visible global function definition for 'convertX' moveTitles: no visible global function definition for 'getGrob' moveTitles: no visible global function definition for 'editGrob' moveTitles: no visible global function definition for 'unit' moveTitles: no visible global function definition for 'grid.newpage' moveTitles: no visible global function definition for 'grid.draw' moveTitles: no visible global function definition for 'pushViewport' moveTitles: no visible global function definition for 'current.transform' moveTitles: no visible global function definition for 'upViewport' moveTitles: no visible global function definition for 'convertY' moveTitles: no visible global function definition for 'convertHeight' moveTitles: no visible global function definition for 'grobHeight' plotGenes: no visible global function definition for 'viewport' plotGenes: no visible global function definition for 'convertX' plotGenes: no visible global function definition for 'browserSession' plotGenes: no visible global function definition for 'genome<-' plotGenes: no visible global function definition for 'ucscTableQuery' plotGenes: no visible global function definition for 'GRangesForUCSCGenome' plotGenes: no visible global function definition for 'IRanges' plotGenes: no visible global function definition for 'getTable' plotGenes: no visible global function definition for 'tableNames' plotGenes: no visible global function definition for 'convertWidth' plotGenes: no visible global function definition for 'grobWidth' plotGenes: no visible global function definition for 'textGrob' plotGenes: no visible global function definition for 'gpar' plotGenes: no visible global function definition for 'unit' plotGenes: no visible global function definition for 'gTree' plotGenes: no visible global function definition for 'gList' plotGenes: no visible global function definition for 'linesGrob' plotGenes: no visible global function definition for 'segmentsGrob' plotGenes: no visible global function definition for 'polygonGrob' plotGenes: no visible global function definition for 'unit.c' plotGenes: no visible global function definition for 'addGrob' plotGenes: no visible global function definition for 'grid.draw' postDrawDetails.ldheatmap: no visible global function definition for 'popViewport' postDrawDetails.symbols: no visible global function definition for 'popViewport' preDrawDetails.ldheatmap: no visible global function definition for 'convertX' preDrawDetails.ldheatmap: no visible global function definition for 'unit' preDrawDetails.ldheatmap: no visible global function definition for 'rectGrob' preDrawDetails.ldheatmap: no visible global function definition for 'pushViewport' preDrawDetails.ldheatmap: no visible global function definition for 'viewport' preDrawDetails.ldheatmap: no visible global function definition for 'gpar' preDrawDetails.symbols: no visible global function definition for 'convertX' preDrawDetails.symbols: no visible global function definition for 'unit' preDrawDetails.symbols: no visible global function definition for 'rectGrob' preDrawDetails.symbols: no visible global function definition for 'pushViewport' preDrawDetails.symbols: no visible global function definition for 'viewport' preDrawDetails.symbols: no visible global function definition for 'gpar' recombRate: no visible global function definition for 'viewport' recombRate: no visible global function definition for 'convertX' recombRate: no visible global function definition for 'browserSession' recombRate: no visible global function definition for 'genome<-' recombRate: no visible global function definition for 'ucscTableQuery' recombRate: no visible global function definition for 'GRangesForUCSCGenome' recombRate: no visible global function definition for 'IRanges' recombRate: no visible global function definition for 'getTable' recombRate: no visible global function definition for 'textGrob' recombRate: no visible global function definition for 'gpar' recombRate: no visible global function definition for 'unit' recombRate: no visible global function definition for 'editGrob' recombRate: no visible global function definition for 'convertWidth' recombRate: no visible global function definition for 'grobWidth' recombRate: no visible global function definition for 'gTree' recombRate: no visible global function definition for 'gList' recombRate: no visible global function definition for 'rectGrob' recombRate: no visible global function definition for 'addGrob' recombRate: no visible global function definition for 'grid.draw' * 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [12s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... [7s] OK * checking re-building of vignette outputs ... [15s] OK * checking PDF version of manual ... OK * DONE NOTE: There were 2 notes.