############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:davidTiling.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings davidTiling_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/davidTiling.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘davidTiling/DESCRIPTION’ ... OK * this is package ‘davidTiling’ version ‘1.44.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘davidTiling’ can be installed ... OK * checking installed package size ... NOTE installed size is 538.5Mb sub-directories of 1Mb or more: celfiles 306.2Mb data 229.6Mb website 2.3Mb * checking package 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘GO.db’ ‘tilingArray’ 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 GOHyperG: no visible global function definition for ‘phyper’ GOHyperG: no visible binding for global variable ‘GOTERM’ GOHyperG: no visible global function definition for ‘replaceSystematicByCommonName’ GOHyperG: no visible global function definition for ‘Term’ GOHyperG: no visible global function definition for ‘abline’ colMedians: no visible binding for global variable ‘median’ getAllGO: no visible binding for global variable ‘GOMFANCESTOR’ getAllGO: no visible binding for global variable ‘GOBPANCESTOR’ getAllGO: no visible binding for global variable ‘GOCCANCESTOR’ movingWindow: no visible global function definition for ‘median’ movingWindow : : no visible global function definition for ‘median’ scatterWithHist: no visible global function definition for ‘hist’ scatterWithHist: no visible global function definition for ‘layout’ scatterWithHist: no visible global function definition for ‘par’ scatterWithHist: no visible global function definition for ‘barplot’ scatterWithHist: no visible global function definition for ‘text’ scoreSegments: no visible global function definition for ‘data’ scoreSegments: no visible binding for global variable ‘yeastFeatures’ scoreSegments: no visible binding for global variable ‘chrs’ scoreSegments: no visible global function definition for ‘otherStrand’ scoreSegments: no visible global function definition for ‘median’ scoreSegments: no visible global function definition for ‘posMin’ showDens: no visible global function definition for ‘hist’ showDens: no visible global function definition for ‘axis’ showDens: no visible global function definition for ‘polygon’ zscore: no visible global function definition for ‘sd’ Undefined global functions or variables: GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM Term abline axis barplot chrs data hist layout median otherStrand par phyper polygon posMin replaceSystematicByCommonName sd text yeastFeatures Consider adding importFrom("graphics", "abline", "axis", "barplot", "hist", "layout", "par", "polygon", "text") importFrom("stats", "median", "phyper", "sd") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples * 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 files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘Archi_RT_positions.txt’ ‘strongConservedNovelIsolated.txt’ ‘utrmap-GOcategories.txt’ 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 davidTiling 25.867 0.884 26.751 probeAnno 5.231 0.144 5.375 * 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: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.19-data-experiment/meat/davidTiling.Rcheck/00check.log’ for details.