############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DeSousa2013_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/DeSousa2013.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘DeSousa2013/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DeSousa2013’ version ‘1.42.0’ * 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 ‘DeSousa2013’ can be installed ... OK * checking installed package size ... NOTE installed size is 43.9Mb sub-directories of 1Mb or more: data 43.7Mb * 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘frmaTools’ ‘hgu133plus2frmavecs’ ‘rgl’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CRCPipeLine: no visible global function definition for ‘data’ CRCPipeLine: no visible global function definition for ‘pdf’ CRCPipeLine: no visible global function definition for ‘graphics.off’ compGapStats: no visible binding for global variable ‘mad’ compGapStats : fun: no visible global function definition for ‘hclust’ compGapStats : fun: no visible global function definition for ‘as.dist’ compGapStats : fun: no visible global function definition for ‘cor’ compGapStats : fun: no visible global function definition for ‘cutree’ compGapStats: no visible binding for global variable ‘median’ figClassify: no visible global function definition for ‘layout’ figClassify: no visible global function definition for ‘par’ figClassify: no visible global function definition for ‘image’ figClassify: no visible global function definition for ‘axis’ figClassify: no visible global function definition for ‘box’ figClassify: no visible global function definition for ‘gray’ figClassify: no visible global function definition for ‘mtext’ figClassify: no visible global function definition for ‘barplot’ figClassify: no visible global function definition for ‘grid’ figGAP: no visible global function definition for ‘par’ figGAP: no visible global function definition for ‘lines’ figGAP: no visible global function definition for ‘title’ figKM: no visible global function definition for ‘axis’ figKM: no visible global function definition for ‘box’ figKM: no visible global function definition for ‘text’ figKM: no visible global function definition for ‘legend’ figPAMCV: no visible global function definition for ‘boxplot’ filterSamples: no visible global function definition for ‘as.dist’ filterSamples: no visible global function definition for ‘cor’ pamClassify: no visible global function definition for ‘hclust’ pamClassify: no visible global function definition for ‘as.dist’ pamClassify: no visible global function definition for ‘cor’ pbs2unigenes: no visible global function definition for ‘mappedkeys’ progAMC: no visible global function definition for ‘pchisq’ selTopVarGenes: no visible binding for global variable ‘mad’ selTopVarGenes: no visible binding for global variable ‘median’ Undefined global functions or variables: as.dist axis barplot box boxplot cor cutree data graphics.off gray grid hclust image layout legend lines mad mappedkeys median mtext par pchisq pdf text title Consider adding importFrom("grDevices", "graphics.off", "gray", "pdf") importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid", "image", "layout", "legend", "lines", "mtext", "par", "text", "title") importFrom("stats", "as.dist", "cor", "cutree", "hclust", "mad", "median", "pchisq") importFrom("utils", "data") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed compGapStats 9.901 0.179 10.082 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/DeSousa2013.Rcheck/00check.log’ for details.