############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GDCRNATools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GDCRNATools_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GDCRNATools/DESCRIPTION’ ... OK * this is package ‘GDCRNATools’ version ‘1.14.0’ * package encoding: UTF-8 * 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 ‘GDCRNATools’ 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 ... 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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE deAnalysislimma: warning in topTable(fit2, coef = 1, n = Inf): partial argument match of 'n' to 'number' gdcDEAnalysis: warning in topTable(fit2, coef = 1, n = Inf): partial argument match of 'n' to 'number' cleanMirFun: no visible global function definition for ‘read.table’ cleanMirFun: no visible global function definition for ‘aggregate’ downloadClientFun: no visible global function definition for ‘download.file’ downloadClientFun: no visible global function definition for ‘unzip’ enrichBarPlotFun: no visible binding for global variable ‘Terms’ enrichBarPlotFun: no visible binding for global variable ‘FDR’ enrichBarPlotFun: no visible binding for global variable ‘Category’ enrichBubblePlotFun: no visible binding for global variable ‘Terms’ enrichBubblePlotFun: no visible binding for global variable ‘foldEnrichment’ enrichBubblePlotFun: no visible binding for global variable ‘FDR’ enrichBubblePlotFun: no visible binding for global variable ‘Counts’ gdcBarPlot: no visible binding for global variable ‘Regulation’ gdcClinicalDownload: no visible global function definition for ‘read.table’ gdcClinicalDownload: no visible global function definition for ‘write.table’ gdcCorPlot: no visible global function definition for ‘cor.test’ gdcDEAnalysis: no visible global function definition for ‘model.matrix’ gdcDEAnalysis: no visible global function definition for ‘p.adjust’ gdcGetURL: no visible global function definition for ‘URLencode’ gdcKMPlot: no visible global function definition for ‘pchisq’ gdcKMPlot: no visible global function definition for ‘qnorm’ gdcRNADownload: no visible global function definition for ‘read.table’ gdcRNADownload: no visible global function definition for ‘write.table’ gdcRNAMerge : : no visible global function definition for ‘read.table’ gdcRNAMerge: no visible global function definition for ‘read.table’ gdcRNAMerge : : no visible global function definition for ‘read.delim’ gdcRNAMerge: no visible global function definition for ‘read.delim’ hyperTestFun: no visible global function definition for ‘phyper’ kmTestFun: no visible global function definition for ‘pchisq’ kmTestFun: no visible global function definition for ‘qnorm’ manifestDownloadFun: no visible global function definition for ‘read.table’ mirCorTestFun: no visible global function definition for ‘cor.test’ multiRegFun: no visible global function definition for ‘cor.test’ Undefined global functions or variables: Category Counts FDR Regulation Terms URLencode aggregate cor.test download.file foldEnrichment model.matrix p.adjust pchisq phyper qnorm read.delim read.table unzip write.table Consider adding importFrom("stats", "aggregate", "cor.test", "model.matrix", "p.adjust", "pchisq", "phyper", "qnorm") importFrom("utils", "URLencode", "download.file", "read.delim", "read.table", "unzip", "write.table") 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/GDCRNATools.Rcheck/00check.log’ for details.