############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ExiMiR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ExiMiR_2.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ExiMiR.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 ‘ExiMiR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ExiMiR’ version ‘2.49.0’ * 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 ‘ExiMiR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields. * 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 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: ‘Biobase’ ‘affyio’ ‘preprocessCore’ All declared Imports should be used. Packages in Depends field not imported from: ‘Biobase’ ‘affy’ ‘limma’ 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 NormiR.bgcorrect.methods: no visible global function definition for ‘bgcorrect.methods’ NormiR.pmcorrect.methods: no visible global function definition for ‘mm’ NormiR.pmcorrect.methods: no visible global function definition for ‘pmcorrect.methods’ NormiR.summary.methods: no visible global function definition for ‘generateExprSet.methods’ ReadExi: no visible global function definition for ‘readTargets’ ReadExi: no visible global function definition for ‘read.maimages’ ReadExi: no visible global function definition for ‘readGAL’ ReadExi: no visible global function definition for ‘getLayout’ ReadExi: no visible global function definition for ‘head’ bg.boxplot: no visible global function definition for ‘boxplot’ bg.correct.miR: no visible global function definition for ‘new’ bg.correct.miR: no visible global function definition for ‘exprs’ bg.correct.miR: no visible global function definition for ‘se.exprs’ bg.correct.miR: no visible global function definition for ‘backgroundCorrect.matrix’ bg.correct.miR: no visible global function definition for ‘exprs<-’ bg.correct.miR: no visible global function definition for ‘se.exprs<-’ bg.correct.miR: no visible global function definition for ‘bgcorrect.methods’ bg.correct.miR: no visible global function definition for ‘bg.correct’ bg.hist: no visible global function definition for ‘hist’ bg.image: no visible global function definition for ‘image’ by.samples.curve: no visible global function definition for ‘points’ by.samples.curve: no visible global function definition for ‘lines’ by.samples.figures: no visible global function definition for ‘dev.new’ by.samples.figures: no visible global function definition for ‘pdf’ by.samples.figures: no visible global function definition for ‘par’ by.samples.figures: no visible global function definition for ‘layout’ by.samples.figures: no visible global function definition for ‘dev.interactive’ by.samples.figures: no visible global function definition for ‘dev.off’ by.samples.legend: no visible global function definition for ‘points’ by.samples.legend: no visible global function definition for ‘text’ by.samples.legend: no visible global function definition for ‘legend’ create.gal.env: no visible global function definition for ‘multiassign’ createAB: no visible global function definition for ‘new’ createAB: no visible global function definition for ‘runif’ createAB: no visible global function definition for ‘notes<-’ createAB: no visible global function definition for ‘notes’ createAB: no visible global function definition for ‘pData<-’ get.bg.ab: no visible global function definition for ‘new’ get.bg.ab: no visible global function definition for ‘se.exprs’ get.bg.ab: no visible global function definition for ‘exprs’ get.bg.ab: no visible global function definition for ‘cdfName’ get.bg.ab: no visible global function definition for ‘phenoData’ get.bg.ab: no visible global function definition for ‘annotation’ get.bg.ab: no visible global function definition for ‘protocolData’ get.bg.ab: no visible global function definition for ‘description’ get.bg.ab: no visible global function definition for ‘notes’ has.bg: no visible global function definition for ‘notes’ is.dual: no visible global function definition for ‘notes’ is.from.createAB: no visible global function definition for ‘notes’ make.gal.env: no visible global function definition for ‘readGAL’ make.gal.env: no visible global function definition for ‘getLayout’ meannorm: no visible global function definition for ‘exprs’ meannorm: no visible global function definition for ‘sampleNames’ mediannorm: no visible global function definition for ‘exprs’ mediannorm: no visible global function definition for ‘sampleNames’ mediannorm: no visible binding for global variable ‘median’ norm.miR: no visible global function definition for ‘getCdfInfo’ norm.miR: no visible global function definition for ‘new’ norm.miR: no visible global function definition for ‘exprs’ norm.miR: no visible global function definition for ‘normalizeQuantiles’ norm.miR: no visible global function definition for ‘normalize’ norm.miR: no visible global function definition for ‘exprs<-’ read.annotation.fromfile: no visible global function definition for ‘read.maimages’ spikeinnorm: no visible global function definition for ‘getCdfInfo’ spikeinnorm: no visible global function definition for ‘exprs’ spikeinnorm: no visible global function definition for ‘sampleNames’ spikeinnorm: no visible global function definition for ‘median’ spikeinnorm: no visible global function definition for ‘cor’ spikeinnorm: no visible binding for global variable ‘sd’ spikeinnorm: no visible global function definition for ‘dev.new’ spikeinnorm: no visible global function definition for ‘pdf’ spikeinnorm: no visible global function definition for ‘dev.cur’ spikeinnorm: no visible global function definition for ‘layout’ spikeinnorm: no visible global function definition for ‘par’ spikeinnorm: no visible global function definition for ‘matplot’ spikeinnorm: no visible global function definition for ‘rainbow’ spikeinnorm: no visible global function definition for ‘axis’ spikeinnorm: no visible global function definition for ‘points’ spikeinnorm: no visible global function definition for ‘text’ spikeinnorm: no visible global function definition for ‘legend’ spikeinnorm: no visible global function definition for ‘dev.interactive’ spikeinnorm: no visible global function definition for ‘dev.off’ spikeinnorm: no visible global function definition for ‘rgb’ spikeinnorm: no visible global function definition for ‘heat.colors’ spikeinnorm: no visible global function definition for ‘image’ spikeinnorm: no visible binding for global variable ‘var’ spikeinnorm: no visible global function definition for ‘barplot’ spikeinnorm: no visible global function definition for ‘lm’ spikeinnorm: no visible global function definition for ‘predict’ spikeinnorm: no visible global function definition for ‘loess.smooth’ spikeinnorm: no visible global function definition for ‘approx’ summarize.miR: no visible global function definition for ‘mm’ summarize.miR: no visible global function definition for ‘computeExprSet’ Undefined global functions or variables: annotation approx axis backgroundCorrect.matrix barplot bg.correct bgcorrect.methods boxplot cdfName computeExprSet cor description dev.cur dev.interactive dev.new dev.off exprs exprs<- generateExprSet.methods getCdfInfo getLayout head heat.colors hist image layout legend lines lm loess.smooth matplot median mm multiassign new normalize normalizeQuantiles notes notes<- pData<- par pdf phenoData pmcorrect.methods points predict protocolData rainbow read.maimages readGAL readTargets rgb runif sampleNames sd se.exprs se.exprs<- text var Consider adding importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new", "dev.off", "heat.colors", "pdf", "rainbow", "rgb") importFrom("graphics", "axis", "barplot", "boxplot", "hist", "image", "layout", "legend", "lines", "matplot", "par", "points", "text") importFrom("methods", "new") importFrom("stats", "approx", "cor", "lm", "loess.smooth", "median", "predict", "runif", "sd", "var") importFrom("utils", "head") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 NormiR 8.439 0.096 8.537 summarize.miR 7.833 0.006 7.839 * 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/ExiMiR.Rcheck/00check.log’ for details.