############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpress_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ArrayExpress.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ArrayExpress/DESCRIPTION’ ... OK * this is package ‘ArrayExpress’ version ‘1.52.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ArrayExpress’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 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 ae2bioc: no visible global function definition for ‘new’ extract.zip : : no visible global function definition for ‘unzip’ getAE : : no visible global function definition for ‘download.file’ getAE: no visible global function definition for ‘download.file’ getDataColsForAE1: no visible global function definition for ‘read.table’ preparePhenoDataFor2channel: no visible global function definition for ‘new’ queryAE: no visible global function definition for ‘download.file’ readDerivedDataFiles: no visible global function definition for ‘read.table’ readDerivedDataFiles: no visible global function definition for ‘new’ readDerivedDataMatrixFile: no visible global function definition for ‘read.table’ readDerivedDataMatrixFile: no visible global function definition for ‘new’ readExperimentData: no visible global function definition for ‘new’ readFeatures: no visible global function definition for ‘read.table’ readFeatures: no visible global function definition for ‘new’ readPhenoData: no visible global function definition for ‘new’ Undefined global functions or variables: download.file new read.table unzip Consider adding importFrom("methods", "new") importFrom("utils", "download.file", "read.table", "unzip") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ArrayExpress 6.386 1.875 23.337 queryAE 6.288 0.413 12.065 getAE 3.524 0.501 14.332 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ArrayExpress.Rcheck/00check.log’ for details.