############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:convert.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings convert_1.83.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/convert.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘convert/DESCRIPTION’ ... OK * this is package ‘convert’ version ‘1.83.0’ * 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 ‘convert’ 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 ... 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 dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘limma’ ‘marray’ ‘methods’ 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 coerce,MAList-ExpressionSet: no visible global function definition for ‘new’ coerce,MAList-ExpressionSet: no visible global function definition for ‘notes<-’ coerce,MAList-marrayNorm: no visible global function definition for ‘new’ coerce,RGList-NChannelSet: no visible global function definition for ‘new’ coerce,RGList-NChannelSet: no visible binding for global variable ‘df’ coerce,RGList-marrayRaw: no visible global function definition for ‘new’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘new’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘notes<-’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘maM’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘maLabels’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘maGnames’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘maInfo’ coerce,marrayNorm-ExpressionSet: no visible global function definition for ‘maTargets’ coerce,marrayNorm-MAList: no visible global function definition for ‘new’ coerce,marrayNorm-MAList: no visible global function definition for ‘getClass’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maRf’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maGf’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maRb’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maGb’ coerce,marrayRaw-NChannelSet: no visible binding for global variable ‘assayDataNew’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maInfo’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maTargets’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘new’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maGnames’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘phenoData<-’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘sampleNames’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘sampleNames<-’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘maLabels’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘featureData<-’ coerce,marrayRaw-NChannelSet: no visible global function definition for ‘featureNames<-’ coerce,marrayRaw-RGList: no visible global function definition for ‘new’ Undefined global functions or variables: assayDataNew df featureData<- featureNames<- getClass maGb maGf maGnames maInfo maLabels maM maRb maRf maTargets new notes<- phenoData<- sampleNames sampleNames<- Consider adding importFrom("methods", "getClass", "new") importFrom("stats", "df") 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/convert.Rcheck/00check.log’ for details.