############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.49.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BiocGenerics.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocGenerics/DESCRIPTION’ ... OK * this is package ‘BiocGenerics’ version ‘0.49.1’ * 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 ‘BiocGenerics’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘utils’ ‘graphics’ ‘stats’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'as.data.frame.Rd': ‘[IRanges]{as.data.frame,IntegerRanges-method}’ Missing link or links in Rd file 'order.Rd': ‘[IRanges]{order,IntegerRanges-method}’ Missing link or links in Rd file 'type.Rd': ‘[DelayedArray]{type,ANY-method}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'funprog.Rd': Reduce Code: function(f, x, init, right = FALSE, accumulate = FALSE, simplify = TRUE) Docs: function(f, x, init, right = FALSE, accumulate = FALSE) Argument names in code not in docs: simplify * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fileName 16.346 0.800 20.081 Ontology 6.938 0.390 8.323 plotMA 6.264 0.251 7.442 plotPCA 5.290 0.085 6.234 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/BiocGenerics.Rcheck/00check.log’ for details.