############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings minfi_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘minfi/DESCRIPTION’ ... OK * this is package ‘minfi’ version ‘1.51.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘minfi’ 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 Unexported objects imported by ':::' calls: ‘DelayedArray:::get_verbose_block_processing’ ‘DelayedArray:::normarg_grid’ ‘bumphunter:::.getEstimate’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.guessArrayTypes’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘minfi/R/IlluminaMethylationManifest-class.R’: unlockBinding(name, env = object@data) * checking Rd files ... NOTE checkRd: (-1) gaphunter.Rd:19: Lost braces 19 | If one of the first two, code{\link{getBeta}} is used to calculate beta values. If a | ^ checkRd: (-1) ratioConvert-methods.Rd:35: Lost braces 35 | \code{\link{RatioSet}} or code{\link{GenomicRatioSet}} for the output | ^ checkRd: (-1) ratioConvert-methods.Rd:36: Lost braces 36 | object and \code{\link{MethylSet}} or code{\link{GenomicMethylSet}} | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combineArrays 85.656 4.239 129.442 bumphunter 36.708 5.352 56.156 read.metharray.exp 12.107 0.209 17.271 densityPlot 7.517 0.351 11.042 read.metharray 7.183 0.296 10.448 preprocessFunnorm 6.864 0.464 10.315 preprocessIllumina 6.637 0.262 10.330 preprocessRaw 5.540 0.133 8.222 IlluminaMethylationManifest-class 5.316 0.254 7.801 densityBeanPlot 4.303 0.145 6.374 compartments 3.616 0.325 5.614 controlStripPlot 3.418 0.171 5.406 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/minfi.Rcheck/00check.log’ for details.