############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/coMethDMR.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘coMethDMR/DESCRIPTION’ ... OK * this is package ‘coMethDMR’ version ‘1.8.0’ * 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 ‘coMethDMR’ 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 whether startup messages can be suppressed ... 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 File ‘coMethDMR/R/zzz.R’: .onLoad calls: packageStartupMessage("Checking for cached SeSAMe data.") packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.") See section ‘Good practice’ in '?.onAttach'. * checking Rd files ... NOTE checkRd: (-1) AnnotateResults.Rd:13: Lost braces in \itemize; meant \describe ? checkRd: (-1) AnnotateResults.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) AnnotateResults.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) CoMethSingleRegion.Rd:55-60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CoMethSingleRegion.Rd:61-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CreateRdrop.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) CreateRdrop.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkComethylatedCpGs.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkComethylatedCpGs.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkComethylatedCpGs.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkComethylatedCpGs.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkMissing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkMissing.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkMissing.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MarkMissing.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly * 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 CoMethSingleRegion 32.668 1.301 35.065 lmmTest 28.292 1.076 30.630 SplitCpGDFbyRegion 20.338 0.764 21.713 CpGsInfoOneRegion 19.148 0.746 20.624 lmmTestAllRegions 18.997 0.613 20.114 CoMethAllRegions 14.306 0.441 14.975 GetCpGsInRegion 13.350 0.431 14.179 AnnotateResults 11.130 0.518 11.909 CloseBySingleRegion 8.732 1.246 13.432 CpGsInfoAllRegions 7.900 0.304 8.411 OrderCpGsByLocation 6.810 0.263 7.480 CreateOutputDF 6.717 0.265 7.181 ImportSesameData 6.088 0.216 6.510 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/coMethDMR.Rcheck/00check.log’ for details.