############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylInheritance.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 ‘methylInheritance/DESCRIPTION’ ... OK * this is package ‘methylInheritance’ version ‘1.29.0’ * 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 ‘methylInheritance’ 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 ... OK * 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 ... NOTE checkRd: (-1) demoForTransgenerationalAnalysis.Rd:59-61: Lost braces 59 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) demoForTransgenerationalAnalysis.Rd:62-63: Lost braces 62 | \item \code{\link{runObservation}} {for running an | ^ checkRd: (-1) isInterGenerationResults.Rd:21: Lost braces; missing escapes or markup? 21 | "_permutation_{permutationID}.RDS" extension.} | ^ checkRd: (-1) methylInheritance-package.Rd:19-21: Lost braces 19 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) methylInheritance-package.Rd:22-23: Lost braces 22 | \item \code{\link{runObservation}} {for running an | ^ checkRd: (-1) methylInheritanceResults.Rd:293-294: Lost braces 293 | \item \code{\link{extractInfo}} {for extracting the | ^ checkRd: (-1) readInterGenerationResults.Rd:25: Lost braces; missing escapes or markup? 25 | "_permutation_{permutationID}.RDS" extension.} | ^ checkRd: (-1) runOnePermutationOnAllGenerations.Rd:144-173: Lost braces 144 | itemize{ | ^ checkRd: (-1) samplesForTransgenerationalAnalysis.Rd:48-50: Lost braces 48 | \item \code{\link{runPermutation}} {for running a | ^ checkRd: (-1) saveInterGenerationResults.Rd:27: Lost braces; missing escapes or markup? 27 | "_permutation_{permutationID}.RDS" extension.} | ^ * 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 runPermutation 290.613 2.245 332.791 runObservation 131.190 1.088 147.560 samplesForTransgenerationalAnalysis 89.444 0.575 103.799 runOnePermutationOnAllGenerations 31.025 0.285 34.792 demoForTransgenerationalAnalysis 13.541 0.319 14.950 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylInheritance.Rcheck/00check.log’ for details.