############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:similaRpeak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings similaRpeak_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/similaRpeak.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 ‘similaRpeak/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘similaRpeak’ version ‘1.39.0’ * 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 ‘similaRpeak’ 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) DiffPosMax.Rd:64-65: Lost braces 64 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) DiffPosMax.Rd:66-67: Lost braces 66 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) DiffPosMax.Rd:68-69: Lost braces 68 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) DiffPosMax.Rd:70-72: Lost braces 70 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) DiffPosMax.Rd:78-79: Lost braces 78 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) Metric.Rd:32-33: Lost braces 32 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) Metric.Rd:34-35: Lost braces 34 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) Metric.Rd:36-37: Lost braces 36 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) Metric.Rd:38-40: Lost braces 38 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) Metric.Rd:46-47: Lost braces 46 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ checkRd: (-1) MetricFactory.Rd:44-45: Lost braces 44 | \item \code{ratioAreaThreshold} { The minimum denominator accepted to | ^ checkRd: (-1) MetricFactory.Rd:46-48: Lost braces 46 | \item \code{ratioMaxMaxThreshold} { The minimum denominator accepted to | ^ checkRd: (-1) MetricFactory.Rd:49-51: Lost braces 49 | \item \code{ratioIntersectThreshold} { The minimum denominator accepted to | ^ checkRd: (-1) MetricFactory.Rd:52-54: Lost braces 52 | \item \code{ratioIntersectThreshold} { The minimum denominator accepted to | ^ checkRd: (-1) MetricFactory.Rd:55-56: Lost braces 55 | \item \code{diffPosMaxThresholdMinValue} { The minimum peak accepted to | ^ checkRd: (-1) MetricFactory.Rd:57-59: Lost braces 57 | \item \code{diffPosMaxThresholdMaxDiff} { The maximum distance accepted | ^ checkRd: (-1) MetricFactory.Rd:60-61: Lost braces 60 | \item \code{diffPosMaxTolerance} {The maximum variation accepted on the | ^ checkRd: (-1) MetricFactory.Rd:62-64: Lost braces 62 | \item\code{spearmanCorrSDThreashold} {The minimum standard deviation | ^ checkRd: (-1) MetricFactory.Rd:118-119: Lost braces 118 | \item \code{\link{similarity}} {for calculating all available metrics | ^ checkRd: (-1) MetricFactory.Rd:120-121: Lost braces 120 | \item \code{\link{demoProfiles}} {for more informations about ChIP-Seq | ^ checkRd: (-1) RatioArea.Rd:43-44: Lost braces 43 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) RatioArea.Rd:45-46: Lost braces 45 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) RatioArea.Rd:47-48: Lost braces 47 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) RatioArea.Rd:49-51: Lost braces 49 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) RatioArea.Rd:57-58: Lost braces 57 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) RatioIntersect.Rd:43-44: Lost braces 43 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) RatioIntersect.Rd:45-46: Lost braces 45 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) RatioIntersect.Rd:47-48: Lost braces 47 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) RatioIntersect.Rd:49-51: Lost braces 49 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) RatioIntersect.Rd:57-58: Lost braces 57 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) RatioMaxMax.Rd:44-45: Lost braces 44 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) RatioMaxMax.Rd:46-47: Lost braces 46 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) RatioMaxMax.Rd:48-49: Lost braces 48 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) RatioMaxMax.Rd:50-52: Lost braces 50 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) RatioMaxMax.Rd:58-59: Lost braces 58 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) RatioNormalizedIntersect.Rd:45-46: Lost braces 45 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) RatioNormalizedIntersect.Rd:47-48: Lost braces 47 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) RatioNormalizedIntersect.Rd:49-50: Lost braces 49 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) RatioNormalizedIntersect.Rd:51-53: Lost braces 51 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) RatioNormalizedIntersect.Rd:59-60: Lost braces 59 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) SpearmanCorrelation.Rd:44-45: Lost braces 44 | \item \code{getMetric} { A function that returns the value of the | ^ checkRd: (-1) SpearmanCorrelation.Rd:46-47: Lost braces 46 | \item \code{getInfo} { A function that returns a description of the metric | ^ checkRd: (-1) SpearmanCorrelation.Rd:48-49: Lost braces 48 | \item \code{getType} { A function that returns the unique name associated | ^ checkRd: (-1) SpearmanCorrelation.Rd:50-52: Lost braces 50 | \item \code{calculateMetric} { A function that modifies the values of the | ^ checkRd: (-1) SpearmanCorrelation.Rd:58-59: Lost braces 58 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) chr7Profiles.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) chr7Profiles.Rd:16-17: Lost braces 16 | \item \code{chr7Profiles$chr7.61968807.61969730} { a \code{list} containing | ^ checkRd: (-1) chr7Profiles.Rd:18-21: Lost braces 18 | \item \code{demoProfiles$chr7.61968807.61969730$H3K27ac} { a numeric vector | ^ checkRd: (-1) chr7Profiles.Rd:22-25: Lost braces 22 | \item \code{demoProfiles$chr7.61968807.61969730$H3K4me1} { a numeric vector | ^ checkRd: (-1) chr7Profiles.Rd:68-69: Lost braces 68 | \item \code{\link{demoProfiles}} { ChIP-seq profiles related to enhancers | ^ checkRd: (-1) chr7Profiles.Rd:70-71: Lost braces 70 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) chr7Profiles.Rd:72-73: Lost braces 72 | \item \code{\link{similarity}} {for calculating all available metrics | ^ checkRd: (-1) demoProfiles.Rd:15-16: Lost braces 15 | \item \code{demoProfiles} { a \code{list} containing all demo ChIP-Seq | ^ checkRd: (-1) demoProfiles.Rd:17-18: Lost braces 17 | \item \code{demoProfiles$chr2.70360770.70361098} { a list containing 2 | ^ checkRd: (-1) demoProfiles.Rd:19-22: Lost braces 19 | \item \code{demoProfiles$chr2.70360770.70361098$H3K27ac} { a numeric vector | ^ checkRd: (-1) demoProfiles.Rd:23-26: Lost braces 23 | \item \code{demoProfiles$chr2.70360770.70361098$H3K4me1} { a numeric vector | ^ checkRd: (-1) demoProfiles.Rd:27-28: Lost braces 27 | \item \code{demoProfiles$chr3.73159773.73160145$H3K4me1} { a list containing | ^ checkRd: (-1) demoProfiles.Rd:29-32: Lost braces 29 | \item \code{demoProfiles$chr3.73159773.73160145$H3K27ac} { a numeric vector | ^ checkRd: (-1) demoProfiles.Rd:33-36: Lost braces 33 | \item \code{demoProfiles$chr3.73159773.73160145$H3K4me1} { a numeric vector | ^ checkRd: (-1) demoProfiles.Rd:72-74: Lost braces 72 | \item \code{\link{chr7Profiles}} { ChIP-Seq profiles of region | ^ checkRd: (-1) demoProfiles.Rd:75-76: Lost braces 75 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) demoProfiles.Rd:77-78: Lost braces 77 | \item \code{\link{similarity}} {for calculating all available metrics | ^ checkRd: (-1) diffPosMaxMethod.Rd:42-43: Lost braces 42 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ checkRd: (-1) ratioAreaMethod.Rd:34-35: Lost braces 34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ checkRd: (-1) ratioIntersectMethod.Rd:34-35: Lost braces 34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ checkRd: (-1) ratioMaxMaxMethod.Rd:34-35: Lost braces 34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ checkRd: (-1) similaRpeak-package.Rd:39-40: Lost braces 39 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) similaRpeak-package.Rd:41-42: Lost braces 41 | \item \code{\link{similarity}} {for calculating all available metrics | ^ checkRd: (-1) similarity.Rd:160-161: Lost braces 160 | \item \code{\link{MetricFactory}} {for using a interface to calculate all | ^ checkRd: (-1) similarity.Rd:162-163: Lost braces 162 | \item \code{\link{demoProfiles}} {for more informations about ChIP-Seq | ^ checkRd: (-1) spearmanCorrMethod.Rd:34-35: Lost braces 34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to | ^ * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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-3.21-bioc/meat/similaRpeak.Rcheck/00check.log’ for details.