############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CNVMetrics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CNVMetrics_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘CNVMetrics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNVMetrics’ version ‘1.10.0’ * 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 ‘CNVMetrics’ 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) CNVMetrics-package.Rd:23-24: Lost braces 23 | \item \code{\link{calculateOverlapMetric}} {for calculating metric | ^ checkRd: (-1) CNVMetrics-package.Rd:25-26: Lost braces 25 | \item \code{\link{calculateLog2ratioMetric}} {for calculating metric | ^ checkRd: (-1) CNVMetrics-package.Rd:27: Lost braces; missing escapes or markup? 27 | \item \code{\link{processSim}} {for generating simulations} | ^ checkRd: (-1) CNVMetrics-package.Rd:28: Lost braces; missing escapes or markup? 28 | \item \code{\link{plotMetric}} {for plotting metrics} | ^ checkRd: (-1) calculateLog2ratioMetric.Rd:42-47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateLog2ratioMetric.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateLog2ratioMetric.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateOneLog2valueMetricT.Rd:37: Lost braces 37 | that have to be excluded for the metric calculation or code{NULL}.} | ^ checkRd: (-1) calculateOneLog2valueMetricT.Rd:42-49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateOneOverlapMetricT.Rd:33-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateOverlapMetric.Rd:39-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateOverlapMetric.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateOverlapMetric.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) processSim.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:26: Lost braces 26 | a code{list} containing one entry per simulation. Each entry is | ^ checkRd: (-1) simChr.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:31-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simChr.Rd:39-40: 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateOverlapMetric 4.704 0.034 5.909 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/CNVMetrics.Rcheck/00check.log’ for details.