############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromstaR_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/chromstaR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chromstaR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chromstaR’ version ‘1.31.0’ * 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 ‘chromstaR’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 4.5Mb * 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 Chromstar: multiple local function definitions for ‘parallel.helper’ with different formal arguments * checking Rd files ... NOTE checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces 66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces 66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces 60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces 60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).} | ^ checkRd: (-1) plotGenomeBrowser.Rd:28-68: Lost braces 28 | plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol='black', peakcols=NULL, style='peaks', peakTrackHeight=5) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:36-41: Lost braces 36 | if (style == 'peaks') { | ^ checkRd: (-1) plotGenomeBrowser.Rd:41-45: Lost braces 41 | } else if (style == 'density') { | ^ checkRd: (-1) plotGenomeBrowser.Rd:45-47: Lost braces 45 | } else { | ^ checkRd: (-1) plotGenomeBrowser.Rd:50-65: Lost braces 50 | if (!is.null(peaklist)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:51-53: Lost braces 51 | if (is.null(peakcols)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:54-64: Lost braces 54 | for (i1 in 1:length(peaklist)) { | ^ checkRd: (-1) plotGenomeBrowser.Rd:57-60: Lost braces 57 | if (length(peaks) > 0) { | ^ * 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combineMultivariates 8.383 0.363 8.784 enrichment_analysis 4.446 0.244 7.253 Chromstar 2.477 0.115 17.380 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/chromstaR.Rcheck/00check.log’ for details.