############################################################################## ############################################################################## ### ### 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 4.4.0 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 ‘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 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.3Mb 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 33.011 0.725 38.237 enrichment_analysis 27.409 0.870 39.454 plotGenomeBrowser 19.274 0.350 22.954 callPeaksMultivariate 15.854 0.395 18.507 callPeaksReplicates 13.189 0.333 15.469 unis2pseudomulti 12.483 0.261 15.073 changePostCutoff 11.330 0.316 13.153 Chromstar 10.374 0.569 86.601 combinatorialStates 9.336 0.245 10.802 changeMaxPostCutoff 7.944 0.198 9.020 readCustomBedFile 7.315 0.135 8.583 plotExpression 5.856 0.221 8.457 * 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.