############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPpeakAnno_3.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPpeakAnno’ version ‘3.38.0’ * 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 ‘ChIPpeakAnno’ can be installed ... OK * checking installed package size ... NOTE installed size is 21.1Mb sub-directories of 1Mb or more: R 1.0Mb data 12.6Mb extdata 7.2Mb * 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) summarizePatternInPeaks.Rd:63: Lost braces; missing escapes or markup? 63 | {shuffle_sequences}} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:69: Lost braces; missing escapes or markup? 69 | \item{"patternNum"}: {number of matched pattern} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:70-71: Lost braces 70 | \item{"totalNumPatternWithSameLen"}: {total number of pattern with the | ^ checkRd: (-1) summarizePatternInPeaks.Rd:72: Lost braces; missing escapes or markup? 72 | \item{"expectedRate"}: {expected rate of pattern for 'binom.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:73: Lost braces; missing escapes or markup? 73 | \item{"patternRate"}: {real rate of pattern for 'permutation.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:74: Lost braces; missing escapes or markup? 74 | \item{"pValueBinomTest"}: {p value of bimom test for 'binom.test' method} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:75-76: Lost braces 75 | \item{"cutOffPermutationTest"}: {cut off of permutation test for | ^ checkRd: (-1) summarizePatternInPeaks.Rd:82: Lost braces; missing escapes or markup? 82 | \item{"motifChr"}: {Chromosome of motif} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:83: Lost braces; missing escapes or markup? 83 | \item{"motifStartInChr"}: {motif start position in chromosome} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:84: Lost braces; missing escapes or markup? 84 | \item{"motifEndInChr"}: {motif end position in chromosome} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:85: Lost braces; missing escapes or markup? 85 | \item{"motifName"}: {motif name} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:86: Lost braces; missing escapes or markup? 86 | \item{"motifPattern"}: {motif pattern} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:87: Lost braces; missing escapes or markup? 87 | \item{"motifStartInPeak"}: {motif start position in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:88: Lost braces; missing escapes or markup? 88 | \item{"motifEndInPeak"}: {motif end position in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:89: Lost braces; missing escapes or markup? 89 | \item{"motifFound"}: {specific motif Found in peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:90-91: Lost braces 90 | \item{"motifFoundStrand"}: {strand of specific motif Found in peak, "-" | ^ checkRd: (-1) summarizePatternInPeaks.Rd:92: Lost braces; missing escapes or markup? 92 | \item{"peakChr"}: {Chromosome of peak} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:93: Lost braces; missing escapes or markup? 93 | \item{"peakStart"}: {peak start position} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:94: Lost braces; missing escapes or markup? 94 | \item{"peakEnd"}: {peak end position} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:95: Lost braces; missing escapes or markup? 95 | \item{"peakWidth"}: {peak width} | ^ checkRd: (-1) summarizePatternInPeaks.Rd:96: Lost braces; missing escapes or markup? 96 | \item{"peakStrand"}: {peak strand} | ^ * 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 LazyData ... 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 findEnhancers 28.874 1.039 30.341 findMotifsInPromoterSeqs 17.057 0.638 18.302 annotatePeakInBatch 16.240 1.010 17.600 summarizeOverlapsByBins 5.734 0.542 6.047 annoPeaks 3.709 0.478 5.232 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’ for details.