############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChIPpeakAnno.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ChIPpeakAnno_3.37.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck' * using R Under development (unstable) (2024-03-16 r86144 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ChIPpeakAnno' version '3.37.4' * 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 whether package 'ChIPpeakAnno' can be installed ... OK * checking installed package size ... NOTE installed size is 21.1Mb sub-directories of 1Mb or more: 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 29.78 1.17 31.62 findMotifsInPromoterSeqs 15.84 0.66 21.33 annotatePeakInBatch 14.67 1.50 17.22 summarizeOverlapsByBins 4.34 0.05 23.89 annoPeaks 3.06 0.52 5.60 addAncestors 1.29 0.23 10.08 tileCount 1.45 0.03 22.14 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/ChIPpeakAnno.Rcheck/00check.log' for details.