############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epigenomix_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epigenomix.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘epigenomix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘epigenomix’ version ‘1.47.0’ * 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 ‘epigenomix’ 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 loading without being on the library search path ... 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) MixModel-class.Rd:77-81: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:85-86: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:87: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:88-89: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:55: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:56-58: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:59-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:65-66: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:67-68: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:69-70: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:71-72: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:51-53: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:58: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:59-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:61: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:50-55: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:56-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:61-63: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:64-72: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:35-38: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:39-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:47-51: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:52-53: Lost braces in \enumerate; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: ChIPseqSet-class.Rd: RangedSummarizedExperiment-class calculateCrossCorrelation.Rd: GRanges, GRanges-class eSet.Rd: ExpressionSet-class integrateData.Rd: ExpressionSet mappedReads.Rd: GRangesList-class, GRanges-class normalize.Rd: ExpressionSet-class summarizeReads.Rd: countOverlaps Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotChains 37.905 0.144 45.113 bayesMixModel 28.963 0.455 30.989 mlMixModel 15.645 0.052 15.733 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/epigenomix.Rcheck/00check.log’ for details.