############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EpiCompare_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EpiCompare.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 ‘EpiCompare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiCompare’ version ‘1.11.0’ * 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 ‘EpiCompare’ 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 ...Warning: program compiled against libxml 212 using older 211 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) EpiCompare.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:76-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:78-79: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:82-84: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:85-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:179: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:180: Lost braces in \itemize; meant \describe ? checkRd: (-1) EpiCompare.Rd:181: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_consensus_peaks.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_consensus_peaks.Rd:48-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:62-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:66-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_corr.Rd:70-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:61-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) gather_files_names.Rd:20-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) liftover_grlist.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) liftover_grlist.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) overlap_stat_plot.Rd:42-43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) overlap_stat_plot.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_corr.Rd:64-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_corr.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_corr.Rd:72-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:47-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:51-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_precision_recall.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:42-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:46-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) precision_recall.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:13-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:32-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:40-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_genome_builds.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:14-15: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:16: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:17: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:18-19: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_peaks.Rd:20-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:39-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:43-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) rebin_peaks.Rd:47-49: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_enrichment 61.411 1.901 66.066 plot_ChIPseeker_annotation 28.545 0.754 29.654 EpiCompare 14.158 0.740 26.135 rebin_peaks 9.588 3.033 5.180 plot_precision_recall 9.545 2.014 6.520 predict_precision_recall 8.574 1.793 5.181 plot_corr 8.778 1.518 8.152 plot_chromHMM 6.349 0.836 46.950 precision_recall 4.275 0.845 5.285 liftover_grlist 4.291 0.592 8.204 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’