############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EpiCompare.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EpiCompare_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/EpiCompare.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EpiCompare/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EpiCompare’ version ‘1.8.1’ * 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 ... 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) 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 50.004 3.674 61.539 plot_ChIPseeker_annotation 27.270 1.023 28.640 EpiCompare 10.292 0.970 11.874 plot_precision_recall 8.030 1.939 5.910 plot_corr 7.935 1.756 7.962 predict_precision_recall 7.134 2.032 5.063 precision_recall 7.091 2.031 4.817 rebin_peaks 5.054 2.144 5.328 plot_chromHMM 5.617 0.414 6.787 liftover_grlist 4.390 0.854 7.613 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 10. └─knitr:::eng_r(options) 11. ├─knitr:::in_input_dir(...) 12. │ └─knitr:::in_dir(input_dir(), expr) 13. └─knitr (local) evaluate(...) 14. └─evaluate::evaluate(...) 15. └─base::withRestarts(...) 16. └─base (local) withRestartList(expr, restarts) 17. └─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 18. └─base (local) docall(restart$handler, restartArgs) 19. ├─base::do.call("fun", lapply(args, enquote)) 20. └─evaluate (local) fun(base::quote(``)) [ FAIL 1 | WARN 7 | SKIP 0 | PASS 78 ] Error: Test failures Execution halted * 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: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/EpiCompare.Rcheck/00check.log’ for details.