############################################################################## ############################################################################## ### ### 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_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * 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 ... 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 ... ERROR Running examples in ‘EpiCompare-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compute_corr > ### Title: Compute correlation matrix > ### Aliases: compute_corr > > ### ** Examples > > data("CnR_H3K27ac") > data("CnT_H3K27ac") > data("encode_H3K27ac") > peakfiles <- list(CnR_H3K27ac=CnR_H3K27ac, CnT_H3K27ac=CnT_H3K27ac) > reference <- list("encode_H3K27ac"=encode_H3K27ac) > > #increasing bin_size for speed but lower values will give more granular corr > corr_mat <- compute_corr(peakfiles = peakfiles, + reference = reference, + genome_build = "hg19", + bin_size = 200000, + workers = 1) Standardising peak files in 16,318 bins of 2e+05 bp. *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges") 2: viewMeans(v, na.rm = na.rm) 3: viewMeans(v, na.rm = na.rm) 4: viewMeans2(v, na.rm = na.rm) 5: FUN(X[[i]], ...) 6: lapply(names(numvar), function(seqname) { v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]]) viewMeans2(v, na.rm = na.rm)}) 7: lapply(names(numvar), function(seqname) { v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]]) viewMeans2(v, na.rm = na.rm)}) 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov, varname = "score", na.rm = FALSE) 9: FUN(X[[i]], ...) 10: lapply(X = S, FUN = FUN, ...) 11: doTryCatch(return(expr), name, parentenv, handler) 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 17: FUN(X[[i]], ...) 18: lapply(seq_len(cores), inner.do) 19: apply_fun(FUN = FUN, X, ...) 20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) { gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols, initial_threshold = 0) gr_names <- names(GenomicRanges::mcols(gr)) intens_col <- gr_names[gr_names %in% paste(intensity_cols, "percentile", sep = "_")][1] data_cov <- GenomicRanges::coverage(gr, weight = intens_col) rm(gr) gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov, varname = "score", na.rm = FALSE) return(gr$score)}, ...) 21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols, bin_size = bin_size, as_sparse = FALSE, workers = workers) 22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19", bin_size = 2e+05, workers = 1) An irrecoverable exception occurred. R is aborting now ... *** caught segfault *** address 0x1, cause 'invalid permissions' Traceback: 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges") 2: viewMeans(v, na.rm = na.rm) 3: viewMeans(v, na.rm = na.rm) 4: viewMeans2(v, na.rm = na.rm) 5: FUN(X[[i]], ...) 6: lapply(names(numvar), function(seqname) { v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]]) viewMeans2(v, na.rm = na.rm)}) 7: lapply(names(numvar), function(seqname) { v <- Views(numvar[[seqname]], bins_per_chrom[[seqname]]) viewMeans2(v, na.rm = na.rm)}) 8: GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov, varname = "score", na.rm = FALSE) 9: FUN(X[[i]], ...) 10: lapply(X = S, FUN = FUN, ...) 11: doTryCatch(return(expr), name, parentenv, handler) 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 15: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 16: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 17: FUN(X[[i]], ...) 18: lapply(seq_len(cores), inner.do) 19: apply_fun(FUN = FUN, X, ...) 20: bpplapply(X = peakfiles, workers = workers, FUN = function(gr) { gr <- compute_percentiles(gr = gr, thresholding_cols = intensity_cols, initial_threshold = 0) gr_names <- names(GenomicRanges::mcols(gr)) intens_col <- gr_names[gr_names %in% paste(intensity_cols, "percentile", sep = "_")][1] data_cov <- GenomicRanges::coverage(gr, weight = intens_col) rm(gr) gr <- GenomicRanges::binnedAverage(bins = gr_windows, numvar = data_cov, varname = "score", na.rm = FALSE) return(gr$score)}, ...) 21: rebin_peaks(peakfiles = all_peaks, genome_build = genome_build, keep_chr = keep_chr, drop_empty_chr = drop_empty_chr, intensity_cols = intensity_cols, bin_size = bin_size, as_sparse = FALSE, workers = workers) 22: compute_corr(peakfiles = peakfiles, reference = reference, genome_build = "hg19", bin_size = 2e+05, workers = 1) An irrecoverable exception occurred. R is aborting now ... Warning in apply_fun(FUN = FUN, X, ...) : scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected Merging data into matrix. Error in `rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), : attempt to set 'rownames' on an object with no dimensions Calls: compute_corr -> rebin_peaks -> rownames<- Execution halted * 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: 1. └─EpiCompare::plot_corr(...) at test-plot_corr.R:9:5 2. └─EpiCompare::compute_corr(...) 3. └─EpiCompare::rebin_peaks(...) 4. └─base::`rownames<-`(...) ── Error ('test-rebin_peaks.R:13:5'): rebin_peaks works ──────────────────────── Error in ``rownames<-`(`*tmp*`, value = paste0(GenomicRanges::seqnames(gr_windows), sep[1], GenomicRanges::start(gr_windows), sep[2], GenomicRanges::end(gr_windows)))`: attempt to set 'rownames' on an object with no dimensions Backtrace: ▆ 1. └─EpiCompare::rebin_peaks(...) at test-rebin_peaks.R:13:5 2. └─base::`rownames<-`(...) [ FAIL 4 | WARN 10 | SKIP 0 | PASS 77 ] 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: 2 ERRORs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/EpiCompare.Rcheck/00check.log’ for details.