############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RLSeq_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/RLSeq.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RLSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RLSeq’ version ‘1.6.0’ * 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 ‘RLSeq’ 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 R 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 startup messages can be suppressed ... 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 ... OK * 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 ‘RLSeq-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: featureEnrich > ### Title: Test Genomic Feature Enrichment > ### Aliases: featureEnrich > > ### ** Examples > > > # Example RLRanges dataset > rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq")) > > # RL Region Test > featureEnrich(rlr) see ?RLHub and browseVignettes('RLHub') for documentation - Calculating enrichment... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... Warning in peak_stats(x, xshuff, y, chromSizesNow, quiet = quiet) : Not enough observations for interval tests... - Done GRanges object with 7 ranges and 6 metadata columns: seqnames ranges strand | V4 | 1 chr14 20343155-20343313 * | /home/UTHSCSA/miller.. 2 chr21 8214588-8214866 * | /home/UTHSCSA/miller.. 3 chr21 8396653-8396835 * | /home/UTHSCSA/miller.. 4 chr22_KI270733v1_ran.. 129919-130080 * | /home/UTHSCSA/miller.. 5 chr22_KI270733v1_ran.. 174979-175184 * | /home/UTHSCSA/miller.. 6 chr6 52995648-52995831 * | /home/UTHSCSA/miller.. 7 chr9 35657778-35657976 * | /home/UTHSCSA/miller.. V5 V6 V7 V8 qval 1 56 . 7.40428 12.1836 5.63076 2 56 . 7.27639 12.2524 5.66372 3 15 . 5.19728 7.7825 1.52856 4 256 . 16.31970 32.6965 25.65290 5 1085 . 30.29480 116.1250 108.58400 6 95 . 9.63809 16.3088 9.58453 7 100 . 9.84017 16.7326 10.04910 ------- seqinfo: 640 sequences (1 circular) from hg38 genome RDIP-Seq +RNH1: Mode: RDIP Genome: hg38 Label: NEG RLSeq Results Available: featureEnrichment, txFeatureOverlap, correlationMat, rlfsRes, noiseAnalysis, geneAnnoRes, predictRes, rlRegionRes prediction: NEG > > # With custom annotations > small_anno <- list( + "Centromeres" = readr::read_csv( + system.file("extdata", "Centromeres.csv.gz", package = "RLSeq"), + show_col_types = FALSE + ) + ) Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value Calls: -> -> vroom_ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 See ‘/Users/biocbuild/bbs-3.17-bioc/meat/RLSeq.Rcheck/00check.log’ for details.