############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomeIntervals_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/genomeIntervals.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genomeIntervals/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genomeIntervals’ version ‘1.56.0’ * 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 ‘genomeIntervals’ 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 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 ... WARNING checkRd: (-1) Genome_intervals-class.Rd:42: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:66: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:67: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:68: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:69: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:70: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:77: Escaped LaTeX specials: \$ checkRd: (-1) Genome_intervals-class.Rd:78: Escaped LaTeX specials: \$ checkRd: (-1) Genome_intervals-class.Rd:86: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals-class.Rd:87: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:88: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:89: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:90: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:91: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:92: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals-class.Rd:97: Escaped LaTeX specials: \_ checkRd: (5) Genome_intervals-ordering.Rd:75-82: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:83-87: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:88-92: \item in \describe must have non-empty label checkRd: (5) Genome_intervals-ordering.Rd:93-98: \item in \describe must have non-empty label checkRd: (-1) Genome_intervals_stranded-class.Rd:12: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:26: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:27: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:29: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:30: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:31: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:36: Escaped LaTeX specials: \_ \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:38: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:39: Escaped LaTeX specials: \_ checkRd: (-1) Genome_intervals_stranded-class.Rd:40: Escaped LaTeX specials: \_ checkRd: (-1) genomeIntervals-package.Rd:32: Escaped LaTeX specials: \_ checkRd: (-1) genomeIntervals-package.Rd:33: Escaped LaTeX specials: \_ \_ checkRd: (-1) interval_overlap-methods.Rd:37: Escaped LaTeX specials: \_ checkRd: (-1) parseGffAttributes.Rd:5: Escaped LaTeX specials: \_ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘benchmarking-tests.R’ Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...15a16,21 > The following objects are masked from 'package:parallel': > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > 26c32 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, --- > Filter, Find, Map, Position, Reduce, anyDuplicated, append, 31c37 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running ‘consistency-tests.R’ Comparing ‘consistency-tests.Rout’ to ‘consistency-tests.Rout.save’ ...12a13,18 > The following objects are masked from 'package:parallel': > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > 23c29 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, --- > Filter, Find, Map, Position, Reduce, anyDuplicated, append, 28c34 < tapply, union, unique, unsplit, which.max, which.min --- > tapply, union, unique, unsplit, which, which.max, which.min Running ‘fullShow.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 WARNING See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/genomeIntervals.Rcheck/00check.log’ for details.