##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:genomeIntervals.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings genomeIntervals_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/genomeIntervals.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 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 ... 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 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 ...
  ‘genomeIntervals.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.