##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyranges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyranges_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/plyranges.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.28.0’
* 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 ‘plyranges’ 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) group_by-ranges.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) group_by-ranges.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:63-64: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'tidyverse-reexports.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_ranges.Rd: Rle, RleList, IRanges, GRanges
  ranges-construct.Rd: tibble
  ranges-filter-overlaps.Rd: GRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
  
      filter
  
  > 
  > test_check("plyranges")
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 396 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-io-bed.R:136:3'): read_narrowpeaks returns correct GRanges ───
  `gr` not identical to `test_gr`.
  Objects equal but not identical
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 396 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/plyranges.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plyranges
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘plyranges’ ...
** this is package ‘plyranges’ version ‘1.28.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plyranges)

R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(plyranges)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'plyranges'

The following object is masked from 'package:IRanges':

    slice

The following object is masked from 'package:stats':

    filter

> 
> test_check("plyranges")
[ FAIL 1 | WARN 8 | SKIP 0 | PASS 396 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-io-bed.R:136:3'): read_narrowpeaks returns correct GRanges ───
`gr` not identical to `test_gr`.
Objects equal but not identical

[ FAIL 1 | WARN 8 | SKIP 0 | PASS 396 ]
Error: Test failures
Execution halted