Mac ARM64 build report for BioC 3.20 - CHECK results for plyranges on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4378
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

##############################################################################
##############################################################################
###
### 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/plyranges.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.25.0’
* 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 ... 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 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 394 ]
  
  ══ 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 394 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/plyranges.Rcheck/00check.log’
for details.

Installation output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘plyranges’ ...
** 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)

Tests output


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 394 ]

══ 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 394 ]
Error: Test failures
Execution halted

Example timings

name	user	system	elapsed
add-nearest-distance	0.348	0.009	0.356
as_ranges	0.091	0.008	0.100
compute_coverage	0.016	0.003	0.019
element-setops	0.112	0.011	0.124
filter-ranges	0.579	0.028	0.606
group_by-ranges	0.298	0.003	0.302
io-bam-read	0.799	0.039	0.839
io-bed-read	3.223	0.574	3.800
io-bed-write	0.000	0.000	0.001
io-bigwig-read	0.111	0.002	0.113
io-bigwig-write	0.000	0.001	0.001
io-gff-read	0.458	0.021	0.480
io-gff-write	0	0	0
io-wig-read	0.365	0.015	0.381
mutate-ranges	0.747	0.010	0.757
n	0.265	0.003	0.266
n_distinct	0.032	0.001	0.031
overlap-joins	0.211	0.002	0.213
ranges-anchor	0.097	0.001	0.100
ranges-arrange	0.041	0.001	0.042
ranges-bind	0.154	0.002	0.157
ranges-chop	0.336	0.007	0.344
ranges-construct	0.111	0.003	0.115
ranges-count-overlaps	0.058	0.000	0.058
ranges-disjoin	0.697	0.004	0.702
ranges-expand	0.520	0.004	0.524
ranges-filter-overlaps	0.147	0.003	0.149
ranges-flank	0.095	0.002	0.096
ranges-follow	0.147	0.002	0.148
ranges-info	0.045	0.001	0.046
ranges-interweave	0.126	0.001	0.127
ranges-names	0.143	0.001	0.143
ranges-nearest	0.375	0.002	0.378
ranges-overlaps-self	0.117	0.001	0.118
ranges-overlaps	0.167	0.002	0.170
ranges-pairs	0.292	0.003	0.295
ranges-precede	0.141	0.002	0.142
ranges-reduce	1.177	0.012	1.189
ranges-select	0.067	0.003	0.069
ranges-setops	0.723	0.004	0.727
ranges-shift	0.133	0.002	0.135
ranges-summarise	0.154	0.001	0.154
ranges-tile	0.084	0.002	0.085
slice-ranges	0.573	0.003	0.576
stretch	0.202	0.002	0.204

CHECK results for plyranges on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings