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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 1600/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.28.0  (landing page)
Michael Love
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: RELEASE_3_21
git_last_commit: 1d0bf92
git_last_commit_date: 2025-04-15 11:20:13 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for plyranges on kunpeng2

To the developers/maintainers of the plyranges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyranges.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: plyranges
Version: 1.28.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings plyranges_1.28.0.tar.gz
StartedAt: 2025-10-14 12:36:51 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 12:42:56 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 365.4 seconds
RetCode: 0
Status:   OK  
CheckDir: plyranges.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings plyranges_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/plyranges.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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 ... 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’
 OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/plyranges.Rcheck/00check.log’
for details.


Installation output

plyranges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL plyranges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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)

Tests output

plyranges.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 0 | WARN 8 | SKIP 0 | PASS 397 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 397 ]
> 
> proc.time()
   user  system elapsed 
 61.426   1.182  62.769 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.6020.0320.635
as_ranges0.1210.0000.121
compute_coverage0.0210.0000.021
element-setops0.1320.0120.144
filter-ranges1.6730.1511.829
group_by-ranges0.4140.0000.414
io-bam-read0.7920.0240.825
io-bed-read1.3290.0241.360
io-bed-write000
io-bigwig-read0.1300.0030.136
io-bigwig-write000
io-gff-read0.4550.0150.471
io-gff-write000
io-wig-read0.4780.0110.491
mutate-ranges0.8130.0160.831
n0.2740.0090.283
n_distinct0.0380.0000.039
overlap-joins0.2450.0040.250
ranges-anchor0.130.000.13
ranges-arrange0.0620.0000.062
ranges-bind0.2270.0000.227
ranges-chop0.4550.0190.476
ranges-construct0.1350.0040.138
ranges-count-overlaps0.0750.0070.084
ranges-disjoin0.9400.0240.966
ranges-expand0.6000.0000.601
ranges-filter-overlaps0.1660.0030.170
ranges-flank0.1320.0000.132
ranges-follow0.2710.0000.270
ranges-info0.0620.0000.063
ranges-interweave0.2230.0000.224
ranges-names0.1540.0000.178
ranges-nearest0.5240.0070.532
ranges-overlaps-self0.1830.0080.191
ranges-overlaps0.2220.0000.222
ranges-pairs0.4360.0040.441
ranges-precede0.2030.0000.203
ranges-reduce1.2800.0161.297
ranges-select0.1030.0000.104
ranges-setops1.0860.0281.116
ranges-shift0.2090.0120.222
ranges-summarise0.2000.0080.208
ranges-tile0.1240.0040.128
slice-ranges0.7720.0120.785
stretch0.2980.0000.299