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This page was generated on 2024-03-04 11:39:42 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1554/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.23.0  (landing page)
Stuart Lee
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: devel
git_last_commit: b5c1421
git_last_commit_date: 2023-10-24 11:04:07 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for plyranges on merida1


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.

raw results


Summary

Package: plyranges
Version: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2024-03-02 08:35:05 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 08:46:42 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 696.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: plyranges.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.23.0’
* 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 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 ... WARNING
group_split:
  function(.tbl, ..., .keep)
group_split.GroupedGenomicRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.GroupedIntegerRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.Ranges:
  function(.data, ..., keep)

group_keys:
  function(.tbl, ...)
group_keys.Ranges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedGenomicRanges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedIntegerRanges:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'ranges-info.Rd':
  ‘[GenomeInfoDb:fetchExtendedChromInfoFromUCSC]{GenomeInfoDb::fetchExtendedChromInfoFromUCSC()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
io-bed-read 4.753  1.143   7.373
* 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 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck/00check.log’
for details.



Installation output

plyranges.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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

plyranges.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 0 | WARN 8 | SKIP 0 | PASS 390 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 390 ]
> 
> proc.time()
   user  system elapsed 
 99.867   3.743 122.421 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.7690.0541.057
as_ranges0.2330.0200.319
compute_coverage0.0340.0030.048
element-setops0.2330.0070.304
filter-ranges1.2650.0581.697
group_by-ranges0.6980.0280.931
io-bam-read1.9840.0622.593
io-bed-read4.7531.1437.373
io-bed-write0.0010.0010.001
io-bigwig-read0.2450.0060.320
io-bigwig-write0.0000.0010.000
io-gff-read0.8220.0321.036
io-gff-write0.0000.0000.001
io-wig-read0.7290.0310.959
mutate-ranges1.6690.0252.077
n0.5620.0050.714
n_distinct0.0730.0020.097
overlap-joins0.4550.0080.565
ranges-anchor0.2440.0050.306
ranges-arrange0.1140.0020.145
ranges-bind0.3900.0070.486
ranges-chop0.6710.0140.846
ranges-construct0.2260.0070.296
ranges-count-overlaps0.1430.0030.173
ranges-disjoin1.6110.0182.015
ranges-expand1.0820.0141.354
ranges-filter-overlaps0.1690.0030.208
ranges-flank0.2170.0040.267
ranges-follow0.4930.0080.627
ranges-info0.1070.0030.141
ranges-interweave0.3190.0040.397
ranges-names0.2680.0030.334
ranges-nearest0.9190.0091.142
ranges-overlaps-self0.2890.0060.364
ranges-overlaps0.380.010.49
ranges-pairs0.7800.0110.988
ranges-precede0.3510.0060.445
ranges-reduce1.7890.0162.224
ranges-select0.1750.0080.218
ranges-setops1.8430.0162.321
ranges-shift0.3290.0070.415
ranges-summarise0.3150.0030.396
ranges-tile0.2080.0060.266
slice-ranges1.3180.0151.636
stretch0.5300.0080.691