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This page was generated on 2023-04-12 11:05:14 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for plyranges on nebbiolo2


To the developers/maintainers of the plyranges package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1499/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.18.0  (landing page)
Stuart Lee
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: RELEASE_3_16
git_last_commit: 580a5e1
git_last_commit_date: 2022-11-01 11:17:28 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: plyranges
Version: 1.18.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings plyranges_1.18.0.tar.gz
StartedAt: 2023-04-10 22:59:35 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:05:37 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 361.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: plyranges.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings plyranges_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/plyranges.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.18.0’
* 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object '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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘an-introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/plyranges.Rcheck/00check.log’
for details.



Installation output

plyranges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL plyranges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, 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 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 
 68.803   1.889  71.415 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.3680.0040.373
as_ranges0.0920.0000.092
compute_coverage0.0160.0000.017
element-setops0.1070.0080.115
filter-ranges0.5780.0800.657
group_by-ranges0.3220.0040.325
io-bam-read0.7540.0400.794
io-bed-read3.3680.1163.486
io-bed-write000
io-bigwig-read0.1050.0000.105
io-bigwig-write000
io-gff-read0.5040.0160.520
io-gff-write000
io-wig-read0.3470.0000.348
mutate-ranges0.8010.0280.828
n0.2600.0160.276
n_distinct0.0340.0000.035
overlap-joins0.2230.0160.239
ranges-anchor0.0990.0000.098
ranges-arrange0.0450.0000.044
ranges-bind0.1560.0040.159
ranges-chop0.3770.0120.389
ranges-construct0.1370.0040.141
ranges-count-overlaps0.0550.0000.055
ranges-disjoin0.8050.0000.805
ranges-expand0.570.000.57
ranges-filter-overlaps0.0780.0000.078
ranges-flank0.1340.0160.150
ranges-follow0.1540.0040.158
ranges-info0.0470.0000.048
ranges-interweave0.1360.0000.137
ranges-names0.1330.0000.134
ranges-nearest0.4260.0040.430
ranges-overlaps-self0.1240.0000.124
ranges-overlaps0.1610.0040.165
ranges-pairs0.3380.0040.342
ranges-precede0.1450.0000.146
ranges-reduce0.8490.0080.857
ranges-select0.0950.0000.094
ranges-setops0.8430.0040.847
ranges-shift0.1430.0200.164
ranges-summarise0.1420.0160.158
ranges-tile0.0900.0040.095
slice-ranges0.6860.0080.693
stretch0.2190.0000.219