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CHECK report for plyranges on merida1

This page was generated on 2021-05-06 12:36:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the plyranges package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1361/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.10.0  (landing page)
Stuart Lee
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/plyranges
Branch: RELEASE_3_12
Last Commit: 5856b8c
Last Changed Date: 2020-10-27 11:34:01 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: plyranges
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plyranges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plyranges_1.10.0.tar.gz
StartedAt: 2021-05-06 04:48:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:53:37 -0400 (Thu, 06 May 2021)
EllapsedTime: 331.8 seconds
RetCode: 0
Status:   OK  
CheckDir: plyranges.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plyranges.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plyranges_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/plyranges.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.10.0’
* 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 ... 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 ... 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

plyranges.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL plyranges
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 object is masked from 'package:base':

    expand.grid

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 7 | SKIP 0 | PASS 390 ]
> 
> proc.time()
   user  system elapsed 
 62.748   1.572  66.163 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.5220.0240.546
as_ranges0.1140.0100.124
compute_coverage0.0200.0030.023
element-setops0.1520.0190.172
filter-ranges0.8170.0780.897
group_by-ranges0.3350.0040.339
io-bam-read1.6730.0401.714
io-bed-read2.9140.4003.317
io-bed-write0.0000.0000.001
io-bigwig-read0.1560.0070.163
io-bigwig-write000
io-gff-read0.6320.0150.648
io-gff-write000
io-wig-read0.5360.0100.546
mutate-ranges0.9560.0270.983
n0.3570.0010.358
n_distinct0.0460.0010.047
overlap-joins0.3000.0030.304
ranges-anchor0.1600.0030.162
ranges-arrange0.0690.0020.070
ranges-bind0.2900.0030.293
ranges-chop0.4390.0080.447
ranges-construct0.1760.0030.177
ranges-count-overlaps0.0700.0010.071
ranges-disjoin1.0410.0061.047
ranges-expand0.7870.0040.791
ranges-filter-overlaps0.0880.0010.089
ranges-flank0.1280.0020.130
ranges-follow0.3180.0150.333
ranges-info0.0790.0010.080
ranges-interweave0.2550.0020.258
ranges-names0.1630.0010.164
ranges-nearest0.6370.0120.650
ranges-overlaps-self0.2150.0070.223
ranges-overlaps0.2870.0060.294
ranges-pairs0.4840.0060.491
ranges-precede0.2340.0040.240
ranges-reduce1.1440.0051.149
ranges-select0.1270.0040.132
ranges-setops1.3410.0061.347
ranges-shift0.2410.0020.243
ranges-summarise0.2190.0020.220
ranges-tile0.1270.0020.130
slice-ranges0.8600.0050.866
stretch0.3490.0040.352