Multiple platform build/check report for BioC 3.10 - CHECK report for plyranges on merida1

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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_1.6.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/plyranges.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.10’
* 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

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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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 348 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 52.643   1.384  54.087

Example timings

name	user	system	elapsed
as_ranges	0.154	0.006	0.159
compute_coverage	0.019	0.001	0.020
element-setops	0.151	0.007	0.159
filter-ranges	0.848	0.027	0.879
flank-ranges	0.135	0.002	0.137
group_by-ranges	0.379	0.004	0.383
io-bam-read	1.451	0.044	1.498
io-bed-read	2.866	0.297	3.167
io-bed-write	0.000	0.001	0.000
io-bigwig-read	0.179	0.021	0.199
io-bigwig-write	0	0	0
io-gff-read	0.614	0.014	0.629
io-gff-write	0.000	0.000	0.001
io-wig-read	0.508	0.007	0.516
mutate-ranges	1.110	0.026	1.138
n	0.370	0.001	0.372
n_distinct	0.052	0.000	0.053
overlap-joins	0.334	0.005	0.339
ranges-anchor	0.166	0.001	0.168
ranges-arrange	0.076	0.001	0.077
ranges-bind	0.325	0.002	0.327
ranges-chop	0.468	0.024	0.492
ranges-construct	0.248	0.002	0.252
ranges-count-overlaps	0.090	0.000	0.092
ranges-disjoin	1.105	0.006	1.113
ranges-expand	0.773	0.006	0.779
ranges-filter-overlaps	0.116	0.001	0.117
ranges-follow	0.378	0.011	0.390
ranges-info	0.058	0.000	0.059
ranges-interweave	0.222	0.001	0.224
ranges-names	0.194	0.001	0.195
ranges-nearest	0.526	0.031	0.556
ranges-overlaps-self	0.210	0.008	0.217
ranges-overlaps	0.241	0.002	0.243
ranges-pairs	0.434	0.002	0.436
ranges-precede	0.236	0.001	0.238
ranges-reduce	0.996	0.002	0.998
ranges-select	0.107	0.002	0.109
ranges-setops	1.245	0.004	1.249
ranges-summarise	0.212	0.001	0.214
ranges-tile	0.106	0.001	0.108
shift-ranges	0.210	0.001	0.212
slice-ranges	0.837	0.003	0.840
stretch	0.238	0.002	0.240

CHECK report for plyranges on merida1

Summary

Command output

Installation output

Tests output

Example timings