Package: plyranges

Version: 1.4.4

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_1.4.4.tar.gz

StartedAt: 2019-10-16 05:38:11 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:44:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 373.0 seconds

RetCode: 0

Status:  OK

CheckDir: plyranges.Rcheck

Warnings: 0

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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_1.4.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/plyranges.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.4’
* 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

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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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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:stats':

    filter

> 
> test_check("plyranges")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 310 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 60.851   2.691  63.528 

name	user	system	elapsed
as_ranges	0.103	0.002	0.106
compute_coverage	0.028	0.003	0.030
element-setops	0.214	0.010	0.224
filter-ranges	1.279	0.099	1.378
flank-ranges	0.133	0.002	0.135
group_by-ranges	0.715	0.010	0.726
io-bam-read	0.993	0.090	1.086
io-bed-read	4.180	0.461	4.653
io-bed-write	0.000	0.000	0.001
io-bigwig-read	0.131	0.002	0.135
io-bigwig-write	0.001	0.001	0.001
io-gff-read	0.593	0.019	0.614
io-gff-write	0	0	0
io-wig-read	0.513	0.010	0.524
mutate-ranges	1.174	0.014	1.189
n	0.627	0.002	0.630
n_distinct	0.058	0.001	0.059
overlap-joins	0.144	0.002	0.145
ranges-anchor	0.155	0.003	0.158
ranges-arrange	0.110	0.002	0.112
ranges-bind	0.280	0.003	0.287
ranges-chop	1.424	0.031	1.457
ranges-construct	0.050	0.003	0.052
ranges-count-overlaps	0.131	0.002	0.133
ranges-disjoin	1.063	0.122	1.189
ranges-expand	1.031	0.123	1.155
ranges-filter-overlaps	0.108	0.001	0.109
ranges-follow	0.164	0.002	0.167
ranges-info	0.041	0.001	0.043
ranges-interweave	0.197	0.002	0.200
ranges-nearest	0.600	0.004	0.606
ranges-overlaps-self	0.163	0.004	0.166
ranges-overlaps	0.238	0.005	0.243
ranges-pairs	0.453	0.006	0.460
ranges-precede	0.159	0.003	0.162
ranges-reduce	0.890	0.008	0.898
ranges-select	0.073	0.003	0.077
ranges-setops	1.186	0.005	1.191
ranges-summarise	0.279	0.001	0.281
ranges-tile	0.098	0.002	0.100
shift-ranges	0.184	0.003	0.186
stretch	0.338	0.003	0.342