Package: plyranges

Version: 1.3.4

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_1.3.4.tar.gz

StartedAt: 2019-04-09 02:55:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:00:03 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 272.8 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_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/plyranges.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.4’
* 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’ ...
** 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
* DONE (plyranges)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, colMeans, colSums, 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, rowMeans, rowSums,
    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: 313 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 43.545   1.190  44.963 

name	user	system	elapsed
as_ranges	0.063	0.001	0.066
compute_coverage	0.021	0.001	0.022
element-setops	0.146	0.003	0.150
filter-ranges	1.384	0.044	1.444
flank-ranges	0.092	0.005	0.099
group_by-ranges	0.521	0.077	0.599
io-bam-read	0.782	0.075	0.863
io-bed-read	3.331	0.217	3.568
io-bed-write	0.001	0.001	0.000
io-bigwig-read	0.073	0.001	0.074
io-bigwig-write	0	0	0
io-gff-read	0.427	0.022	0.451
io-gff-write	0	0	0
io-wig-read	0.444	0.036	0.481
mutate-ranges	0.917	0.017	0.940
n	0.454	0.009	0.465
n_distinct	0.042	0.004	0.044
overlap-joins	0.055	0.000	0.055
ranges-anchor	0.113	0.001	0.116
ranges-arrange	0.069	0.000	0.070
ranges-bind	0.229	0.002	0.235
ranges-chop	0.514	0.015	0.530
ranges-construct	0.041	0.001	0.041
ranges-count-overlaps	0.102	0.001	0.103
ranges-disjoin	0.622	0.005	0.630
ranges-filter-overlaps	0.083	0.001	0.083
ranges-follow	0.141	0.002	0.143
ranges-info	0.040	0.001	0.040
ranges-interweave	0.151	0.001	0.151
ranges-nearest	0.465	0.001	0.469
ranges-overlaps-self	0.123	0.001	0.127
ranges-overlaps	0.171	0.002	0.173
ranges-pairs	0.279	0.002	0.282
ranges-precede	0.122	0.002	0.124
ranges-reduce	0.821	0.003	0.829
ranges-select	0.084	0.002	0.086
ranges-setops	0.914	0.003	0.919
ranges-summarise	0.187	0.000	0.187
ranges-tile	0.059	0.000	0.060
ranges-unnest	0.207	0.001	0.211
shift-ranges	0.121	0.001	0.124
stretch	0.168	0.001	0.169