Multiple platform build/check report for BioC 3.9 - CHECK report for plyranges on celaya2

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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) (2019-03-18 r76245)
* 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

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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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 
 55.379   2.442  57.813

Example timings

name	user	system	elapsed
as_ranges	0.066	0.002	0.068
compute_coverage	0.022	0.002	0.024
element-setops	0.130	0.004	0.134
filter-ranges	1.841	0.090	1.933
flank-ranges	0.092	0.007	0.099
group_by-ranges	0.825	0.150	0.975
io-bam-read	0.891	0.122	1.017
io-bed-read	4.311	0.471	4.797
io-bed-write	0.000	0.001	0.001
io-bigwig-read	0.121	0.002	0.124
io-bigwig-write	0.000	0.001	0.000
io-gff-read	0.645	0.049	0.695
io-gff-write	0.000	0.001	0.001
io-wig-read	0.570	0.070	0.641
mutate-ranges	1.112	0.058	1.170
n	0.520	0.004	0.524
n_distinct	0.035	0.000	0.035
overlap-joins	0.104	0.012	0.117
ranges-anchor	0.122	0.007	0.129
ranges-arrange	0.060	0.001	0.060
ranges-bind	0.183	0.002	0.185
ranges-chop	0.416	0.023	0.438
ranges-construct	0.028	0.001	0.031
ranges-count-overlaps	0.109	0.001	0.111
ranges-disjoin	0.791	0.013	0.804
ranges-filter-overlaps	0.089	0.002	0.090
ranges-follow	0.176	0.003	0.179
ranges-info	0.045	0.001	0.046
ranges-interweave	0.219	0.002	0.221
ranges-nearest	0.452	0.004	0.455
ranges-overlaps-self	0.174	0.003	0.176
ranges-overlaps	0.207	0.003	0.210
ranges-pairs	0.360	0.003	0.362
ranges-precede	0.190	0.003	0.193
ranges-reduce	0.743	0.005	0.749
ranges-select	0.095	0.003	0.099
ranges-setops	0.975	0.003	0.978
ranges-summarise	0.310	0.001	0.311
ranges-tile	0.094	0.002	0.096
ranges-unnest	0.259	0.002	0.260
shift-ranges	0.192	0.002	0.195
stretch	0.310	0.002	0.312

CHECK report for plyranges on celaya2

Summary

Command output

Installation output

Tests output

Example timings