Multiple platform build/check report for BioC 3.7 - CHECK report for plyranges on tokay2

Package: plyranges

Version: 1.0.3

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings plyranges_1.0.3.tar.gz

StartedAt: 2018-10-17 04:01:17 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:07:04 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 347.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: plyranges.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings plyranges_1.0.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/plyranges.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plyranges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plyranges' version '1.0.3'
* 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 whether package 'plyranges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/as_ranges.Rd:32: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/as_ranges.Rd:32: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/compute_coverage.Rd:37: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/compute_coverage.Rd:37: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/flank-ranges.Rd:59: file link 'flank' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-bed-read.Rd:75: file link 'BEDFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-bed-write.Rd:57: file link 'BEDFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-gff-read.Rd:57: file link 'GFFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-gff-write.Rd:44: file link 'GFFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-wig-read.Rd:36: file link 'WIGFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-wig-write.Rd:23: file link 'WIGFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/overscope_ranges.Rd:24: file link 'new_data_mask' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-construct.Rd:50: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-filter-overlaps.Rd:60: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-overlaps.Rd:122: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-overlaps.Rd:122: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-summarise.Rd:15: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:52: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:52: file link 'tile' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:54: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:54: file link 'slidingWindows' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:47: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'enquo' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'quos' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'UQS' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'UQ' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/shift-ranges.Rd:49: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/plyranges.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/plyranges.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/plyranges_1.0.3.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL plyranges_1.0.3.zip && rm plyranges_1.0.3.tar.gz plyranges_1.0.3.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  434k  100  434k    0     0  6837k      0 --:--:-- --:--:-- --:--:-- 7751k

install for i386

* installing *source* package 'plyranges' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'plyranges'
    finding HTML links ... done
    as_ranges                               html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/as_ranges.Rd:32: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/as_ranges.Rd:32: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
    compute_coverage                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/compute_coverage.Rd:37: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/compute_coverage.Rd:37: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
    element-setops                          html  
    filter-ranges                           html  
    flank-ranges                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/flank-ranges.Rd:59: file link 'flank' in package 'GenomicRanges' does not exist and so has been treated as a topic
    group_by-ranges                         html  
    io-bam-read                             html  
    io-bed-read                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-bed-read.Rd:75: file link 'BEDFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    io-bed-write                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-bed-write.Rd:57: file link 'BEDFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    io-bigwig-read                          html  
    io-bigwig-write                         html  
    io-gff-read                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-gff-read.Rd:57: file link 'GFFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    io-gff-write                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-gff-write.Rd:44: file link 'GFFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    io-wig-read                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-wig-read.Rd:36: file link 'WIGFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    io-wig-write                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/io-wig-write.Rd:23: file link 'WIGFile' in package 'rtracklayer' does not exist and so has been treated as a topic
    mutate-ranges                           html  
    n                                       html  
    overlap-joins                           html  
    overscope_ranges                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/overscope_ranges.Rd:24: file link 'new_data_mask' in package 'rlang' does not exist and so has been treated as a topic
    plyranges-package                       html  
    ranges-anchor                           html  
    ranges-arrange                          html  
    ranges-bind                             html  
    ranges-chop                             html  
    ranges-class                            html  
    ranges-construct                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-construct.Rd:50: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    ranges-count-overlaps                   html  
    ranges-deferred                         html  
    ranges-disjoin                          html  
    ranges-filter-overlaps                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-filter-overlaps.Rd:60: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    ranges-follow                           html  
    ranges-info                             html  
    ranges-interweave                       html  
    ranges-nearest                          html  
    ranges-overlaps-self                    html  
    ranges-overlaps                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-overlaps.Rd:122: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-overlaps.Rd:122: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    ranges-pairs                            html  
    ranges-precede                          html  
    ranges-reduce                           html  
    ranges-select                           html  
    ranges-setops                           html  
    ranges-setters                          html  
    ranges-summarise                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-summarise.Rd:15: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    ranges-tile                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:52: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:52: file link 'tile' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:54: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/ranges-tile.Rd:54: file link 'slidingWindows' in package 'GenomicRanges' does not exist and so has been treated as a topic
    ranges-unnest                           html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:45: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:47: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'enquo' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'quos' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'UQS' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/reexports.Rd:49: file link 'UQ' in package 'rlang' does not exist and so has been treated as a topic
    shift-ranges                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcLfsda/R.INSTALL102c267f2617/plyranges/man/shift-ranges.Rd:49: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
    stretch                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'plyranges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plyranges' as plyranges_1.0.3.zip
* DONE (plyranges)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, lengths, 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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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: 285 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.15    2.12   35.34


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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, lengths, 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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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: 285 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  37.70    1.12   38.82

name	user	system	elapsed
as_ranges	0.07	0.00	0.07
compute_coverage	0.03	0.00	0.03
element-setops	0.09	0.02	0.11
filter-ranges	0.38	0.11	0.48
flank-ranges	0.06	0.00	0.06
group_by-ranges	0.22	0.00	0.22
io-bam-read	0.81	0.01	0.83
io-bed-read	2.92	0.94	3.86
io-bed-write	0	0	0
io-bigwig-read	0	0	0
io-bigwig-write	0	0	0
io-gff-read	0.35	0.00	0.34
io-gff-write	0.01	0.00	0.02
io-wig-read	0.39	0.00	0.39
mutate-ranges	0.66	0.25	0.91
n	0.29	0.00	0.29
overlap-joins	0.05	0.00	0.05
ranges-anchor	0.08	0.00	0.08
ranges-arrange	0.03	0.00	0.03
ranges-bind	0.17	0.00	0.17
ranges-chop	0.32	0.03	0.34
ranges-construct	0.03	0.00	0.04
ranges-count-overlaps	0.06	0.00	0.06
ranges-disjoin	1.41	0.02	1.42
ranges-filter-overlaps	0.06	0.00	0.06
ranges-follow	0.11	0.00	0.11
ranges-info	0.03	0.00	0.03
ranges-interweave	0.09	0.00	0.10
ranges-nearest	0.39	0.00	0.39
ranges-overlaps-self	0.10	0.00	0.09
ranges-overlaps	0.12	0.00	0.13
ranges-pairs	0.25	0.00	0.25
ranges-precede	0.10	0.00	0.09
ranges-reduce	0.71	0.03	0.75
ranges-select	0.05	0.00	0.04
ranges-setops	0.53	0.00	0.53
ranges-summarise	0.11	0.00	0.11
ranges-tile	0.07	0.00	0.06
ranges-unnest	0.12	0.00	0.13
shift-ranges	0.08	0.00	0.07
stretch	0.12	0.00	0.13

name	user	system	elapsed
as_ranges	0.10	0.00	0.09
compute_coverage	0.03	0.00	0.04
element-setops	0.17	0.00	0.17
filter-ranges	0.83	0.00	0.83
flank-ranges	0.13	0.00	0.13
group_by-ranges	0.53	0.02	0.55
io-bam-read	1.72	0.05	1.76
io-bed-read	2.86	0.81	3.67
io-bed-write	0	0	0
io-bigwig-read	0	0	0
io-bigwig-write	0	0	0
io-gff-read	0.42	0.04	0.47
io-gff-write	0	0	0
io-wig-read	0.45	0.02	0.47
mutate-ranges	0.89	0.00	0.90
n	0.30	0.00	0.29
overlap-joins	0.04	0.00	0.05
ranges-anchor	0.08	0.00	0.08
ranges-arrange	0.05	0.00	0.04
ranges-bind	0.20	0.00	0.21
ranges-chop	0.35	0.02	0.36
ranges-construct	0.03	0.00	0.03
ranges-count-overlaps	0.07	0.00	0.08
ranges-disjoin	1.65	0.00	1.64
ranges-filter-overlaps	0.07	0.00	0.07
ranges-follow	0.11	0.00	0.11
ranges-info	0.03	0.00	0.04
ranges-interweave	0.14	0.00	0.14
ranges-nearest	0.72	0.00	0.71
ranges-overlaps-self	0.11	0.00	0.11
ranges-overlaps	0.14	0.00	0.14
ranges-pairs	0.3	0.0	0.3
ranges-precede	0.25	0.00	0.25
ranges-reduce	0.86	0.00	0.86
ranges-select	0.09	0.00	0.09
ranges-setops	0.64	0.00	0.64
ranges-summarise	0.14	0.00	0.15
ranges-tile	0.11	0.00	0.10
ranges-unnest	0.23	0.00	0.24
shift-ranges	0.14	0.00	0.14
stretch	0.16	0.00	0.16

CHECK report for plyranges on tokay2

Summary

Command output

Installation output

Tests output

Example timings