Multiple platform build/check report for BioC 3.9 - CHECK report for plyranges on tokay2

Package: plyranges

Version: 1.3.4

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plyranges_1.3.4.tar.gz

StartedAt: 2019-04-09 04:58:43 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:05:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 382.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: plyranges.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plyranges_1.3.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/plyranges.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.3.4'
* 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 whether package 'plyranges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/shift-ranges.Rd:49: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:31: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:33: file link '!!!' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:33: file link '!!' in package 'rlang' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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-3.9-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/3.9/bioc/src/contrib/plyranges_1.3.4.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.3.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL plyranges_1.3.4.zip && rm plyranges_1.3.4.tar.gz plyranges_1.3.4.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 1393k    1 16384    0     0   258k      0  0:00:05 --:--:--  0:00:05  285k
100 1393k  100 1393k    0     0  18.4M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'plyranges/inst/NEWS' to 'plyranges/NEWS.md'
* 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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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  
    n_distinct                              html  
    overlap-joins                           html  
    overscope_ranges                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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  
    shift-ranges                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/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  
    tidyverse-reexports                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:29: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:31: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:33: file link '!!!' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6J1HBI/R.INSTALL21301ceb4514/plyranges/man/tidyverse-reexports.Rd:33: file link '!!' in package 'rlang' does not exist and so has been treated as a topic
*** 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

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'plyranges/inst/NEWS' to 'plyranges/NEWS.md'
* installing *source* package 'plyranges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plyranges' as plyranges_1.3.4.zip
* DONE (plyranges)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, 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: 308 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  39.32    2.09   41.42


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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, 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: 308 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  48.32    1.28   49.79

name	user	system	elapsed
as_ranges	0.04	0.00	0.04
compute_coverage	0.02	0.00	0.02
element-setops	0.14	0.03	0.17
filter-ranges	0.99	0.06	1.04
flank-ranges	0.11	0.00	0.11
group_by-ranges	0.45	0.00	0.46
io-bam-read	1.52	0.05	1.56
io-bed-read	3.00	1.28	4.28
io-bed-write	0	0	0
io-bigwig-read	0.00	0.02	0.02
io-bigwig-write	0	0	0
io-gff-read	0.53	0.03	0.57
io-gff-write	0	0	0
io-wig-read	0.55	0.00	0.55
mutate-ranges	2.06	0.09	2.15
n	0.46	0.00	0.46
n_distinct	0.04	0.00	0.04
overlap-joins	0.10	0.02	0.11
ranges-anchor	0.14	0.03	0.17
ranges-arrange	0.09	0.01	0.11
ranges-bind	0.24	0.02	0.25
ranges-chop	0.50	0.11	0.61
ranges-construct	0.03	0.00	0.04
ranges-count-overlaps	0.09	0.00	0.09
ranges-disjoin	0.69	0.00	0.69
ranges-filter-overlaps	0.08	0.00	0.07
ranges-follow	0.14	0.00	0.15
ranges-info	0.03	0.00	0.03
ranges-interweave	0.17	0.00	0.17
ranges-nearest	0.35	0.00	0.34
ranges-overlaps-self	0.07	0.00	0.08
ranges-overlaps	0.10	0.00	0.09
ranges-pairs	0.18	0.00	0.19
ranges-precede	0.07	0.00	0.06
ranges-reduce	0.43	0.00	0.44
ranges-select	0.05	0.00	0.04
ranges-setops	0.53	0.02	0.55
ranges-summarise	0.13	0.00	0.13
ranges-tile	0.04	0.00	0.04
ranges-unnest	0.13	0.00	0.13
shift-ranges	0.08	0.00	0.08
stretch	0.14	0.00	0.14

name	user	system	elapsed
as_ranges	0.06	0.00	0.06
compute_coverage	0.02	0.00	0.02
element-setops	0.13	0.00	0.13
filter-ranges	0.91	0.00	0.90
flank-ranges	0.12	0.00	0.13
group_by-ranges	1.13	0.00	1.12
io-bam-read	0.78	0.09	0.90
io-bed-read	2.89	0.72	3.61
io-bed-write	0	0	0
io-bigwig-read	0	0	0
io-bigwig-write	0	0	0
io-gff-read	0.44	0.02	0.45
io-gff-write	0	0	0
io-wig-read	0.39	0.01	0.41
mutate-ranges	0.72	0.04	0.75
n	0.43	0.00	0.43
n_distinct	0.02	0.00	0.02
overlap-joins	0.08	0.00	0.08
ranges-anchor	0.09	0.00	0.09
ranges-arrange	0.05	0.00	0.05
ranges-bind	0.17	0.00	0.17
ranges-chop	0.42	0.03	0.45
ranges-construct	0.03	0.00	0.03
ranges-count-overlaps	0.08	0.00	0.08
ranges-disjoin	0.78	0.00	0.78
ranges-filter-overlaps	0.07	0.00	0.07
ranges-follow	0.10	0.00	0.11
ranges-info	0.03	0.00	0.03
ranges-interweave	0.24	0.00	0.24
ranges-nearest	0.32	0.00	0.33
ranges-overlaps-self	0.10	0.00	0.09
ranges-overlaps	0.12	0.00	0.12
ranges-pairs	0.27	0.00	0.27
ranges-precede	0.10	0.00	0.09
ranges-reduce	0.72	0.00	0.72
ranges-select	0.06	0.00	0.06
ranges-setops	0.72	0.00	0.72
ranges-summarise	0.15	0.00	0.16
ranges-tile	0.05	0.00	0.04
ranges-unnest	0.14	0.00	0.14
shift-ranges	0.08	0.00	0.08
stretch	0.18	0.00	0.18

CHECK report for plyranges on tokay2

Summary

Command output

Installation output

Tests output

Example timings