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CHECK report for plyranges on tokay2

This page was generated on 2020-10-17 11:57:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE plyranges PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1327/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.8.0
Stuart Lee
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/plyranges
Branch: RELEASE_3_11
Last Commit: da4f008
Last Changed Date: 2020-04-27 15:15:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plyranges
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings plyranges_1.8.0.tar.gz
StartedAt: 2020-10-17 06:58:00 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:05:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 462.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: plyranges.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings plyranges_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/plyranges.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.8.0'
* 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/as_ranges.Rd:33: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/as_ranges.Rd:33: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-bam-read.Rd:79: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-bed-read.Rd:82: file link 'BEDFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-gff-read.Rd:53: file link 'GFFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-construct.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-overlaps.Rd:131: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-overlaps.Rd:131: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/shift-ranges.Rd:51: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'groups' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:38: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:40: file link '!!' in package 'rlang' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:40: file link '!!!' in package 'rlang' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/meat/plyranges.Rcheck/00check.log'
for details.



Installation output

plyranges.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/plyranges_1.8.0.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL plyranges_1.8.0.zip && rm plyranges_1.8.0.tar.gz plyranges_1.8.0.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  580k  100  580k    0     0  9049k      0 --:--:-- --:--:-- --:--:--  9.9M

install for i386

* installing *source* package 'plyranges' ...
** using staged installation
** 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/as_ranges.Rd:33: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/as_ranges.Rd:33: 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-bam-read.Rd:79: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
    io-bed-read                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-bed-read.Rd:82: 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/io-gff-read.Rd:53: 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-construct.Rd:56: 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-expand                           html  
    ranges-filter-overlaps                  html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-names                            html  
    ranges-nearest                          html  
    ranges-overlaps-self                    html  
    ranges-overlaps                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-overlaps.Rd:131: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-overlaps.Rd:131: 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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/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-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/ranges-tile.Rd:54: file link 'slidingWindows' in package 'GenomicRanges' does not exist and so has been treated as a topic
    shift-ranges                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/shift-ranges.Rd:51: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
    slice-ranges                            html  
    stretch                                 html  
    tidyverse-reexports                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'groups' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:36: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:38: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:40: file link '!!' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQrZpay/R.INSTALL225c1b3b571d/plyranges/man/tidyverse-reexports.Rd:40: 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

* installing *source* package 'plyranges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plyranges' as plyranges_1.8.0.zip
* DONE (plyranges)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked

Tests output

plyranges.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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


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:IRanges':

    slice

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

    filter

> 
> test_check("plyranges")
== testthat results  ===========================================================
[ OK: 347 | SKIPPED: 1 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.39    2.53   51.54 

plyranges.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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


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:IRanges':

    slice

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

    filter

> 
> test_check("plyranges")
== testthat results  ===========================================================
[ OK: 347 | SKIPPED: 1 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  54.81    1.28   59.23 

Example timings

plyranges.Rcheck/examples_i386/plyranges-Ex.timings

nameusersystemelapsed
as_ranges0.130.000.12
compute_coverage0.030.000.03
element-setops0.110.000.11
filter-ranges0.810.060.88
flank-ranges0.950.000.95
group_by-ranges0.460.000.46
io-bam-read0.990.151.13
io-bed-read3.591.374.98
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.650.050.70
io-gff-write0.000.010.01
io-wig-read0.600.080.68
mutate-ranges0.710.030.75
n0.250.190.43
n_distinct0.000.050.05
overlap-joins0.290.000.28
ranges-anchor0.110.000.11
ranges-arrange0.040.000.05
ranges-bind0.250.000.25
ranges-chop0.420.000.42
ranges-construct0.240.000.23
ranges-count-overlaps0.090.000.09
ranges-disjoin0.910.000.91
ranges-expand0.550.000.55
ranges-filter-overlaps0.040.020.06
ranges-follow0.190.000.19
ranges-info0.050.000.04
ranges-interweave0.150.000.16
ranges-names0.110.000.11
ranges-nearest0.420.000.42
ranges-overlaps-self0.130.000.13
ranges-overlaps0.190.000.18
ranges-pairs0.320.000.33
ranges-precede0.150.000.14
ranges-reduce1.620.001.63
ranges-select0.090.000.09
ranges-setops0.910.000.91
ranges-summarise0.140.000.14
ranges-tile0.090.000.09
shift-ranges0.160.000.16
slice-ranges0.550.000.55
stretch0.20.00.2

plyranges.Rcheck/examples_x64/plyranges-Ex.timings

nameusersystemelapsed
as_ranges0.200.020.22
compute_coverage0.030.000.03
element-setops0.180.020.20
filter-ranges0.680.000.67
flank-ranges0.110.000.11
group_by-ranges0.310.010.34
io-bam-read1.500.081.58
io-bed-read3.010.643.66
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.740.000.73
io-gff-write000
io-wig-read0.420.020.44
mutate-ranges0.910.010.92
n0.290.000.30
n_distinct0.050.000.05
overlap-joins0.270.000.26
ranges-anchor0.20.00.2
ranges-arrange0.090.000.10
ranges-bind0.410.000.40
ranges-chop0.360.020.38
ranges-construct0.230.000.23
ranges-count-overlaps0.10.00.1
ranges-disjoin0.840.000.84
ranges-expand0.640.000.64
ranges-filter-overlaps0.060.010.08
ranges-follow0.190.000.19
ranges-info0.060.000.06
ranges-interweave0.190.000.19
ranges-names0.220.000.22
ranges-nearest0.550.000.54
ranges-overlaps-self0.220.000.22
ranges-overlaps0.290.000.30
ranges-pairs0.630.000.62
ranges-precede0.260.000.27
ranges-reduce1.240.001.23
ranges-select0.090.000.10
ranges-setops1.140.001.14
ranges-summarise0.160.000.15
ranges-tile0.090.000.10
shift-ranges0.240.000.23
slice-ranges0.950.000.95
stretch0.410.000.41