Multiple platform build/check report for BioC 3.14 - CHECK results for plyranges on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: plyranges

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings plyranges_1.14.0.tar.gz

StartedAt: 2022-04-13 00:38:04 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:45:07 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 423.4 seconds

RetCode: 0

Status: OK

CheckDir: plyranges.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings plyranges_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/plyranges.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.14.0'
* 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 ... 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
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/plyranges_1.14.0.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL plyranges_1.14.0.zip && rm plyranges_1.14.0.tar.gz plyranges_1.14.0.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  674k  100  674k    0     0  1281k      0 --:--:-- --:--:-- --:--:-- 1282k

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
    add-nearest-distance                    html  
    as_ranges                               html  
    finding level-2 HTML links ... done

    compute_coverage                        html  
    element-setops                          html  
    filter-ranges                           html  
    group_by-ranges                         html  
    io-bam-read                             html  
    io-bed-read                             html  
    io-bed-write                            html  
    io-bigwig-read                          html  
    io-bigwig-write                         html  
    io-gff-read                             html  
    io-gff-write                            html  
    io-wig-read                             html  
    io-wig-write                            html  
    mutate-ranges                           html  
    n                                       html  
    n_distinct                              html  
    overlap-joins                           html  
    overscope_ranges                        html  
    plyranges-package                       html  
    ranges-anchor                           html  
    ranges-arrange                          html  
    ranges-bind                             html  
    ranges-chop                             html  
    ranges-class                            html  
    ranges-construct                        html  
    ranges-count-overlaps                   html  
    ranges-deferred                         html  
    ranges-disjoin                          html  
    ranges-expand                           html  
    ranges-filter-overlaps                  html  
    ranges-flank                            html  
    ranges-follow                           html  
    ranges-info                             html  
    ranges-interweave                       html  
    ranges-names                            html  
    ranges-nearest                          html  
    ranges-overlaps-self                    html  
    ranges-overlaps                         html  
    ranges-pairs                            html  
    ranges-precede                          html  
    ranges-reduce                           html  
    ranges-select                           html  
    ranges-setops                           html  
    ranges-setters                          html  
    ranges-shift                            html  
    ranges-summarise                        html  
    ranges-tile                             html  
    slice-ranges                            html  
    stretch                                 html  
    tidyverse-reexports                     html  
*** 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_1.14.0.zip
* DONE (plyranges)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


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")
[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]

== Skipped tests ===============================================================
* On Windows (2)

[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
  51.70    2.90   54.59


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


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")
[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]

== Skipped tests ===============================================================
* On Windows (2)

[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
  59.42    1.70   61.28

name	user	system	elapsed
add-nearest-distance	0.46	0.05	0.50
as_ranges	0.79	0.01	0.81
compute_coverage	0.04	0.00	0.03
element-setops	0.09	0.02	0.11
filter-ranges	0.58	0.14	0.72
group_by-ranges	0.28	0.25	0.53
io-bam-read	0.76	0.19	0.95
io-bed-read	3.55	1.11	4.65
io-bed-write	0	0	0
io-bigwig-read	0	0	0
io-bigwig-write	0	0	0
io-gff-read	0.39	0.01	0.44
io-gff-write	0	0	0
io-wig-read	0.37	0.02	0.39
mutate-ranges	0.80	0.09	0.89
n	0.28	0.00	0.28
n_distinct	0.03	0.00	0.04
overlap-joins	0.24	0.00	0.23
ranges-anchor	0.12	0.00	0.12
ranges-arrange	0.05	0.00	0.05
ranges-bind	0.22	0.00	0.22
ranges-chop	0.36	0.05	0.41
ranges-construct	0.14	0.00	0.14
ranges-count-overlaps	0.07	0.00	0.08
ranges-disjoin	0.71	0.02	0.71
ranges-expand	0.58	0.03	0.61
ranges-filter-overlaps	0.07	0.00	0.08
ranges-flank	0.16	0.00	0.16
ranges-follow	0.22	0.00	0.22
ranges-info	0.06	0.00	0.06
ranges-interweave	0.19	0.00	0.19
ranges-names	0.12	0.00	0.12
ranges-nearest	0.52	0.00	0.52
ranges-overlaps-self	0.2	0.0	0.2
ranges-overlaps	0.27	0.00	0.27
ranges-pairs	0.45	0.00	0.45
ranges-precede	0.22	0.00	0.22
ranges-reduce	0.83	0.00	0.83
ranges-select	0.14	0.00	0.14
ranges-setops	1.01	0.00	1.01
ranges-shift	0.40	0.00	0.39
ranges-summarise	0.21	0.00	0.22
ranges-tile	0.16	0.00	0.16
slice-ranges	0.69	0.00	0.69
stretch	0.28	0.00	0.28

name	user	system	elapsed
add-nearest-distance	0.5	0.0	0.5
as_ranges	0.12	0.00	0.13
compute_coverage	0.03	0.00	0.03
element-setops	0.13	0.00	0.13
filter-ranges	0.62	0.02	0.64
group_by-ranges	0.38	0.01	0.39
io-bam-read	1.56	0.03	1.59
io-bed-read	2.89	0.69	3.58
io-bed-write	0	0	0
io-bigwig-read	0	0	0
io-bigwig-write	0	0	0
io-gff-read	0.67	0.00	0.72
io-gff-write	0	0	0
io-wig-read	0.42	0.02	0.43
mutate-ranges	1	0	1
n	0.40	0.00	0.41
n_distinct	0.03	0.00	0.03
overlap-joins	0.29	0.00	0.28
ranges-anchor	0.12	0.00	0.12
ranges-arrange	0.06	0.00	0.07
ranges-bind	0.30	0.00	0.29
ranges-chop	0.47	0.00	0.47
ranges-construct	0.17	0.00	0.17
ranges-count-overlaps	0.08	0.00	0.08
ranges-disjoin	0.89	0.00	0.89
ranges-expand	1.5	0.0	1.5
ranges-filter-overlaps	0.09	0.00	0.10
ranges-flank	0.14	0.00	0.14
ranges-follow	0.27	0.00	0.26
ranges-info	0.06	0.00	0.07
ranges-interweave	0.22	0.01	0.23
ranges-names	0.16	0.00	0.16
ranges-nearest	0.56	0.00	0.56
ranges-overlaps-self	0.22	0.00	0.22
ranges-overlaps	0.31	0.00	0.31
ranges-pairs	0.52	0.00	0.52
ranges-precede	0.25	0.00	0.25
ranges-reduce	0.97	0.00	0.97
ranges-select	0.25	0.00	0.25
ranges-setops	1.24	0.02	1.25
ranges-shift	0.21	0.01	0.23
ranges-summarise	0.18	0.00	0.18
ranges-tile	0.11	0.02	0.12
slice-ranges	0.64	0.00	0.64
stretch	0.26	0.00	0.27

CHECK results for plyranges on tokay2

Summary

Command output

Installation output

Tests output

Example timings