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This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).

CHECK results for plyranges on tokay2

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raw results

Package 1406/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.12.1  (landing page)
Stuart Lee
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: RELEASE_3_13
git_last_commit: e3563e8
git_last_commit_date: 2021-06-27 21:18:53 -0400 (Sun, 27 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: plyranges
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings plyranges_1.12.1.tar.gz
StartedAt: 2021-10-15 03:30:52 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:37:48 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 416.2 seconds
RetCode: 0
Status:   OK  
CheckDir: plyranges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings plyranges_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/plyranges.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.12.1'
* 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


Installation output

plyranges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/plyranges_1.12.1.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL plyranges_1.12.1.zip && rm plyranges_1.12.1.tar.gz plyranges_1.12.1.zip
###
##############################################################################
##############################################################################


  % 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  653k  100  653k    0     0  1681k      0 --:--:-- --:--:-- --:--:-- 1684k

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_1.12.1.zip
* DONE (plyranges)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked

Tests output

plyranges.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.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")
== Skipped tests ===============================================================
* On Windows (2)

[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
  54.39    3.00   57.39 

plyranges.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.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")
== Skipped tests ===============================================================
* On Windows (2)

[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
  56.90    1.45   58.34 

Example timings

plyranges.Rcheck/examples_i386/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance1.080.031.11
as_ranges0.090.000.10
compute_coverage0.010.000.02
element-setops0.100.000.09
filter-ranges0.570.290.88
group_by-ranges0.380.220.59
io-bam-read0.840.110.95
io-bed-read2.881.073.94
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.450.010.49
io-gff-write000
io-wig-read0.340.050.39
mutate-ranges0.800.000.79
n0.340.080.43
n_distinct0.020.000.01
overlap-joins0.250.000.25
ranges-anchor0.110.000.11
ranges-arrange0.050.000.05
ranges-bind0.230.000.23
ranges-chop0.380.060.44
ranges-construct0.170.000.17
ranges-count-overlaps0.060.000.06
ranges-disjoin0.830.000.83
ranges-expand0.690.000.69
ranges-filter-overlaps0.110.000.11
ranges-flank0.140.000.14
ranges-follow0.260.000.26
ranges-info0.10.00.1
ranges-interweave0.280.000.28
ranges-names0.150.000.16
ranges-nearest0.640.000.64
ranges-overlaps-self0.240.000.23
ranges-overlaps1.090.001.09
ranges-pairs0.470.000.47
ranges-precede0.250.000.25
ranges-reduce0.840.000.85
ranges-select0.140.000.14
ranges-setops101
ranges-shift0.240.000.23
ranges-summarise0.140.000.14
ranges-tile0.120.000.12
slice-ranges0.610.000.61
stretch0.270.000.27

plyranges.Rcheck/examples_x64/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.500.010.52
as_ranges0.080.020.09
compute_coverage0.010.010.03
element-setops0.130.000.12
filter-ranges0.670.000.68
group_by-ranges0.340.080.43
io-bam-read1.780.031.82
io-bed-read2.720.963.67
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.610.010.63
io-gff-write000
io-wig-read1.120.021.14
mutate-ranges0.830.030.86
n0.310.000.32
n_distinct0.030.000.03
overlap-joins0.270.000.26
ranges-anchor0.100.000.11
ranges-arrange0.070.000.07
ranges-bind0.220.000.21
ranges-chop0.360.010.38
ranges-construct0.140.000.14
ranges-count-overlaps0.070.000.08
ranges-disjoin0.790.000.78
ranges-expand0.680.000.69
ranges-filter-overlaps0.100.000.09
ranges-flank0.140.000.14
ranges-follow0.260.000.27
ranges-info0.080.000.07
ranges-interweave0.220.000.22
ranges-names0.140.000.14
ranges-nearest0.660.000.66
ranges-overlaps-self0.230.000.23
ranges-overlaps0.330.000.33
ranges-pairs0.510.000.52
ranges-precede0.240.020.25
ranges-reduce0.910.000.90
ranges-select0.150.000.16
ranges-setops1.110.001.11
ranges-shift0.280.000.28
ranges-summarise0.190.000.19
ranges-tile0.160.000.16
slice-ranges0.70.00.7
stretch0.310.000.31