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This page was generated on 2022-03-18 11:08:19 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

CHECK results for plyranges on riesling1


To the developers/maintainers of the plyranges package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyranges.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1441/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.15.0  (landing page)
Stuart Lee
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: master
git_last_commit: 1263a98
git_last_commit_date: 2021-10-26 12:43:21 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: plyranges
Version: 1.15.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plyranges_1.15.0.tar.gz
StartedAt: 2022-03-17 19:53:30 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:57:20 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 230.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: plyranges.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plyranges_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/plyranges.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.15.0'
* 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
* 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 ... WARNING
Missing link or links in documentation object 'ranges-info.Rd':
  '[GenomeInfoDb:fetchExtendedChromInfoFromUCSC]{GenomeInfoDb::fetchExtendedChromInfoFromUCSC()}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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
  'D:/biocbuild/bbs-3.15-bioc/meat/plyranges.Rcheck/00check.log'
for details.



Installation output

plyranges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL plyranges
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (plyranges)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TFBSTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'VarCon' is missing or broken
 done

Tests output

plyranges.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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

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 
  31.32    2.43   33.73 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.480.000.48
as_ranges0.080.000.08
compute_coverage0.020.000.02
element-setops0.080.000.08
filter-ranges0.390.080.47
group_by-ranges0.290.020.31
io-bam-read1.330.041.37
io-bed-read2.890.923.81
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.330.000.33
io-gff-write000
io-wig-read0.250.000.25
mutate-ranges0.600.000.61
n0.180.000.17
n_distinct0.030.000.03
overlap-joins0.120.000.13
ranges-anchor0.070.020.07
ranges-arrange0.030.000.04
ranges-bind0.110.000.11
ranges-chop0.260.000.26
ranges-construct0.080.000.08
ranges-count-overlaps0.050.000.05
ranges-disjoin0.620.000.63
ranges-expand0.390.000.39
ranges-filter-overlaps0.060.000.06
ranges-flank0.070.000.06
ranges-follow0.110.000.11
ranges-info0.030.000.03
ranges-interweave0.090.000.10
ranges-names0.160.000.15
ranges-nearest0.280.000.28
ranges-overlaps-self0.090.000.10
ranges-overlaps0.110.000.11
ranges-pairs0.270.000.26
ranges-precede0.120.000.13
ranges-reduce0.570.000.56
ranges-select0.040.000.05
ranges-setops0.490.000.48
ranges-shift0.090.000.10
ranges-summarise0.140.000.14
ranges-tile0.060.000.06
slice-ranges0.390.000.39
stretch0.160.000.16