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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1541/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.25.0  (landing page)
Michael Love
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/plyranges
git_branch: devel
git_last_commit: 0dc7403
git_last_commit_date: 2024-04-30 11:05:19 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for plyranges on palomino6

To the developers/maintainers of the plyranges package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: plyranges
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings plyranges_1.25.0.tar.gz
StartedAt: 2024-07-16 02:48:54 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:53:13 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 258.1 seconds
RetCode: 0
Status:   OK  
CheckDir: plyranges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings plyranges_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/plyranges.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'plyranges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plyranges' version '1.25.0'
* 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 code 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 ... NOTE
checkRd: (-1) group_by-ranges.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) group_by-ranges.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ranges-anchor.Rd:63-64: Lost braces in \itemize; meant \describe ?
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/plyranges.Rcheck/00check.log'
for details.


Installation output

plyranges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL plyranges
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'plyranges' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** 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)

Tests output

plyranges.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, aperm, 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, 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 object is masked from 'package:utils':

    findMatches

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 8 | SKIP 2 | PASS 388 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Windows (2): 'test-io-bed.R:112:3', 'test-io-bw.R:15:3'

[ FAIL 0 | WARN 8 | SKIP 2 | PASS 388 ]
> 
> proc.time()
   user  system elapsed 
  39.64    6.25   46.23 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
add-nearest-distance0.290.040.31
as_ranges0.070.010.09
compute_coverage0.020.000.02
element-setops0.090.000.09
filter-ranges0.470.030.50
group_by-ranges0.300.020.32
io-bam-read0.520.040.55
io-bed-read2.901.264.20
io-bed-write000
io-bigwig-read000
io-bigwig-write000
io-gff-read0.330.010.34
io-gff-write000
io-wig-read0.340.020.38
mutate-ranges0.580.010.59
n1.420.021.51
n_distinct0.030.000.03
overlap-joins0.140.000.14
ranges-anchor0.10.00.1
ranges-arrange0.030.000.03
ranges-bind0.140.000.16
ranges-chop0.250.010.26
ranges-construct0.060.020.08
ranges-count-overlaps0.050.000.05
ranges-disjoin0.580.000.57
ranges-expand0.340.020.36
ranges-filter-overlaps0.090.000.10
ranges-flank0.100.000.09
ranges-follow0.140.000.14
ranges-info0.040.000.05
ranges-interweave0.110.000.11
ranges-names0.080.000.09
ranges-nearest0.330.000.33
ranges-overlaps-self0.110.000.11
ranges-overlaps0.140.000.14
ranges-pairs0.250.000.25
ranges-precede0.140.000.14
ranges-reduce0.750.000.75
ranges-select0.060.000.06
ranges-setops0.60.00.6
ranges-shift0.230.000.23
ranges-summarise0.110.000.11
ranges-tile0.060.010.08
slice-ranges0.550.000.72
stretch0.170.000.17