##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings plyranges_1.23.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.23.0'
* 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 ... WARNING
group_split:
  function(.tbl, ..., .keep)
group_split.GroupedGenomicRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.GroupedIntegerRanges:
  function(.data, ..., keep)

group_split:
  function(.tbl, ..., .keep)
group_split.Ranges:
  function(.data, ..., keep)

group_keys:
  function(.tbl, ...)
group_keys.Ranges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedGenomicRanges:
  function(.data, ...)

group_keys:
  function(.tbl, ...)
group_keys.GroupedIntegerRanges:
  function(.data, ...)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* 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 ... WARNING
Missing link or links in Rd file '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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
io-bed-read 3.77   1.73    5.56
* 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: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL plyranges
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.19-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)

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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 383 ]

══ 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 383 ]
> 
> proc.time()
   user  system elapsed 
  49.01    3.21   52.59