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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyinteractions_1.9.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/plyinteractions.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyinteractions/DESCRIPTION’ ... OK
* this is package ‘plyinteractions’ version ‘1.9.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘plyinteractions’ 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 whether startup messages can be suppressed ... 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 ... NOTE
count.GInteractions: no visible binding for global variable ‘group’
group_size.GroupedGInteractions: no visible global function definition
  for ‘group_rows’
pair_granges: no visible global function definition for ‘combn’
write_bedpe: no visible binding for global variable ‘name’
write_bedpe: no visible binding for global variable ‘score’
write_pairs: no visible binding for global variable ‘name’
Undefined global functions or variables:
  combn group group_rows name score
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/plyinteractions.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plyinteractions
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘plyinteractions’ ...
** this is package ‘plyinteractions’ version ‘1.9.2’
** using staged installation
** R
** data
** 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 (plyinteractions)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(plyinteractions)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

Loading required package: plyranges
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:matrixStats':

    count

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

    intersect, setdiff, union

The following object is masked from 'package:Seqinfo':

    intersect

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

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

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

    combine, intersect, setdiff, setequal, union

The following object is masked from 'package:generics':

    explain

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'plyranges'

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

    between, n, n_distinct


Attaching package: 'plyinteractions'

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

    flank_downstream, flank_left, flank_right, flank_upstream,
    shift_downstream, shift_left, shift_right, shift_upstream

> 
> gi <- read.table(text = "
+     chr1 11 20 chr1 21 30 + +
+     chr1 11 20 chr1 51 55 + +
+     chr1 11 30 chr1 51 55 - -
+     chr1 11 30 chr2 51 60 - -",
+     col.names = c(
+     "seqnames1", "start1", "end1", 
+     "seqnames2", "start2", "end2", "strand1", "strand2")
+ ) |> 
+     as_ginteractions() |> 
+     mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
> 
> test_check("plyinteractions")
GInteractions object with 4 interactions and 2 metadata columns:
      seqnames1   ranges1 strand1     seqnames2   ranges2 strand2 |      score
          <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle> |  <numeric>
  [1]      chr1     11-20       + ---      chr1     21-30       + | 0.86091538
  [2]      chr1     11-20       + ---      chr1     51-55       + | 0.64031061
  [3]      chr1     11-30       - ---      chr1     51-55       - | 0.00949576
  [4]      chr1     11-30       - ---      chr2     51-60       - | 0.23255051
             type
      <character>
  [1]         cis
  [2]         cis
  [3]         cis
  [4]       trans
  -------
  regions: 6 ranges and 0 metadata columns
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
PinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2
      seqnames1   ranges1 strand1     seqnames2   ranges2 strand2 |      score
          <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle> |  <numeric>
  [1]      chr1     11-20       + ---      chr1     21-30       + | 0.86091538
  [2]      chr1     11-20       + ---      chr1     51-55       + | 0.64031061
  [3]      chr1     11-30       - ---      chr1     51-55       - | 0.00949576
  [4]      chr1     11-30       - ---      chr2     51-60       - | 0.23255051
             type
      <character>
  [1]         cis
  [2]         cis
  [3]         cis
  [4]       trans
  -------
  regions: 6 ranges and 0 metadata columns
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2 | Anchored by: 5p
      seqnames1   ranges1 strand1     seqnames2   ranges2 strand2 |      score
          <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle> |  <numeric>
  [1]      chr1     11-20       + ---      chr1     21-30       + | 0.86091538
  [2]      chr1     11-20       + ---      chr1     51-55       + | 0.64031061
  [3]      chr1     11-30       - ---      chr1     51-55       - | 0.00949576
  [4]      chr1     11-30       - ---      chr2     51-60       - | 0.23255051
             type
      <character>
  [1]         cis
  [2]         cis
  [3]         cis
  [4]       trans
  -------
  regions: 6 ranges and 0 metadata columns
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
GroupedGInteractions object with 4 interactions and 3 metadata columns:
Groups: group [2]
      seqnames1   ranges1 strand1     seqnames2   ranges2 strand2 |      score
          <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle> |  <numeric>
  [1]      chr1     11-20       + ---      chr1     21-30       + | 0.86091538
  [2]      chr1     11-20       + ---      chr1     51-55       + | 0.64031061
  [3]      chr1     11-30       - ---      chr1     51-55       - | 0.00949576
  [4]      chr1     11-30       - ---      chr2     51-60       - | 0.23255051
             type     group
      <character> <numeric>
  [1]         cis         1
  [2]         cis         1
  [3]         cis         2
  [4]       trans         2
  -------
  regions: 6 ranges and 0 metadata columns
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2 | Anchored by: 5p
      seqnames1   ranges1 strand1     seqnames2   ranges2 strand2 |      score
          <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle> |  <numeric>
  [1]      chr1     11-20       + ---      chr1     21-30       + | 0.86091538
  [2]      chr1     11-20       + ---      chr1     51-55       + | 0.64031061
  [3]      chr1     11-30       - ---      chr1     51-55       - | 0.00949576
  [4]      chr1     11-30       - ---      chr2     51-60       - | 0.23255051
             type
      <character>
  [1]         cis
  [2]         cis
  [3]         cis
  [4]       trans
  -------
  regions: 6 ranges and 0 metadata columns
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
Detected `seqlengths:`
chr1 chr2 
  55   60 
Provided `seqlengths:`
chr1 chr2 
 100   30 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 189 ]
> 
> proc.time()
   user  system elapsed 
  8.190   0.315   9.037