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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings plyinteractions_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/plyinteractions.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘plyinteractions/DESCRIPTION’ ... OK
* this is package ‘plyinteractions’ version ‘1.9.0’
* 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘plyranges::mutate’
* 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’
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 name score
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ginteractions-construct.Rd: DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘plyinteractions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate
> ### Title: Annotate both anchors of a GInteractions
> ### Aliases: annotate annotate_directed ginteractions-annotate
> ###   annotate,GInteractions,GRanges,character-method
> ###   annotate_directed,GInteractions,GRanges,character-method
> 
> ### ** Examples
> 
> ####################################################################
> # 1. Basic example
> ####################################################################
> 
> gi <- read.table(text = "  
+     chr1 11 20 - chr1 21 30 + 
+     chr1 21 30 + chr2 51 60 +",  
+     col.names = c(
+         "seqnames1", "start1", "end1", "strand1", 
+         "seqnames2", "start2", "end2", "strand2"
+     )
+ ) |> as_ginteractions() 
> 
> gr <- GenomicRanges::GRanges(c("chr1:20-30:+", "chr2:55-65:+")) |>
+     plyranges::mutate(id = 1:2)
Error: 'mutate' is not an exported object from 'namespace:plyranges'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_setup(".", env)
    7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(...)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. └─base::.handleSimpleError(...) at ./setup.R:16:1
   15.   └─testthat (local) h(simpleError(msg, call))
   16.     └─cli::cli_abort(...)
   17.       └─rlang::abort(...)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/plyinteractions.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL plyinteractions
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘plyinteractions’ ...
** this is package ‘plyinteractions’ version ‘1.9.0’
** 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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)

Attaching package: 'plyinteractions'

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

    filter

> 
> 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")
Error in `source_dir()`:
! Failed to evaluate './setup.R'.
Caused by error:
! 'mutate' is not an exported object from 'namespace:plyranges'
Backtrace:
     ▆
  1. ├─testthat::test_check("plyinteractions")
  2. │ └─testthat::test_dir(...)
  3. │   └─testthat:::test_files(...)
  4. │     └─testthat:::test_files_serial(...)
  5. │       └─testthat:::test_files_setup_state(...)
  6. │         └─testthat::source_test_setup(".", env)
  7. │           └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
  8. │             └─base::lapply(...)
  9. │               └─testthat (local) FUN(X[[i]], ...)
 10. │                 └─testthat::source_file(...)
 11. │                   ├─base::withCallingHandlers(...)
 12. │                   └─base::eval(exprs, env)
 13. │                     └─base::eval(exprs, env)
 14. └─base::.handleSimpleError(...) at ./setup.R:16:1
 15.   └─testthat (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted