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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:wiggleplotr.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings wiggleplotr_1.35.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/wiggleplotr.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-28 09:29:14 UTC
* checking for file ‘wiggleplotr/DESCRIPTION’ ... OK
* this is package ‘wiggleplotr’ version ‘1.35.2’
* 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 ‘wiggleplotr’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
coverageParquetToGRangesList: no visible binding for global variable
  ‘seqnames’
coverageParquetToGRangesList: no visible binding for global variable
  ‘end’
coverageParquetToGRangesList: no visible binding for global variable
  ‘start’
coverageParquetToGRangesList: no visible binding for global variable
  ‘sample_id’
extractCoverageData: no visible global function definition for ‘is’
extractCoverageData: no visible binding for global variable ‘sample_id’
extractCoverageData: no visible binding for global variable ‘coverage’
extractCoverageData: no visible binding for global variable
  ‘scaling_factor’
makeCoveragePlot: no visible binding for global variable ‘bins’
makeCoveragePlot: no visible binding for global variable ‘coverage’
makeCoveragePlot: no visible binding for global variable ‘sample_id’
makeCoveragePlot: no visible binding for global variable ‘colour_group’
makeManhattanPlot: no visible binding for global variable ‘pos’
makeManhattanPlot: no visible binding for global variable ‘p_nominal’
makeManhattanPlot: no visible binding for global variable ‘R2’
meanCoverage: no visible binding for global variable ‘track_id’
meanCoverage: no visible binding for global variable ‘colour_group’
meanCoverage: no visible binding for global variable ‘bins’
meanCoverage: no visible binding for global variable ‘coverage’
plotTranscriptStructure: no visible binding for global variable
  ‘feature_type’
plotTranscriptStructure: no visible binding for global variable ‘start’
plotTranscriptStructure: no visible binding for global variable
  ‘transcript_rank’
plotTranscriptStructure: no visible binding for global variable ‘end’
plotTranscripts: no visible global function definition for ‘is’
Undefined global functions or variables:
  R2 bins colour_group coverage end feature_type is p_nominal pos
  sample_id scaling_factor seqnames start track_id transcript_rank
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "end", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'extractCoverageData.Rd':
extractCoverageData
  Code: function(exons, cdss = NULL, transcript_annotations = NULL,
                 track_data, rescale_introns = TRUE, new_intron_length
                 = 50, flanking_length = c(50, 50), plot_fraction =
                 0.1, mean_only = TRUE, region_coords = NULL,
                 coverage_ranges_pq = NULL)
  Docs: function(exons, cdss = NULL, transcript_annotations = NULL,
                 track_data, rescale_introns = TRUE, new_intron_length
                 = 50, flanking_length = c(50, 50), plot_fraction =
                 0.1, mean_only = TRUE, region_coords = NULL)
  Argument names in code not in docs:
    coverage_ranges_pq

Codoc mismatches from Rd file 'plotCoverage.Rd':
plotCoverage
  Code: function(exons, cdss = NULL, transcript_annotations = NULL,
                 track_data, rescale_introns = TRUE, new_intron_length
                 = 50, flanking_length = c(50, 50), plot_fraction =
                 0.1, heights = c(0.75, 0.25), alpha = 1, fill_palette
                 = c("#a1dab4", "#41b6c4", "#225ea8"), mean_only =
                 TRUE, connect_exons = TRUE, transcript_label = TRUE,
                 return_subplots_list = FALSE, region_coords = NULL,
                 coverage_type = "area", coverage_ranges_pq = NULL,
                 show_legend = FALSE)
  Docs: function(exons, cdss = NULL, transcript_annotations = NULL,
                 track_data, rescale_introns = TRUE, new_intron_length
                 = 50, flanking_length = c(50, 50), plot_fraction =
                 0.1, heights = c(0.75, 0.25), alpha = 1, fill_palette
                 = c("#a1dab4", "#41b6c4", "#225ea8"), mean_only =
                 TRUE, connect_exons = TRUE, transcript_label = TRUE,
                 return_subplots_list = FALSE, region_coords = NULL,
                 coverage_type = "area", show_legend = FALSE)
  Argument names in code not in docs:
    coverage_ranges_pq
  Mismatches in argument names:
    Position: 18 Code: coverage_ranges_pq Docs: show_legend

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
plotCoverageFromEnsembldb 9.93   0.67  10.805
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/wiggleplotr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL wiggleplotr
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘wiggleplotr’ ...
** this is package ‘wiggleplotr’ version ‘1.35.2’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (wiggleplotr)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

> library(testthat)
> library(wiggleplotr)
> 
> test_check("wiggleplotr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  7.230   0.670   9.578