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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:tadar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings tadar_1.8.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/tadar.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘tadar/DESCRIPTION’ ... OK
* this is package ‘tadar’ version ‘1.8.0’
* 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 ‘tadar’ 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotChrDar-methods       13.695  0.664  14.362
flipRanges-methods        6.773  0.311   7.084
modP-methods              6.554  0.003   6.558
assignFeatureDar-methods  6.122  0.333   6.457
* 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: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL tadar
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘tadar’ ...
** this is package ‘tadar’ version ‘1.8.0’
** using staged installation
** R
** data
** 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 (tadar)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(tadar)
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: ggplot2
> 
> test_check("tadar")
<ggplot2::ggplot>
 @ data       :'data.frame':	2500 obs. of  3 variables:
 .. $ Chromosome : Factor w/ 25 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
 .. $ dar        : num  0.7969 0.205 0.4685 0.7778 0.0317 ...
 .. $ line_colour: Factor w/ 25 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
 @ layers     :List of 1
 .. $ stat_ecdf:Classes 'LayerInstance', 'Layer', 'ggproto', 'gg' <ggproto object: Class LayerInstance, Layer, gg>
    aes_params: list
    compute_aesthetics: function
    compute_geom_1: function
    compute_geom_2: function
    compute_position: function
    compute_statistic: function
    computed_geom_params: NULL
    computed_mapping: NULL
    computed_stat_params: NULL
    constructor: call
    data: waiver
    draw_geom: function
    finish_statistics: function
    geom: <ggproto object: Class GeomStep, GeomPath, Geom, gg>
        aesthetics: function
        default_aes: ggplot2::mapping, uneval, gg, S7_object
        draw_group: function
        draw_key: function
        draw_layer: function
        draw_panel: function
        extra_params: na.rm orientation
        handle_na: function
        non_missing_aes: linewidth colour linetype
        optional_aes: 
        parameters: function
        rename_size: TRUE
        required_aes: x y
        setup_data: function
        setup_params: function
        use_defaults: function
        super:  <ggproto object: Class GeomPath, Geom, gg>
    geom_params: list
    inherit.aes: TRUE
    layer_data: function
    layout: NULL
    map_statistic: function
    mapping: NULL
    name: NULL
    position: <ggproto object: Class PositionIdentity, Position, gg>
        aesthetics: function
        compute_layer: function
        compute_panel: function
        default_aes: ggplot2::mapping, uneval, gg, S7_object
        required_aes: 
        setup_data: function
        setup_params: function
        use_defaults: function
        super:  <ggproto object: Class Position, gg>
    print: function
    setup_layer: function
    show.legend: NA
    stat: <ggproto object: Class StatEcdf, Stat, gg>
        aesthetics: function
        compute_group: function
        compute_layer: function
        compute_panel: function
        default_aes: ggplot2::mapping, uneval, gg, S7_object
        dropped_aes: weight
        extra_params: na.rm
        finish_layer: function
        non_missing_aes: 
        optional_aes: 
        parameters: function
        required_aes: x|y
        retransform: TRUE
        setup_data: function
        setup_params: function
        super:  <ggproto object: Class Stat, gg>
    stat_params: list
    super:  <ggproto object: Class Layer, gg> 
 @ scales     :Classes 'ScalesList', 'ggproto', 'gg' <ggproto object: Class ScalesList, gg>
    add: function
    add_defaults: function
    add_missing: function
    backtransform_df: function
    clone: function
    find: function
    get_scales: function
    has_scale: function
    input: function
    map_df: function
    n: function
    non_position_scales: function
    scales: list
    set_palettes: function
    train_df: function
    transform_df: function
    super:  <ggproto object: Class ScalesList, gg> 
 @ guides     :Classes 'Guides', 'ggproto', 'gg' <ggproto object: Class Guides, gg>
    add: function
    assemble: function
    build: function
    draw: function
    get_custom: function
    get_guide: function
    get_params: function
    get_position: function
    guides: NULL
    merge: function
    missing: <ggproto object: Class GuideNone, Guide, gg>
        add_title: function
        arrange_layout: function
        assemble_drawing: function
        available_aes: any
        build_decor: function
        build_labels: function
        build_ticks: function
        build_title: function
        draw: function
        draw_early_exit: function
        elements: list
        extract_decor: function
        extract_key: function
        extract_params: function
        get_layer_key: function
        hashables: list
        measure_grobs: function
        merge: function
        override_elements: function
        params: list
        process_layers: function
        setup_elements: function
        setup_params: function
        train: function
        transform: function
        super:  <ggproto object: Class GuideNone, Guide, gg>
    package_box: function
    print: function
    process_layers: function
    setup: function
    subset_guides: function
    train: function
    update_params: function
    super:  <ggproto object: Class Guides, gg> 
 @ mapping    : <ggplot2::mapping> List of 3
 .. $ x     : language ~dar
 ..  ..- attr(*, ".Environment")=<environment: 0x63167977bb98> 
 .. $ group : language ~Chromosome
 ..  ..- attr(*, ".Environment")=<environment: 0x63167977bb98> 
 .. $ colour: language ~line_colour
 ..  ..- attr(*, ".Environment")=<environment: 0x63167977bb98> 
 @ theme      : <theme>  Named list()
 .. @ complete: logi FALSE
 .. @ validate: logi TRUE
 @ coordinates:Classes 'CoordCartesian', 'Coord', 'ggproto', 'gg' <ggproto object: Class CoordCartesian, Coord, gg>
    aspect: function
    backtransform_range: function
    clip: on
    default: TRUE
    distance: function
    draw_panel: function
    expand: TRUE
    is_free: function
    is_linear: function
    labels: function
    limits: list
    modify_scales: function
    range: function
    ratio: NULL
    render_axis_h: function
    render_axis_v: function
    render_bg: function
    render_fg: function
    reverse: none
    setup_data: function
    setup_layout: function
    setup_panel_guides: function
    setup_panel_params: function
    setup_params: function
    train_panel_guides: function
    transform: function
    super:  <ggproto object: Class CoordCartesian, Coord, gg> 
 @ facet      :Classes 'FacetNull', 'Facet', 'ggproto', 'gg' <ggproto object: Class FacetNull, Facet, gg>
    attach_axes: function
    attach_strips: function
    compute_layout: function
    draw_back: function
    draw_front: function
    draw_labels: function
    draw_panel_content: function
    draw_panels: function
    finish_data: function
    format_strip_labels: function
    init_gtable: function
    init_scales: function
    map_data: function
    params: list
    set_panel_size: function
    setup_data: function
    setup_panel_params: function
    setup_params: function
    shrink: TRUE
    train_scales: function
    vars: function
    super:  <ggproto object: Class FacetNull, Facet, gg> 
 @ layout     :Classes 'Layout', 'ggproto', 'gg' <ggproto object: Class Layout, gg>
    coord: NULL
    coord_params: list
    facet: NULL
    facet_params: list
    finish_data: function
    get_scales: function
    layout: NULL
    map_position: function
    panel_params: NULL
    panel_scales_x: NULL
    panel_scales_y: NULL
    render: function
    render_labels: function
    reset_scales: function
    resolve_label: function
    setup: function
    setup_panel_guides: function
    setup_panel_params: function
    train_position: function
    super:  <ggproto object: Class Layout, gg> 
 @ labels     : <ggplot2::labels> List of 3
 .. $ x     : chr "DAR"
 .. $ y     : chr "F(DAR)"
 .. $ colour: chr "Chromosome"
 @ meta       : list()
 @ plot_env   :<environment: 0x63167977bb98> 
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 127 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
 80.651   2.553  83.198