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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2068/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tadar 1.3.0  (landing page)
Lachlan Baer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/tadar
git_branch: devel
git_last_commit: 61ecdbe
git_last_commit_date: 2024-04-30 11:51:44 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for tadar on kjohnson1

To the developers/maintainers of the tadar package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tadar.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: tadar
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tadar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tadar_1.3.0.tar.gz
StartedAt: 2024-06-11 10:28:53 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 10:38:03 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 550.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: tadar.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tadar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tadar_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/tadar.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tadar/DESCRIPTION’ ... OK
* this is package ‘tadar’ version ‘1.3.0’
* 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 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
flipRanges-methods       21.402  0.564  22.029
plotChrDar-methods       16.139  0.334  16.529
assignFeatureDar-methods 10.441  0.187  10.665
* 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:
    ..$ colour: chr "Chromosome"
    ..$ group : chr "Chromosome"
   - attr(*, "class")= chr [1:2] "gg" "ggplot"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 126 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-countsToProps.R:18:5'): countsToProps returns proportions ────
  unique(unlist(rowsums)) (`actual`) not equal to 1 (`expected`).
  
    `actual`: 1 1
  `expected`: 1  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 126 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/tadar.Rcheck/00check.log’
for details.


Installation output

tadar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tadar
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘tadar’ ...
** 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)

Tests output

tadar.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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/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

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: 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: GenomeInfoDb
Loading required package: ggplot2
> 
> test_check("tadar")
List of 11
 $ 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 [1:2500] 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
  ..$ :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: uneval
        draw_group: function
        draw_key: function
        draw_layer: function
        draw_panel: function
        extra_params: na.rm
        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
    map_statistic: function
    mapping: NULL
    position: <ggproto object: Class PositionIdentity, Position, gg>
        compute_layer: function
        compute_panel: function
        required_aes: 
        setup_data: function
        setup_params: 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: uneval
        dropped_aes: 
        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
    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    :List of 3
  ..$ x     : language ~dar
  .. ..- attr(*, ".Environment")=<environment: 0x2a0cd2a20> 
  ..$ group : language ~Chromosome
  .. ..- attr(*, ".Environment")=<environment: 0x2a0cd2a20> 
  ..$ colour: language ~line_colour
  .. ..- attr(*, ".Environment")=<environment: 0x2a0cd2a20> 
  ..- attr(*, "class")= chr "uneval"
 $ theme      : list()
 $ coordinates:Classes 'CoordCartesian', 'Coord', 'ggproto', 'gg' <ggproto object: Class CoordCartesian, Coord, gg>
    aspect: function
    backtransform_range: function
    clip: on
    default: TRUE
    distance: function
    expand: TRUE
    is_free: function
    is_linear: function
    labels: function
    limits: list
    modify_scales: function
    range: function
    render_axis_h: function
    render_axis_v: function
    render_bg: function
    render_fg: function
    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>
    compute_layout: function
    draw_back: function
    draw_front: function
    draw_labels: function
    draw_panels: function
    finish_data: function
    init_scales: function
    map_data: function
    params: list
    setup_data: function
    setup_params: function
    shrink: TRUE
    train_scales: function
    vars: function
    super:  <ggproto object: Class FacetNull, Facet, gg> 
 $ plot_env   :<environment: 0x2a0cd2a20> 
 $ 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     :List of 4
  ..$ x     : chr "DAR"
  ..$ y     : chr "F(DAR)"
  ..$ colour: chr "Chromosome"
  ..$ group : chr "Chromosome"
 - attr(*, "class")= chr [1:2] "gg" "ggplot"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 126 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-countsToProps.R:18:5'): countsToProps returns proportions ────
unique(unlist(rowsums)) (`actual`) not equal to 1 (`expected`).

  `actual`: 1 1
`expected`: 1  

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 126 ]
Error: Test failures
Execution halted

Example timings

tadar.Rcheck/tadar-Ex.timings

nameusersystemelapsed
assignFeatureDar-methods10.441 0.18710.665
countAlleles-methods3.1270.0263.159
countsToProps-methods3.2380.0213.276
dar-methods4.1570.0324.204
filterLoci-methods3.4970.0223.540
flipRanges-methods21.402 0.56422.029
plotChrDar-methods16.139 0.33416.529
plotDarECDF-methods1.1700.0191.193
readGenotypes-methods2.3970.0202.423
unphaseGT-methods2.7830.4513.251