Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 2113/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tadar 1.4.0 (landing page) Lachlan Baer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: tadar |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tadar.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tadar_1.4.0.tar.gz |
StartedAt: 2024-11-29 07:38:14 -0500 (Fri, 29 Nov 2024) |
EndedAt: 2024-11-29 07:49:22 -0500 (Fri, 29 Nov 2024) |
EllapsedTime: 667.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tadar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tadar.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tadar_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tadar.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘tadar/DESCRIPTION’ ... OK * this is package ‘tadar’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 11.678 0.628 12.307 flipRanges-methods 7.867 0.180 8.048 assignFeatureDar-methods 5.462 0.268 5.733 * 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
tadar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tadar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)
tadar.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 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, saveRDS, 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: 0x57c0d17f1b68> ..$ group : language ~Chromosome .. ..- attr(*, ".Environment")=<environment: 0x57c0d17f1b68> ..$ colour: language ~line_colour .. ..- attr(*, ".Environment")=<environment: 0x57c0d17f1b68> ..- 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: 0x57c0d17f1b68> $ 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 0 | WARN 0 | SKIP 0 | PASS 129 ] > > proc.time() user system elapsed 65.257 2.112 67.362
tadar.Rcheck/tadar-Ex.timings
name | user | system | elapsed | |
assignFeatureDar-methods | 5.462 | 0.268 | 5.733 | |
countAlleles-methods | 2.940 | 0.052 | 2.992 | |
countsToProps-methods | 3.006 | 0.002 | 3.009 | |
dar-methods | 3.718 | 0.023 | 3.742 | |
filterLoci-methods | 3.096 | 0.019 | 3.116 | |
flipRanges-methods | 7.867 | 0.180 | 8.048 | |
modP-methods | 3.795 | 0.000 | 3.795 | |
plotChrDar-methods | 11.678 | 0.628 | 12.307 | |
plotDarECDF-methods | 0.909 | 0.004 | 0.914 | |
readGenotypes-methods | 2.251 | 0.010 | 2.262 | |
unphaseGT-methods | 2.447 | 0.082 | 2.529 | |