Louis Le Nézet
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/Pedixplorer |
| git_branch: RELEASE_3_20 |
| git_last_commit: 16276b4 |
| git_last_commit_date: 2024-10-29 11:27:43 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:07 -0500 (Thu, 06 Feb 2025).
| 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" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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 1525/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pedixplorer 1.2.0 (landing page) Louis Le Nézet
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the Pedixplorer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pedixplorer.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: Pedixplorer |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pedixplorer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Pedixplorer_1.2.0.tar.gz |
| StartedAt: 2025-02-04 04:48:52 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 04:52:24 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 212.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pedixplorer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pedixplorer.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Pedixplorer_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Pedixplorer.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Pedixplorer/DESCRIPTION' ... OK
* this is package 'Pedixplorer' version '1.2.0'
* 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 whether package 'Pedixplorer' 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
shrink 7.06 0.08 7.17
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
Pedixplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Pedixplorer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Pedixplorer' ... ** 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 (Pedixplorer)
Pedixplorer.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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(Pedixplorer)
> library(shinytest2)
Loading required package: testthat
> library(R.devices)
R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
>
> ## Clean up any open devices
> all_dev <- dev.list()
> for (devi in all_dev) {
+ dev.off(devi)
+ }
>
> ## Set up the plotting device
> par_lst <- list(
+ "pin" = c(8, 8), "cex" = 1, "mai" = c(1, 1, 1, 1),
+ "fin" = c(6, 6), "bg" = "white", "family" = "HersheySans",
+ "usr" = c(0, 1, 0, 1), xaxp = c(0, 1, 5), yaxp = c(0, 1, 5),
+ "fig" = c(0, 1, 0, 1), "mar" = c(1, 1, 1, 1), xpd = TRUE,
+ lwd = 0.5
+ )
> R.devices::devNew("pdf", width = 10, height = 10, par = par_lst)
> plot.new()
>
> ## Set up the environment
> withr::local_options(width = 150, digits = 8, browser = "firefox")
> withr::local_options(width = 150, digits = 8, browser = "google-chrome")
> options(shiny.testmode = TRUE, shinytest2.load_timeout = 60000)
> Sys.setenv("R_TESTS" = "")
>
> ## Run the tests
> test_check("Pedixplorer")
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Google Chrome was not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave.
Error in initialize(...) : Invalid path to Chrome
Multiple families present, only plotting family 1
[ FAIL 0 | WARN 0 | SKIP 39 | PASS 221 ]
══ Skipped tests (39) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (29): 'test-align.R:28:5', 'test-align.R:74:5', 'test-align.R:90:5', 'test-class.R:18:5', 'test-class.R:127:5', 'test-class.R:170:5',
'test-class.R:215:5', 'test-fix_parents.R:5:5', 'test-fix_parents.R:20:5', 'test-fix_parents.R:34:5', 'test-fix_parents.R:50:5',
'test-ibdmatrix.R:11:5', 'test-is_informative.R:70:5', 'test-kindepth.R:43:5', 'test-kinship.R:127:5', 'test-norm_data.R:24:5',
'test-norm_data.R:47:5', 'test-ped_to_legdf.R:35:5', 'test-plot.R:28:5', 'test-plot.R:59:5', 'test-plot.R:78:5', 'test-plot.R:101:5',
'test-plot_fct.R:11:5', 'test-plot_fct.R:79:5', 'test-plot_fct.R:83:5', 'test-shrink.R:20:5', 'test-shrink.R:130:5', 'test-useful_inds.R:39:5',
'test-utils.R:74:5'
• `shinytest2::AppDriver` can not be initialized as {chromote} can not be started (10): 'test-app.R:2:5', 'test-modules.R:2:5',
'test-modules.R:18:5', 'test-modules.R:34:5', 'test-modules.R:47:5', 'test-modules.R:72:5', 'test-modules.R:106:5', 'test-modules.R:129:5',
'test-modules.R:138:5', 'test-modules.R:177:5'
[ FAIL 0 | WARN 0 | SKIP 39 | PASS 221 ]
Deleting unused snapshots:
• align/sampleped-norel.svg
• kindepth/double-marriage.svg
• linux-4.4/app/ped_shiny-001-Ped_F2_K3_T_IAll_SF1.png
• linux-4.4/app/ped_shiny-002-Ped_F1_K2_I1_121-1_131_SF2.csv
• linux-4.4/modules/color_picker-001.json
• linux-4.4/modules/color_picker-001_.png
• linux-4.4/modules/color_picker-002.json
• linux-4.4/modules/color_picker-002_.png
• linux-4.4/modules/data_col_sel-001.json
• linux-4.4/modules/data_col_sel-001_.png
• linux-4.4/modules/data_col_sel-002.json
• linux-4.4/modules/data_col_sel-002_.png
• linux-4.4/modules/data_download-001.download
• linux-4.4/modules/data_import-001.json
• linux-4.4/modules/data_import-001_.png
• linux-4.4/modules/data_import-002.json
• linux-4.4/modules/data_import-002_.png
• linux-4.4/modules/health_sel-001.json
• linux-4.4/modules/health_sel-001_.png
• linux-4.4/modules/health_sel-002.json
• linux-4.4/modules/health_sel-002_.png
• linux-4.4/modules/health_sel-003.json
• linux-4.4/modules/health_sel-003_.png
• linux-4.4/modules/inf_sel-001.json
• linux-4.4/modules/inf_sel-001_.png
• linux-4.4/modules/inf_sel-002.json
• linux-4.4/modules/inf_sel-002_.png
• linux-4.4/modules/inf_sel-003.json
• linux-4.4/modules/inf_sel-003_.png
• linux-4.4/modules/ped_avaf_infos-001.json
• linux-4.4/modules/ped_avaf_infos-001_.png
• ped_to_legdf/legend-alone.svg
• ped_to_legdf/plot-with-legend.svg
• plot/ped-2-affections-ggplot.svg
• plot/ped-simple-affection-ggplot.svg
• plot/ped1reorder.svg
• plot_fct/subregion.svg
• shrink/pedigree-shrink-2.svg
• shrink/shrinked-ped.svg
• windows-4.3/app/ped_shiny-001-Ped_F2_K3_T_IAll_SF1.png
• windows-4.3/app/ped_shiny-002-Ped_F1_K2_I1_121-1_131_SF2.csv
• windows-4.3/modules/color_picker-001.json
• windows-4.3/modules/color_picker-001_.png
• windows-4.3/modules/color_picker-002.json
• windows-4.3/modules/color_picker-002_.png
• windows-4.3/modules/data_col_sel-001.json
• windows-4.3/modules/data_col_sel-001_.png
• windows-4.3/modules/data_col_sel-002.json
• windows-4.3/modules/data_col_sel-002_.png
• windows-4.3/modules/data_download-001.download
• windows-4.3/modules/data_import-001.json
• windows-4.3/modules/data_import-001_.png
• windows-4.3/modules/data_import-002.json
• windows-4.3/modules/data_import-002_.png
• windows-4.3/modules/health_sel-001.json
• windows-4.3/modules/health_sel-001_.png
• windows-4.3/modules/health_sel-002.json
• windows-4.3/modules/health_sel-002_.png
• windows-4.3/modules/health_sel-003.json
• windows-4.3/modules/health_sel-003_.png
• windows-4.3/modules/inf_sel-001.json
• windows-4.3/modules/inf_sel-001_.png
• windows-4.3/modules/inf_sel-002.json
• windows-4.3/modules/inf_sel-002_.png
• windows-4.3/modules/inf_sel-003.json
• windows-4.3/modules/inf_sel-003_.png
• windows-4.3/modules/ped_avaf_infos-001.json
• windows-4.3/modules/ped_avaf_infos-001_.png
• windows-4.4/app/ped_shiny-001-Ped_F2_K3_T_IAll_SF1.png
• windows-4.4/app/ped_shiny-002-Ped_F1_K2_I1_121-1_131_SF2.csv
• windows-4.4/modules/color_picker-001.json
• windows-4.4/modules/color_picker-001_.png
• windows-4.4/modules/color_picker-002.json
• windows-4.4/modules/color_picker-002_.png
• windows-4.4/modules/data_col_sel-001.json
• windows-4.4/modules/data_col_sel-001_.png
• windows-4.4/modules/data_col_sel-002.json
• windows-4.4/modules/data_col_sel-002_.png
• windows-4.4/modules/data_download-001.download
• windows-4.4/modules/data_import-001.json
• windows-4.4/modules/data_import-001_.png
• windows-4.4/modules/data_import-002.json
• windows-4.4/modules/data_import-002_.png
• windows-4.4/modules/health_sel-001.json
• windows-4.4/modules/health_sel-001_.png
• windows-4.4/modules/health_sel-002.json
• windows-4.4/modules/health_sel-002_.png
• windows-4.4/modules/health_sel-003.json
• windows-4.4/modules/health_sel-003_.png
• windows-4.4/modules/inf_sel-001.json
• windows-4.4/modules/inf_sel-001_.png
• windows-4.4/modules/inf_sel-002.json
• windows-4.4/modules/inf_sel-002_.png
• windows-4.4/modules/inf_sel-003.json
• windows-4.4/modules/inf_sel-003_.png
• windows-4.4/modules/ped_avaf_infos-001.json
• windows-4.4/modules/ped_avaf_infos-001_.png
>
> dev.off()
null device
1
>
> proc.time()
user system elapsed
49.39 2.10 57.20
Ran 2/2 deferred expressions
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
| name | user | system | elapsed | |
| Hints-class | 0.01 | 0.00 | 0.02 | |
| Ped-class | 0.38 | 0.02 | 0.39 | |
| Pedigree-class | 0.78 | 0.03 | 0.82 | |
| Pedixplorer_package | 0 | 0 | 0 | |
| Rel-class | 0.01 | 0.00 | 0.01 | |
| Scales-class | 0 | 0 | 0 | |
| align | 0.75 | 0.05 | 0.80 | |
| alignped1 | 0.46 | 0.01 | 0.47 | |
| alignped2 | 0.43 | 0.02 | 0.45 | |
| alignped3 | 0.41 | 0.00 | 0.41 | |
| alignped4 | 0.44 | 0.00 | 0.43 | |
| ancestors | 0 | 0 | 0 | |
| anchor_to_factor | 0 | 0 | 0 | |
| auto_hint | 0.14 | 0.02 | 0.16 | |
| best_hint | 0.65 | 0.03 | 0.69 | |
| bit_size | 0.14 | 0.01 | 0.15 | |
| check_columns | 0 | 0 | 0 | |
| circfun | 0 | 0 | 0 | |
| color_picker | 0 | 0 | 0 | |
| create_text_column | 0 | 0 | 0 | |
| data_col_sel | 0 | 0 | 0 | |
| data_download | 0 | 0 | 0 | |
| data_import | 0.00 | 0.02 | 0.02 | |
| descendants | 0.17 | 0.01 | 0.18 | |
| family_check | 0.22 | 0.00 | 0.22 | |
| family_infos_table | 0.28 | 0.00 | 0.28 | |
| family_sel | 0 | 0 | 0 | |
| find_avail_affected | 1.50 | 0.03 | 1.53 | |
| find_avail_noninform | 0.22 | 0.04 | 0.25 | |
| find_unavailable | 0.19 | 0.03 | 0.22 | |
| fix_parents | 0.03 | 0.01 | 0.05 | |
| generate_aff_inds | 0 | 0 | 0 | |
| generate_border | 0 | 0 | 0 | |
| generate_colors | 0.22 | 0.02 | 0.23 | |
| generate_fill | 0 | 0 | 0 | |
| get_dataframe | 0 | 0 | 0 | |
| get_famid | 0 | 0 | 0 | |
| get_families_table | 0.03 | 0.00 | 0.03 | |
| get_title | 0 | 0 | 0 | |
| health_sel | 0 | 0 | 0 | |
| ibd_matrix | 0.02 | 0.00 | 0.01 | |
| inf_sel | 0 | 0 | 0 | |
| is_disconnected | 0.02 | 0.00 | 0.02 | |
| is_founder | 0 | 0 | 0 | |
| is_informative | 0.34 | 0.00 | 0.35 | |
| is_parent | 0.14 | 0.00 | 0.14 | |
| kindepth | 0.17 | 0.00 | 0.17 | |
| kinship | 0.47 | 0.02 | 0.48 | |
| make_class_info | 0 | 0 | 0 | |
| make_famid | 0.24 | 0.01 | 0.25 | |
| make_rownames | 0 | 0 | 0 | |
| min_dist_inf | 0.26 | 0.00 | 0.27 | |
| minnbreast | 2.49 | 0.11 | 2.59 | |
| na_to_length | 0 | 0 | 0 | |
| norm_ped | 0 | 0 | 0 | |
| norm_rel | 0.03 | 0.00 | 0.03 | |
| num_child | 0.39 | 0.00 | 0.40 | |
| parent_of | 0.25 | 0.00 | 0.25 | |
| ped_avaf_infos | 0 | 0 | 0 | |
| ped_server | 0 | 0 | 0 | |
| ped_shiny | 0 | 0 | 0 | |
| ped_to_legdf | 0.29 | 0.02 | 0.31 | |
| ped_to_plotdf | 0.32 | 0.00 | 0.31 | |
| ped_ui | 0 | 0 | 0 | |
| plot_download | 0 | 0 | 0 | |
| plot_fromdf | 0.64 | 0.01 | 0.66 | |
| plot_legend_app | 0 | 0 | 0 | |
| plot_ped | 0.01 | 0.00 | 0.01 | |
| plot_pedigree | 0.19 | 0.02 | 0.21 | |
| polyfun | 0 | 0 | 0 | |
| polygons | 0.02 | 0.00 | 0.01 | |
| read_data | 0 | 0 | 0 | |
| rel_code_to_factor | 0 | 0 | 0 | |
| relped | 0.23 | 0.01 | 0.25 | |
| sampleped | 0.17 | 0.00 | 0.17 | |
| sex_to_factor | 0 | 0 | 0 | |
| shrink | 7.06 | 0.08 | 7.17 | |
| unrelated | 0.19 | 0.00 | 0.19 | |
| upd_famid | 0.49 | 0.00 | 0.50 | |
| useful_inds | 0.22 | 0.03 | 0.25 | |
| vect_to_binary | 0 | 0 | 0 | |