Multiple platform build/check report for BioC 3.22 - CHECK results for Pedixplorer on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4822
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4617
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4564
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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*

CHECK results for Pedixplorer on lconway

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.

raw results

Summary

Package: Pedixplorer

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pedixplorer_1.5.6.tar.gz

StartedAt: 2025-09-03 22:47:50 -0400 (Wed, 03 Sep 2025)

EndedAt: 2025-09-03 22:51:51 -0400 (Wed, 03 Sep 2025)

EllapsedTime: 240.8 seconds

RetCode: 0

Status: OK

CheckDir: Pedixplorer.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pedixplorer_1.5.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pedixplorer.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.5.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘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 7.002  0.046   7.081
* 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

Installation output

Pedixplorer.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Pedixplorer’ ...
** this is package ‘Pedixplorer’ version ‘1.5.6’
** 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)

Tests output

Pedixplorer.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
> 
> ## Beware when testing with shinytest2
> ## the package version used will be the one avalailable through
> ## `library(Pedixplorer)` as an independant R session is launched
> ## To do so you need to `unload("Pedixplorer")`, `build()`
> ## and `install("../Pedixplorer*.tar.gz")` the package before running the tests
> 
> 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.
> library(rlang)

Attaching package: 'rlang'

The following objects are masked from 'package:testthat':

    is_false, is_null, is_true

> 
> ## Set up the environment
> Sys.setenv(
+     CHROMOTE_CHROME = Sys.getenv("CHROMOTE_CHROME"),
+     CHROMOTE_HEADLESS = Sys.getenv("CHROMOTE_HEADLESS"),
+     SKIP_SHINY_TESTS = Sys.getenv("SKIP_SHINY_TESTS"),
+     CHROMOTE_ARGS = Sys.getenv("CHROMOTE_ARGS"),
+     R_TESTS = ""
+ )
> 
> print(Sys.getenv("CHROMOTE_CHROME"))
[1] ""
> 
> ## Set up the environment
> options(
+     shiny.testmode = TRUE,
+     shinytest2.load_timeout = 120000,
+     shiny.fullstacktrace = TRUE,
+     shiny.port = 3929,
+     chromote.verbose = TRUE,
+     digits = 4, width = 150,
+     browser = Sys.getenv("CHROMOTE_CHROME"),
+     keep.source = TRUE,
+     pager = "internal",
+     papersize = "a4",
+     pkgType = "source",
+     showErrorCalls = TRUE,
+     timeout = 600,
+     unzip = "internal",
+     error = rlang::entrace,
+     rlang_backtrace_on_error_report = "full",
+     rlang_backtrace_on_warning_report = "full"
+ )
> 
> rlang::global_entrace()
> 
> 
> ## Clean up any open devices
> all_dev <- grDevices::dev.list()
> for (devi in all_dev) {
+     grDevices::dev.off(devi)
+ }
> 
> ## Set up the plotting device
> par_lst <- list(
+     "pin" = c(8, 8), "cex" = 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" = rep(1, 4), "xpd" = TRUE,
+     "lwd" = 1, "oma" = rep(1, 4)
+ )
> 
> op <- par(par_lst)
> 
> R.devices::devNew("pdf", width = 10, height = 10, par = par_lst)
> 
> ## Run the tests
> test_check("Pedixplorer")
Individuals:  1_113 won't be plotted
Individuals:  113 won't be plotted
Individuals:  1_113 won't be plotted
Multiple families present, only plotting family 1
Individuals:  1_113 won't be plotted
Multiple families present, only plotting family 1
Individuals:  1_113 won't be plotted
Multiple families present, only plotting family 1
Individuals:  1_113 won't be plotted
Multiple families present, only plotting family 1
Individuals:  1_113 won't be plotted
Multiple families present, only plotting family 1
Individuals:  1_113 won't be plotted
Individuals:  1_113 won't be plotted
Individuals:  1_113 won't be plotted
Individuals:  1_113 won't be plotted
Individuals:  5_26050, 5_26051, 5_68, 5_71, 5_72, 5_73, 5_74, 5_75, 5_76, 5_77, 5_78 won't be plotted
[ FAIL 0 | WARN 3 | SKIP 48 | PASS 356 ]

══ Skipped tests (48) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (48): 'test-align.R:34:5', 'test-align.R:80:5', 'test-align.R:96:5', 'test-app.R:6:5', '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:61:5',
  'test-fix_parents.R:80:5', 'test-ibdmatrix.R:11:5', 'test-is_informative.R:69:5', 'test-kindepth.R:42:5', 'test-kinship.R:127:5',
  'test-modules.R:6:5', 'test-modules.R:22:5', 'test-modules.R:38:5', 'test-modules.R:48:5', 'test-modules.R:74:5', 'test-modules.R:109:5',
  'test-modules.R:139:5', 'test-modules.R:149:5', 'test-modules.R:189:5', 'test-norm_data.R:26:5', 'test-norm_data.R:156:5', 'test-parameters.R:2:5',
  'test-parameters.R:34:5', 'test-ped_to_legdf.R:20:5', 'test-plot.R:27:5', 'test-plot.R:64:5', 'test-plot.R:89:5', 'test-plot.R:113:5',
  'test-plot.R:119:5', 'test-plot.R:176:5', 'test-plot.R:204:5', 'test-plot.R:235:5', 'test-plot.R:258:5', 'test-plot_fct.R:11:5',
  'test-plot_fct.R:78:5', 'test-plot_fct.R:82:5', 'test-plot_fct.R:105:5', 'test-shrink.R:20:5', 'test-shrink.R:130:5', 'test-twins.R:14:5',
  'test-useful_inds.R:36:5', 'test-utils.R:76:5'

[ FAIL 0 | WARN 3 | SKIP 48 | PASS 356 ]
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_SF1.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-mtcars_data_file.csv
• 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/ped-with-all-annotations-ggplot.svg
• plot/ped1reorder.svg
• plot_fct/subregion.svg
• shrink/pedigree-shrink-2.svg
• shrink/shrinked-ped.svg
• 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_SF1.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-mtcars_data_file.csv
• 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()
pdf 
  2 
> par(op)
> 
> proc.time()
   user  system elapsed 
 88.889   2.544  92.142

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

name	user	system	elapsed
Hints-class	0.015	0.002	0.018
Ped-class	0.305	0.037	0.343
Pedigree-class	0.776	0.025	0.803
Pedixplorer_package	0.000	0.000	0.001
Rel-class	0.105	0.001	0.107
Scales-class	0.007	0.000	0.007
align	0.976	0.012	0.993
alignped1	0.485	0.006	0.492
alignped2	0.506	0.008	0.517
alignped3	0.465	0.007	0.474
alignped4	0.488	0.006	0.495
ancestors	0.001	0.000	0.001
anchor_to_factor	0.001	0.000	0.001
app_plot_all	0	0	0
app_resize_plot	0	0	0
auto_hint	0.238	0.004	0.242
best_hint	0.728	0.013	0.743
bit_size	0.195	0.005	0.200
char_to_date	0.001	0.000	0.000
check_col_config	0.001	0.001	0.001
check_columns	0.003	0.001	0.003
circfun	0.001	0.001	0.002
color_picker	0	0	0
complete_twins	0.075	0.002	0.077
compute_stress	0.234	0.003	0.238
create_text_column	0.007	0.001	0.008
data_col_sel	0	0	0
data_download	0	0	0
data_import	0	0	0
descendants	0.206	0.003	0.209
distribute_by	0.000	0.001	0.000
eval_perm	0.231	0.002	0.235
family_check	0.285	0.003	0.289
family_infos_table	0.258	0.003	0.262
family_sel	0.001	0.000	0.000
fertility_to_factor	0.001	0.000	0.001
find_avail_affected	1.499	0.012	1.520
find_avail_noninform	0.294	0.003	0.300
find_ray_intersections	0.000	0.000	0.001
find_unavailable	0.301	0.003	0.305
fix_parents	0.052	0.002	0.054
generate_aff_inds	0.003	0.000	0.003
generate_border	0.003	0.000	0.003
generate_colors	0.271	0.006	0.277
generate_fill	0.008	0.001	0.009
get_dataframe	0	0	0
get_famid	0.000	0.000	0.001
get_families_table	0.058	0.003	0.062
get_title	0.000	0.000	0.001
health_sel	0	0	0
ibd_matrix	0.015	0.000	0.015
inf_sel	0.000	0.000	0.001
is_disconnected	0.018	0.001	0.018
is_founder	0.001	0.000	0.000
is_informative	0.447	0.006	0.456
is_parent	0.213	0.004	0.220
kindepth	0.184	0.003	0.187
kinship	0.514	0.019	0.534
make_class_info	0.001	0.001	0.001
make_famid	0.237	0.005	0.243
make_reactive	0.008	0.001	0.009
make_rownames	0.000	0.001	0.001
min_dist_inf	0.259	0.004	0.263
minnbreast	3.501	0.113	3.631
miscarriage_to_factor	0.001	0.000	0.001
na_to_length	0.000	0.001	0.001
norm_ped	0.043	0.002	0.044
norm_rel	0.018	0.001	0.019
num_child	0.342	0.010	0.355
parent_of	0.192	0.003	0.196
paste0max	0	0	0
ped_avaf_infos	0.000	0.000	0.001
ped_server	0.000	0.001	0.001
ped_shiny	0	0	0
ped_to_legdf	0.244	0.006	0.251
ped_to_plotdf	0.368	0.009	0.381
ped_ui	0.000	0.000	0.001
permute	0.000	0.000	0.001
plink_to_pedigree	0.001	0.000	0.001
plot_download	0	0	0
plot_fromdf	0.733	0.006	0.745
plot_legend_app	0	0	0
plot_ped	0.185	0.002	0.188
plot_pedigree	0.159	0.002	0.161
polyfun	0.008	0.000	0.009
polygons	0.016	0.003	0.019
read_data	0.000	0.000	0.001
rel_code_to_factor	0.001	0.000	0.001
relped	0.221	0.004	0.225
rescale	0.001	0.001	0.001
sampleped	0.155	0.003	0.158
sex_to_factor	0.001	0.000	0.001
shrink	7.002	0.046	7.081
unrelated	0.277	0.003	0.281
upd_famid	0.462	0.011	0.476
useful_inds	0.225	0.005	0.231
validate_and_rename_df	0.002	0.000	0.003
vect_to_binary	0.000	0.000	0.001