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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Pedixplorer_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Pedixplorer.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 ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.6.0’
* 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 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
shrink 5.856  0.038   5.895
* 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 Pedixplorer
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Pedixplorer’ ...
** this is package ‘Pedixplorer’ version ‘1.6.0’
** 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 (Pedixplorer)

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
> 
> ## 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)
> 
> ## 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:  113 won't be plotted
Individuals:  1_113 won't be plotted
Saving _problems/test-plot-50.R
Individuals:  1_113 won't be plotted
Individuals:  1_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
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:  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
Individuals:  8_160, 8_164, 8_167, 8_168, 8_169, 8_170, 8_171, 8_172, 8_173, 8_174 won't be plotted
[ FAIL 1 | WARN 3 | SKIP 48 | PASS 445 ]

══ Skipped tests (48) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (48): 'test-align.R:23:1', 'test-align.R:61:1', 'test-align.R:88:1', 'test-app.R:6:5', 'test-class.R:1:1', 'test-class.R:111:1',
  'test-class.R:150:1', 'test-class.R:204:1', 'test-fix_parents.R:1:1', 'test-fix_parents.R:10:1', 'test-fix_parents.R:54:1',
  'test-fix_parents.R:75:1', 'test-ibdmatrix.R:1:1', 'test-is_informative.R:47:1', 'test-kindepth.R:1:1', 'test-kinship.R:103:1',
  '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:1:1', 'test-norm_data.R:137:1', 'test-parameters.R:1:1',
  'test-parameters.R:5:1', 'test-ped_to_legdf.R:1:1', 'test-plot.R:1:1', 'test-plot.R:59:1', 'test-plot.R:81:1', 'test-plot.R:102:1',
  'test-plot.R:116:1', 'test-plot.R:131:1', 'test-plot.R:189:1', 'test-plot.R:209:1', 'test-plot.R:246:1', 'test-plot_fct.R:1:1',
  'test-plot_fct.R:47:1', 'test-plot_fct.R:81:1', 'test-plot_fct.R:87:1', 'test-shrink.R:4:1', 'test-shrink.R:124:1', 'test-twins.R:1:1',
  'test-useful_inds.R:27:1', 'test-utils.R:70:1'

══ Failed tests ══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
── Failure ('test-plot.R:47:5'): Pedigree plotting test ──────────────────────────────────────────────────────────────────────────────────────────────
Expected `round(lst$par_usr$usr, 3)` to equal `c(-0.064, 3.064, 4.248, 1)`.
Differences:
  `actual`: -0.0630 3.0630 4.2480 1.0000
`expected`: -0.0640 3.0640 4.2480 1.0000


[ FAIL 1 | WARN 3 | SKIP 48 | PASS 445 ]
Deleting unused snapshots: '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', …, 'windows-4.4/modules/ped_avaf_infos-001.json', and 'windows-4.4/modules/ped_avaf_infos-001_.png'
Error:
! Test failures.
Error during wrapup: 
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
> 
> dev.off()
pdf 
  2 
> par(op)
> 
> proc.time()
   user  system elapsed 
  92.43    1.16   93.61