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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 1539/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pedixplorer 1.3.4  (landing page)
Louis Le Nezet
Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025)
git_url: https://git.bioconductor.org/packages/Pedixplorer
git_branch: devel
git_last_commit: 7eacf67
git_last_commit_date: 2025-03-15 16:21:06 -0400 (Sat, 15 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Pedixplorer on kjohnson3

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: 1.3.4
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_1.3.4.tar.gz
StartedAt: 2025-03-19 20:50:58 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 20:52:02 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 63.8 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_1.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Pedixplorer.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.3.4’
* 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 ‘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
* 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-arm64/Resources/library’
* installing *source* package ‘Pedixplorer’ ...
** this is package ‘Pedixplorer’ version ‘1.3.4’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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
> 
> ## 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] ""
> 
> ## 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,
+     "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)
> 
> ## 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()
> 
> ## 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
Multiple families present, only plotting family 1
Multiple families present, only plotting family 1
Multiple families present, only plotting family 1
Multiple families present, only plotting family 1
[ FAIL 0 | WARN 0 | SKIP 44 | PASS 333 ]

══ Skipped tests (44) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (34): 'test-align.R:34:5', 'test-align.R:80:5', 'test-align.R:96:5', '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-norm_data.R:26:5',
  'test-norm_data.R:143:5', 'test-parameters.R:2:5', 'test-parameters.R:29:5', 'test-ped_to_legdf.R:20:5', 'test-plot.R:27:5', 'test-plot.R:63:5',
  'test-plot.R:82:5', 'test-plot.R:106:5', 'test-plot.R:112:5', 'test-plot.R:169:5', 'test-plot_fct.R:11:5', 'test-plot_fct.R:81:5',
  'test-plot_fct.R:85:5', 'test-plot_fct.R:108:5', 'test-shrink.R:20:5', 'test-shrink.R:130:5', 'test-useful_inds.R:36:5', 'test-utils.R:74:5'
• `shinytest2::AppDriver` can not be initialized as {chromote} can not be started (10): 'test-app.R:7:5', '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:108:5', 'test-modules.R:138:5',
  'test-modules.R:148:5', 'test-modules.R:188:5'

[ FAIL 0 | WARN 0 | SKIP 44 | PASS 333 ]
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-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_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-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 
 16.296   1.012  17.458 

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

nameusersystemelapsed
Hints-class0.0040.0010.004
Ped-class0.0910.0090.101
Pedigree-class0.1750.0080.182
Pedixplorer_package000
Rel-class0.0040.0000.004
Scales-class0.0020.0000.002
align0.2430.0020.245
alignped10.1090.0010.111
alignped20.1000.0010.102
alignped30.0980.0010.100
alignped40.0990.0020.101
ancestors000
anchor_to_factor0.0010.0000.000
auto_hint0.0470.0010.048
best_hint0.1700.0030.172
bit_size0.0450.0030.047
char_to_date000
check_col_config000
check_columns0.0020.0010.003
circfun0.0000.0000.001
color_picker000
create_text_column0.0030.0000.002
data_col_sel000
data_download000
data_import000
descendants0.0400.0010.040
distribute_by000
family_check0.0600.0010.061
family_infos_table0.0610.0010.062
family_sel000
fertility_to_factor0.0000.0000.001
find_avail_affected0.3440.0030.346
find_avail_noninform0.0630.0010.064
find_ray_intersections000
find_unavailable0.0580.0010.059
fix_parents0.0110.0010.012
generate_aff_inds0.0010.0000.001
generate_border0.0010.0000.001
generate_colors0.0590.0010.061
generate_fill0.0020.0000.002
get_dataframe0.0000.0010.000
get_famid0.0010.0000.000
get_families_table0.0130.0010.014
get_title000
health_sel000
ibd_matrix0.0050.0000.005
inf_sel0.0010.0000.000
is_disconnected0.0050.0000.006
is_founder000
is_informative0.0870.0020.089
is_parent0.0450.0010.047
kindepth0.0400.0010.041
kinship0.1180.0090.134
make_class_info000
make_famid0.0530.0010.066
make_rownames0.0000.0010.000
min_dist_inf0.0640.0010.065
minnbreast0.8450.0460.951
miscarriage_to_factor0.0010.0000.000
na_to_length000
norm_ped0.0120.0000.012
norm_rel0.0050.0010.006
num_child0.0700.0010.071
parent_of0.0420.0030.045
paste0max000
ped_avaf_infos000
ped_server0.0000.0000.001
ped_shiny000
ped_to_legdf0.0640.0040.067
ped_to_plotdf0.0940.0020.108
ped_ui000
permute000
plot_download000
plot_fromdf0.1780.0010.180
plot_legend_app000
plot_ped000
plot_pedigree0.0470.0020.052
polyfun0.0070.0000.007
polygons0.0060.0010.007
read_data000
rel_code_to_factor000
relped0.0500.0010.051
sampleped0.0400.0010.041
sex_to_factor0.0000.0000.001
shrink1.7130.0051.785
unrelated0.0590.0010.059
upd_famid0.1020.0030.107
useful_inds0.0570.0010.058
validate_and_rename_df0.0010.0000.001
vect_to_binary000