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This page was generated on 2025-08-25 12:08 -0400 (Mon, 25 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1543/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pedixplorer 1.5.5  (landing page)
Louis Le Nezet
Snapshot Date: 2025-08-24 13:45 -0400 (Sun, 24 Aug 2025)
git_url: https://git.bioconductor.org/packages/Pedixplorer
git_branch: devel
git_last_commit: 2a9e176
git_last_commit_date: 2025-07-23 14:59:33 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Pedixplorer on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Pedixplorer
Version: 1.5.5
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pedixplorer_1.5.5.tar.gz
StartedAt: 2025-08-22 10:56:47 -0000 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 11:01:16 -0000 (Fri, 22 Aug 2025)
EllapsedTime: 269.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Pedixplorer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pedixplorer_1.5.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Pedixplorer.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.5.5’
* 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 8.678   0.04   8.739
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Pedixplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Pedixplorer’ ...
** this is package ‘Pedixplorer’ version ‘1.5.5’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)

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:  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 47 | PASS 356 ]

══ Skipped tests (47) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (47): '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_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 47 | 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 
106.219   1.208 107.839 

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

nameusersystemelapsed
Hints-class0.0200.0010.020
Ped-class0.3810.0630.447
Pedigree-class0.9950.1441.141
Pedixplorer_package000
Rel-class0.1400.0120.152
Scales-class0.0050.0040.009
align1.4420.0321.477
alignped10.6060.0040.612
alignped20.6320.0160.650
alignped30.6030.0000.605
alignped40.6090.0240.635
ancestors0.0010.0000.001
anchor_to_factor0.0020.0000.001
app_plot_all000
app_resize_plot0.0000.0000.001
auto_hint0.2860.0040.291
best_hint0.9660.0120.979
bit_size0.2470.0320.279
char_to_date0.0010.0000.000
check_col_config0.0010.0000.000
check_columns0.0040.0000.003
circfun0.0020.0000.001
color_picker000
complete_twins0.0960.0020.100
compute_stress0.2870.0040.292
create_text_column0.0090.0000.009
data_col_sel0.0000.0000.001
data_download000
data_import000
descendants0.2520.0000.253
distribute_by000
eval_perm0.3090.0040.313
family_check0.3450.0000.345
family_infos_table0.3290.0080.338
family_sel000
fertility_to_factor0.0010.0000.001
find_avail_affected1.7280.0151.748
find_avail_noninform0.3330.0050.338
find_ray_intersections000
find_unavailable0.3440.0150.360
fix_parents0.0580.0010.058
generate_aff_inds0.0040.0000.004
generate_border0.0030.0000.003
generate_colors0.3180.0030.323
generate_fill0.0090.0000.010
get_dataframe000
get_famid0.0000.0000.001
get_families_table0.0490.0030.052
get_title0.0010.0000.001
health_sel000
ibd_matrix0.0180.0030.021
inf_sel000
is_disconnected0.0230.0000.022
is_founder000
is_informative0.4850.0080.494
is_parent0.2450.0000.245
kindepth0.2360.0010.237
kinship0.6470.0070.657
make_class_info0.0010.0000.001
make_famid0.2980.0080.306
make_reactive0.0050.0040.009
make_rownames0.0010.0000.001
min_dist_inf0.3270.0000.328
minnbreast4.3170.1164.441
miscarriage_to_factor0.0010.0000.001
na_to_length0.0000.0000.001
norm_ped0.0510.0000.052
norm_rel0.0260.0000.026
num_child0.3880.0040.393
parent_of0.2390.0040.244
paste0max0.0000.0000.001
ped_avaf_infos000
ped_server000
ped_shiny000
ped_to_legdf0.3000.0200.324
ped_to_plotdf0.5080.0040.513
ped_ui000
permute0.0010.0000.001
plink_to_pedigree000
plot_download000
plot_fromdf0.9680.0000.970
plot_legend_app000
plot_ped0.2460.0000.247
plot_pedigree0.2220.0000.223
polyfun0.0140.0000.014
polygons0.0170.0000.017
read_data000
rel_code_to_factor0.0010.0000.001
relped0.3140.0040.318
rescale0.0010.0000.001
sampleped0.2410.0000.242
sex_to_factor0.0010.0000.000
shrink8.6780.0408.739
unrelated0.2880.0000.289
upd_famid0.5370.0280.566
useful_inds0.2800.0120.293
validate_and_rename_df0.0030.0000.003
vect_to_binary0.0010.0000.001