Multiple platform build/check report for BioC 3.21 - CHECK results for Pedixplorer on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
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 nebbiolo1

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: 1.3.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Pedixplorer_1.3.0.tar.gz

StartedAt: 2024-11-28 03:59:17 -0500 (Thu, 28 Nov 2024)

EndedAt: 2024-11-28 04:06:15 -0500 (Thu, 28 Nov 2024)

EllapsedTime: 417.4 seconds

RetCode: 0

Status: OK

CheckDir: Pedixplorer.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Pedixplorer_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Pedixplorer.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 5.861  0.082   5.943
* 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

Installation output

Pedixplorer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Pedixplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)

Tests output

Pedixplorer.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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
> 
> 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`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
Error in initialize(...) : Invalid path to Chrome
`google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
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 
 36.757   0.939  37.688 
Ran 2/2 deferred expressions

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

name	user	system	elapsed
Hints-class	0.207	0.012	0.219
Ped-class	0.232	0.033	0.264
Pedigree-class	0.492	0.046	0.537
Pedixplorer_package	0.001	0.000	0.000
Rel-class	0.011	0.002	0.013
Scales-class	0.005	0.000	0.005
align	0.727	0.002	0.731
alignped1	0.280	0.003	0.283
alignped2	0.294	0.004	0.298
alignped3	0.279	0.003	0.282
alignped4	0.273	0.019	0.292
ancestors	0	0	0
anchor_to_factor	0.001	0.000	0.001
auto_hint	0.140	0.005	0.145
best_hint	0.518	0.024	0.542
bit_size	0.113	0.001	0.115
check_columns	0.001	0.002	0.003
circfun	0.000	0.002	0.002
color_picker	0	0	0
create_text_column	0.006	0.000	0.006
data_col_sel	0	0	0
data_download	0	0	0
data_import	0	0	0
descendants	0.114	0.000	0.114
family_check	0.178	0.001	0.179
family_infos_table	0.161	0.001	0.162
family_sel	0	0	0
find_avail_affected	0.871	0.032	0.903
find_avail_noninform	0.169	0.001	0.170
find_unavailable	0.165	0.000	0.165
fix_parents	0.039	0.001	0.040
generate_aff_inds	0.002	0.001	0.003
generate_border	0.000	0.002	0.002
generate_colors	0.160	0.003	0.163
generate_fill	0.006	0.000	0.006
get_dataframe	0	0	0
get_famid	0.001	0.000	0.001
get_families_table	0.03	0.00	0.03
get_title	0.000	0.000	0.001
health_sel	0	0	0
ibd_matrix	0.012	0.002	0.014
inf_sel	0.001	0.000	0.001
is_disconnected	0.012	0.003	0.015
is_founder	0.001	0.000	0.001
is_informative	0.282	0.004	0.286
is_parent	0.118	0.008	0.126
kindepth	0.112	0.010	0.122
kinship	0.316	0.035	0.351
make_class_info	0.001	0.000	0.001
make_famid	0.141	0.005	0.145
make_rownames	0.000	0.000	0.001
min_dist_inf	0.141	0.003	0.143
minnbreast	1.397	0.064	1.461
na_to_length	0	0	0
norm_ped	0.000	0.002	0.002
norm_rel	0.019	0.000	0.020
num_child	0.220	0.003	0.223
parent_of	0.120	0.005	0.125
ped_avaf_infos	0.001	0.000	0.000
ped_server	0.000	0.000	0.001
ped_shiny	0	0	0
ped_to_legdf	0.169	0.007	0.175
ped_to_plotdf	0.245	0.001	0.245
ped_ui	0	0	0
plot_download	0	0	0
plot_fromdf	0.410	0.002	0.412
plot_legend_app	0	0	0
plot_ped	0	0	0
plot_pedigree	0.168	0.004	0.171
polyfun	0.001	0.000	0.002
polygons	0.004	0.002	0.006
read_data	0.001	0.000	0.000
rel_code_to_factor	0.001	0.000	0.001
relped	0.137	0.001	0.138
sampleped	0.120	0.002	0.122
sex_to_factor	0.000	0.001	0.001
shrink	5.861	0.082	5.943
unrelated	0.166	0.004	0.170
upd_famid	0.317	0.003	0.320
useful_inds	0.148	0.004	0.152
vect_to_binary	0.000	0.000	0.001