Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1525/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pedixplorer 1.2.0 (landing page) Louis Le Nézet
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: Pedixplorer |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pedixplorer_1.2.0.tar.gz |
StartedAt: 2024-11-20 07:19:39 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 07:22:28 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 169.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pedixplorer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Pedixplorer_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/Pedixplorer.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘1.2.0’ * 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 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 * 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
Pedixplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Pedixplorer ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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)
Pedixplorer.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 28.152 0.636 29.530 Ran 2/2 deferred expressions
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
name | user | system | elapsed | |
Hints-class | 0.008 | 0.000 | 0.008 | |
Ped-class | 0.186 | 0.037 | 0.232 | |
Pedigree-class | 0.371 | 0.050 | 0.424 | |
Pedixplorer_package | 0.000 | 0.001 | 0.000 | |
Rel-class | 0.008 | 0.000 | 0.009 | |
Scales-class | 0.004 | 0.000 | 0.004 | |
align | 0.581 | 0.001 | 1.010 | |
alignped1 | 0.239 | 0.001 | 0.481 | |
alignped2 | 0.267 | 0.001 | 0.440 | |
alignped3 | 0.220 | 0.001 | 0.224 | |
alignped4 | 0.212 | 0.001 | 0.215 | |
ancestors | 0.000 | 0.000 | 0.001 | |
anchor_to_factor | 0.001 | 0.000 | 0.001 | |
auto_hint | 0.108 | 0.000 | 0.111 | |
best_hint | 0.413 | 0.009 | 0.435 | |
bit_size | 0.092 | 0.000 | 0.096 | |
check_columns | 0.002 | 0.000 | 0.002 | |
circfun | 0.000 | 0.001 | 0.001 | |
color_picker | 0.000 | 0.000 | 0.001 | |
create_text_column | 0.004 | 0.000 | 0.004 | |
data_col_sel | 0 | 0 | 0 | |
data_download | 0 | 0 | 0 | |
data_import | 0 | 0 | 0 | |
descendants | 0.088 | 0.001 | 0.089 | |
family_check | 0.144 | 0.000 | 0.146 | |
family_infos_table | 0.13 | 0.00 | 0.13 | |
family_sel | 0.001 | 0.000 | 0.000 | |
find_avail_affected | 0.664 | 0.002 | 0.669 | |
find_avail_noninform | 0.128 | 0.000 | 0.128 | |
find_unavailable | 0.126 | 0.000 | 0.126 | |
fix_parents | 0.026 | 0.001 | 0.026 | |
generate_aff_inds | 0.002 | 0.000 | 0.002 | |
generate_border | 0.001 | 0.001 | 0.002 | |
generate_colors | 0.127 | 0.000 | 0.127 | |
generate_fill | 0.005 | 0.000 | 0.005 | |
get_dataframe | 0 | 0 | 0 | |
get_famid | 0 | 0 | 0 | |
get_families_table | 0.023 | 0.001 | 0.024 | |
get_title | 0.000 | 0.000 | 0.001 | |
health_sel | 0 | 0 | 0 | |
ibd_matrix | 0.011 | 0.000 | 0.011 | |
inf_sel | 0 | 0 | 0 | |
is_disconnected | 0.010 | 0.001 | 0.012 | |
is_founder | 0 | 0 | 0 | |
is_informative | 0.222 | 0.001 | 0.223 | |
is_parent | 0.089 | 0.001 | 0.091 | |
kindepth | 0.086 | 0.001 | 0.087 | |
kinship | 0.241 | 0.004 | 0.255 | |
make_class_info | 0.001 | 0.000 | 0.000 | |
make_famid | 0.109 | 0.001 | 0.114 | |
make_rownames | 0.000 | 0.001 | 0.001 | |
min_dist_inf | 0.115 | 0.000 | 0.114 | |
minnbreast | 1.047 | 0.051 | 1.102 | |
na_to_length | 0 | 0 | 0 | |
norm_ped | 0.001 | 0.000 | 0.001 | |
norm_rel | 0.015 | 0.001 | 0.016 | |
num_child | 0.161 | 0.000 | 0.235 | |
parent_of | 0.090 | 0.000 | 0.091 | |
ped_avaf_infos | 0 | 0 | 0 | |
ped_server | 0 | 0 | 0 | |
ped_shiny | 0 | 0 | 0 | |
ped_to_legdf | 0.130 | 0.002 | 0.132 | |
ped_to_plotdf | 0.190 | 0.001 | 0.199 | |
ped_ui | 0 | 0 | 0 | |
plot_download | 0 | 0 | 0 | |
plot_fromdf | 0.318 | 0.002 | 0.320 | |
plot_legend_app | 0 | 0 | 0 | |
plot_ped | 0 | 0 | 0 | |
plot_pedigree | 0.139 | 0.000 | 0.142 | |
polyfun | 0.001 | 0.000 | 0.001 | |
polygons | 0.002 | 0.001 | 0.003 | |
read_data | 0 | 0 | 0 | |
rel_code_to_factor | 0.001 | 0.000 | 0.000 | |
relped | 0.107 | 0.000 | 0.106 | |
sampleped | 0.090 | 0.001 | 0.091 | |
sex_to_factor | 0.001 | 0.000 | 0.001 | |
shrink | 4.198 | 0.002 | 4.236 | |
unrelated | 0.123 | 0.000 | 0.123 | |
upd_famid | 0.226 | 0.004 | 0.231 | |
useful_inds | 0.104 | 0.002 | 0.106 | |
vect_to_binary | 0.000 | 0.001 | 0.001 | |