Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
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" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1517/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pedixplorer 1.3.0 (landing page) Louis Le Nézet
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 1.3.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pedixplorer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Pedixplorer_1.3.0.tar.gz |
StartedAt: 2024-12-24 03:36:28 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:39:57 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 208.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Pedixplorer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pedixplorer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Pedixplorer_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Pedixplorer.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 ... 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed shrink 7.84 0.11 7.95 * 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
Pedixplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Pedixplorer ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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 [ FAIL 0 | WARN 0 | SKIP 39 | PASS 217 ] ══ 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 217 ] 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 51.64 2.39 54.73 Ran 2/2 deferred expressions
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
name | user | system | elapsed | |
Hints-class | 0.02 | 0.00 | 0.01 | |
Ped-class | 0.28 | 0.00 | 0.28 | |
Pedigree-class | 0.54 | 0.06 | 0.67 | |
Pedixplorer_package | 0 | 0 | 0 | |
Rel-class | 0.01 | 0.00 | 0.02 | |
Scales-class | 0.02 | 0.00 | 0.02 | |
align | 0.95 | 0.01 | 0.96 | |
alignped1 | 0.41 | 0.02 | 0.43 | |
alignped2 | 0.48 | 0.00 | 0.48 | |
alignped3 | 0.45 | 0.00 | 0.45 | |
alignped4 | 0.39 | 0.02 | 0.41 | |
ancestors | 0 | 0 | 0 | |
anchor_to_factor | 0 | 0 | 0 | |
auto_hint | 0.21 | 0.01 | 0.22 | |
best_hint | 0.59 | 0.05 | 0.64 | |
bit_size | 0.13 | 0.00 | 0.12 | |
check_columns | 0.01 | 0.00 | 0.02 | |
circfun | 0 | 0 | 0 | |
color_picker | 0 | 0 | 0 | |
create_text_column | 0.02 | 0.00 | 0.02 | |
data_col_sel | 0 | 0 | 0 | |
data_download | 0 | 0 | 0 | |
data_import | 0 | 0 | 0 | |
descendants | 0.12 | 0.00 | 0.12 | |
family_check | 0.27 | 0.01 | 0.28 | |
family_infos_table | 0.19 | 0.02 | 0.20 | |
family_sel | 0 | 0 | 0 | |
find_avail_affected | 1.26 | 0.00 | 1.27 | |
find_avail_noninform | 0.31 | 0.00 | 0.31 | |
find_unavailable | 0.30 | 0.01 | 0.32 | |
fix_parents | 0.03 | 0.02 | 0.04 | |
generate_aff_inds | 0 | 0 | 0 | |
generate_border | 0.02 | 0.00 | 0.02 | |
generate_colors | 0.22 | 0.02 | 0.23 | |
generate_fill | 0.01 | 0.00 | 0.02 | |
get_dataframe | 0 | 0 | 0 | |
get_famid | 0 | 0 | 0 | |
get_families_table | 0.05 | 0.00 | 0.04 | |
get_title | 0.01 | 0.00 | 0.02 | |
health_sel | 0 | 0 | 0 | |
ibd_matrix | 0.02 | 0.00 | 0.02 | |
inf_sel | 0 | 0 | 0 | |
is_disconnected | 0.03 | 0.00 | 0.03 | |
is_founder | 0 | 0 | 0 | |
is_informative | 0.52 | 0.00 | 0.51 | |
is_parent | 0.22 | 0.00 | 0.22 | |
kindepth | 0.2 | 0.0 | 0.2 | |
kinship | 0.44 | 0.01 | 0.46 | |
make_class_info | 0 | 0 | 0 | |
make_famid | 0.19 | 0.00 | 0.19 | |
make_rownames | 0.00 | 0.02 | 0.00 | |
min_dist_inf | 0.25 | 0.00 | 0.25 | |
minnbreast | 2.23 | 0.08 | 2.31 | |
na_to_length | 0 | 0 | 0 | |
norm_ped | 0 | 0 | 0 | |
norm_rel | 0.04 | 0.00 | 0.03 | |
num_child | 0.28 | 0.00 | 0.28 | |
parent_of | 0.2 | 0.0 | 0.2 | |
ped_avaf_infos | 0 | 0 | 0 | |
ped_server | 0 | 0 | 0 | |
ped_shiny | 0 | 0 | 0 | |
ped_to_legdf | 0.27 | 0.01 | 0.29 | |
ped_to_plotdf | 0.35 | 0.00 | 0.36 | |
ped_ui | 0 | 0 | 0 | |
plot_download | 0 | 0 | 0 | |
plot_fromdf | 0.55 | 0.00 | 0.54 | |
plot_legend_app | 0.00 | 0.02 | 0.02 | |
plot_ped | 0 | 0 | 0 | |
plot_pedigree | 0.24 | 0.00 | 0.23 | |
polyfun | 0 | 0 | 0 | |
polygons | 0.00 | 0.01 | 0.02 | |
read_data | 0 | 0 | 0 | |
rel_code_to_factor | 0 | 0 | 0 | |
relped | 0.15 | 0.02 | 0.17 | |
sampleped | 0.16 | 0.01 | 0.17 | |
sex_to_factor | 0 | 0 | 0 | |
shrink | 7.84 | 0.11 | 7.95 | |
unrelated | 0.25 | 0.00 | 0.25 | |
upd_famid | 0.47 | 0.03 | 0.50 | |
useful_inds | 0.22 | 0.02 | 0.25 | |
vect_to_binary | 0 | 0 | 0 | |