Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1539/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pedixplorer 1.3.4 (landing page) Louis Le Nezet
| 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 24.03 LTS) / 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: 1.3.4 |
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 |
############################################################################## ############################################################################## ### ### 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
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)
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
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
name | user | system | elapsed | |
Hints-class | 0.004 | 0.001 | 0.004 | |
Ped-class | 0.091 | 0.009 | 0.101 | |
Pedigree-class | 0.175 | 0.008 | 0.182 | |
Pedixplorer_package | 0 | 0 | 0 | |
Rel-class | 0.004 | 0.000 | 0.004 | |
Scales-class | 0.002 | 0.000 | 0.002 | |
align | 0.243 | 0.002 | 0.245 | |
alignped1 | 0.109 | 0.001 | 0.111 | |
alignped2 | 0.100 | 0.001 | 0.102 | |
alignped3 | 0.098 | 0.001 | 0.100 | |
alignped4 | 0.099 | 0.002 | 0.101 | |
ancestors | 0 | 0 | 0 | |
anchor_to_factor | 0.001 | 0.000 | 0.000 | |
auto_hint | 0.047 | 0.001 | 0.048 | |
best_hint | 0.170 | 0.003 | 0.172 | |
bit_size | 0.045 | 0.003 | 0.047 | |
char_to_date | 0 | 0 | 0 | |
check_col_config | 0 | 0 | 0 | |
check_columns | 0.002 | 0.001 | 0.003 | |
circfun | 0.000 | 0.000 | 0.001 | |
color_picker | 0 | 0 | 0 | |
create_text_column | 0.003 | 0.000 | 0.002 | |
data_col_sel | 0 | 0 | 0 | |
data_download | 0 | 0 | 0 | |
data_import | 0 | 0 | 0 | |
descendants | 0.040 | 0.001 | 0.040 | |
distribute_by | 0 | 0 | 0 | |
family_check | 0.060 | 0.001 | 0.061 | |
family_infos_table | 0.061 | 0.001 | 0.062 | |
family_sel | 0 | 0 | 0 | |
fertility_to_factor | 0.000 | 0.000 | 0.001 | |
find_avail_affected | 0.344 | 0.003 | 0.346 | |
find_avail_noninform | 0.063 | 0.001 | 0.064 | |
find_ray_intersections | 0 | 0 | 0 | |
find_unavailable | 0.058 | 0.001 | 0.059 | |
fix_parents | 0.011 | 0.001 | 0.012 | |
generate_aff_inds | 0.001 | 0.000 | 0.001 | |
generate_border | 0.001 | 0.000 | 0.001 | |
generate_colors | 0.059 | 0.001 | 0.061 | |
generate_fill | 0.002 | 0.000 | 0.002 | |
get_dataframe | 0.000 | 0.001 | 0.000 | |
get_famid | 0.001 | 0.000 | 0.000 | |
get_families_table | 0.013 | 0.001 | 0.014 | |
get_title | 0 | 0 | 0 | |
health_sel | 0 | 0 | 0 | |
ibd_matrix | 0.005 | 0.000 | 0.005 | |
inf_sel | 0.001 | 0.000 | 0.000 | |
is_disconnected | 0.005 | 0.000 | 0.006 | |
is_founder | 0 | 0 | 0 | |
is_informative | 0.087 | 0.002 | 0.089 | |
is_parent | 0.045 | 0.001 | 0.047 | |
kindepth | 0.040 | 0.001 | 0.041 | |
kinship | 0.118 | 0.009 | 0.134 | |
make_class_info | 0 | 0 | 0 | |
make_famid | 0.053 | 0.001 | 0.066 | |
make_rownames | 0.000 | 0.001 | 0.000 | |
min_dist_inf | 0.064 | 0.001 | 0.065 | |
minnbreast | 0.845 | 0.046 | 0.951 | |
miscarriage_to_factor | 0.001 | 0.000 | 0.000 | |
na_to_length | 0 | 0 | 0 | |
norm_ped | 0.012 | 0.000 | 0.012 | |
norm_rel | 0.005 | 0.001 | 0.006 | |
num_child | 0.070 | 0.001 | 0.071 | |
parent_of | 0.042 | 0.003 | 0.045 | |
paste0max | 0 | 0 | 0 | |
ped_avaf_infos | 0 | 0 | 0 | |
ped_server | 0.000 | 0.000 | 0.001 | |
ped_shiny | 0 | 0 | 0 | |
ped_to_legdf | 0.064 | 0.004 | 0.067 | |
ped_to_plotdf | 0.094 | 0.002 | 0.108 | |
ped_ui | 0 | 0 | 0 | |
permute | 0 | 0 | 0 | |
plot_download | 0 | 0 | 0 | |
plot_fromdf | 0.178 | 0.001 | 0.180 | |
plot_legend_app | 0 | 0 | 0 | |
plot_ped | 0 | 0 | 0 | |
plot_pedigree | 0.047 | 0.002 | 0.052 | |
polyfun | 0.007 | 0.000 | 0.007 | |
polygons | 0.006 | 0.001 | 0.007 | |
read_data | 0 | 0 | 0 | |
rel_code_to_factor | 0 | 0 | 0 | |
relped | 0.050 | 0.001 | 0.051 | |
sampleped | 0.040 | 0.001 | 0.041 | |
sex_to_factor | 0.000 | 0.000 | 0.001 | |
shrink | 1.713 | 0.005 | 1.785 | |
unrelated | 0.059 | 0.001 | 0.059 | |
upd_famid | 0.102 | 0.003 | 0.107 | |
useful_inds | 0.057 | 0.001 | 0.058 | |
validate_and_rename_df | 0.001 | 0.000 | 0.001 | |
vect_to_binary | 0 | 0 | 0 | |