Louis Le Nézet
| Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024) |
| git_url: https://git.bioconductor.org/packages/Pedixplorer |
| git_branch: devel |
| git_last_commit: 569e94f |
| git_last_commit_date: 2024-04-30 11:54:20 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:40 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 1490/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pedixplorer 1.1.0 (landing page) Louis Le Nézet
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2024-05-02 09:04:11 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 09:10:02 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 351.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pedixplorer.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Pedixplorer.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.1.0’
* 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 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 ... NOTE
checkRd: (-1) Pedixplorer_package.Rd:19: Lost braces
19 | \\url{https://cran.r-project.org/package=kinship2} for the
| ^
* 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 13.235 0.092 15.165
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/Pedixplorer.Rcheck/00check.log’
for details.
Pedixplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pedixplorer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
>
> library(withr)
> library(testthat)
> library(Pedixplorer)
> library(vdiffr)
>
> withr::local_options(width = 150)
> test_check("Pedixplorer")
[ FAIL 0 | WARN 0 | SKIP 22 | PASS 200 ]
══ Skipped tests (22) ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
• On CRAN (22): 'test-align.R:28:5', 'test-align.R:74:5', 'test-align.R:90:5', 'test-class.R:18:5', 'test-class.R:126:5', 'test-class.R:169:5',
'test-class.R:214:5', '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-is_informative.R:70:5', 'test-kindepth.R:43:5', 'test-kinship.R:136:5', 'test-norm_data.R:24:5', 'test-norm_data.R:47:5',
'test-ped_to_legdf.R:27:5', 'test-plot.R:29:5', 'test-plot.R:57:5', 'test-shrink.R:20:5', 'test-shrink.R:130:5', 'test-useful_inds.R:32:5'
[ FAIL 0 | WARN 0 | SKIP 22 | PASS 200 ]
Deleting unused snapshots:
• align/sampleped-norel.svg
• kindepth/double-marriage.svg
• 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
• shrink/pedigree-shrink-2.svg
• shrink/shrinked-ped.svg
> TRUE
[1] TRUE
>
> proc.time()
user system elapsed
79.325 2.186 92.444
Ran 1/1 deferred expressions
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
| name | user | system | elapsed | |
| Hints-class | 0.026 | 0.004 | 0.037 | |
| Ped-class | 0.895 | 0.079 | 1.298 | |
| Pedigree-class | 1.336 | 0.130 | 1.892 | |
| Pedixplorer_package | 0.001 | 0.001 | 0.000 | |
| Rel-class | 0.024 | 0.001 | 0.034 | |
| Scales-class | 0.015 | 0.002 | 0.018 | |
| align | 1.728 | 0.025 | 2.168 | |
| alignped1 | 0.758 | 0.015 | 0.902 | |
| alignped2 | 0.755 | 0.017 | 0.886 | |
| alignped3 | 0.742 | 0.014 | 0.869 | |
| alignped4 | 0.753 | 0.013 | 0.872 | |
| ancestors | 0.001 | 0.001 | 0.002 | |
| anchor_to_factor | 0.002 | 0.001 | 0.004 | |
| auto_hint | 0.391 | 0.007 | 0.458 | |
| best_hint | 1.611 | 0.034 | 1.904 | |
| bit_size | 0.317 | 0.005 | 0.373 | |
| check_columns | 0.007 | 0.003 | 0.013 | |
| circfun | 0.002 | 0.006 | 0.011 | |
| descendants | 0.320 | 0.005 | 0.403 | |
| family_check | 0.501 | 0.007 | 0.647 | |
| find_avail_affected | 2.201 | 0.049 | 2.771 | |
| find_avail_noninform | 0.455 | 0.006 | 0.533 | |
| find_unavailable | 0.460 | 0.007 | 0.538 | |
| fix_parents | 0.084 | 0.009 | 0.105 | |
| generate_aff_inds | 0.008 | 0.002 | 0.015 | |
| generate_border | 0.006 | 0.002 | 0.009 | |
| generate_colors | 0.461 | 0.014 | 0.549 | |
| generate_fill | 0.020 | 0.004 | 0.026 | |
| is_disconnected | 0.040 | 0.001 | 0.048 | |
| is_founder | 0.000 | 0.001 | 0.001 | |
| is_informative | 0.374 | 0.008 | 0.429 | |
| is_parent | 0.316 | 0.006 | 0.358 | |
| kindepth | 0.309 | 0.007 | 0.340 | |
| kinship | 0.827 | 0.074 | 1.025 | |
| make_famid | 0.407 | 0.030 | 0.486 | |
| min_dist_inf | 0.471 | 0.008 | 0.521 | |
| minnbreast | 3.810 | 0.104 | 4.496 | |
| na_to_length | 0.000 | 0.001 | 0.001 | |
| norm_ped | 0.005 | 0.001 | 0.006 | |
| norm_rel | 0.046 | 0.002 | 0.061 | |
| num_child | 0.565 | 0.008 | 0.681 | |
| ped_to_legdf | 0.440 | 0.018 | 0.520 | |
| ped_to_plotdf | 0.679 | 0.010 | 0.782 | |
| plot-Pedigree-missing-method | 0.317 | 0.004 | 0.359 | |
| plot_fromdf | 1.166 | 0.018 | 1.385 | |
| polyfun | 0.003 | 0.002 | 0.004 | |
| polygons | 0.009 | 0.009 | 0.022 | |
| rel_code_to_factor | 0.002 | 0.001 | 0.004 | |
| sampleped | 0.631 | 0.009 | 0.761 | |
| sex_to_factor | 0.002 | 0.000 | 0.002 | |
| shrink | 13.235 | 0.092 | 15.165 | |
| unrelated | 0.413 | 0.006 | 0.481 | |
| upd_famid_id | 0.782 | 0.041 | 0.963 | |
| useful_inds | 0.376 | 0.026 | 0.466 | |
| vect_to_binary | 0.002 | 0.001 | 0.004 | |