| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:14 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 1539/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pedixplorer 1.0.0 (landing page) Louis Le Nézet
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | 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 | ||||||||||
| kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Pedixplorer |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Pedixplorer_1.0.0.tar.gz |
| StartedAt: 2024-05-09 10:27:56 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 10:30:53 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 177.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pedixplorer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Pedixplorer_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Pedixplorer.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pedixplorer/DESCRIPTION’ ... OK
* this is package ‘Pedixplorer’ version ‘1.0.0’
* 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 ... 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 7.896 0.056 7.97
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/Pedixplorer.Rcheck/00check.log’
for details.
Pedixplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Pedixplorer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(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
46.564 0.965 47.628
Ran 1/1 deferred expressions
Pedixplorer.Rcheck/Pedixplorer-Ex.timings
| name | user | system | elapsed | |
| Hints-class | 0.015 | 0.000 | 0.016 | |
| Ped-class | 0.338 | 0.028 | 0.366 | |
| Pedigree-class | 0.697 | 0.024 | 0.723 | |
| Pedixplorer_package | 0 | 0 | 0 | |
| Rel-class | 0.012 | 0.000 | 0.012 | |
| Scales-class | 0.006 | 0.000 | 0.007 | |
| align | 0.912 | 0.000 | 0.914 | |
| alignped1 | 0.422 | 0.000 | 0.422 | |
| alignped2 | 0.435 | 0.000 | 0.436 | |
| alignped3 | 0.410 | 0.004 | 0.414 | |
| alignped4 | 0.427 | 0.024 | 0.453 | |
| ancestors | 0.001 | 0.000 | 0.001 | |
| anchor_to_factor | 0.001 | 0.000 | 0.002 | |
| auto_hint | 0.219 | 0.004 | 0.223 | |
| best_hint | 0.835 | 0.024 | 0.861 | |
| bit_size | 0.182 | 0.004 | 0.186 | |
| check_columns | 0.003 | 0.000 | 0.003 | |
| circfun | 0.000 | 0.001 | 0.001 | |
| descendants | 0.188 | 0.002 | 0.190 | |
| family_check | 0.283 | 0.024 | 0.308 | |
| find_avail_affected | 1.305 | 0.004 | 1.312 | |
| find_avail_noninform | 0.271 | 0.004 | 0.276 | |
| find_unavailable | 0.256 | 0.012 | 0.269 | |
| fix_parents | 0.046 | 0.004 | 0.051 | |
| generate_aff_inds | 0.002 | 0.002 | 0.005 | |
| generate_border | 0.002 | 0.002 | 0.003 | |
| generate_colors | 0.243 | 0.012 | 0.256 | |
| generate_fill | 0.01 | 0.00 | 0.01 | |
| is_disconnected | 0.024 | 0.000 | 0.024 | |
| is_founder | 0.001 | 0.000 | 0.000 | |
| is_informative | 0.211 | 0.000 | 0.212 | |
| is_parent | 0.180 | 0.000 | 0.181 | |
| kindepth | 0.178 | 0.000 | 0.179 | |
| kinship | 0.469 | 0.015 | 0.486 | |
| make_famid | 0.214 | 0.016 | 0.230 | |
| min_dist_inf | 0.261 | 0.000 | 0.261 | |
| minnbreast | 2.378 | 0.056 | 2.440 | |
| na_to_length | 0.001 | 0.000 | 0.000 | |
| norm_ped | 0.003 | 0.000 | 0.002 | |
| norm_rel | 0.028 | 0.000 | 0.028 | |
| num_child | 0.332 | 0.000 | 0.334 | |
| ped_to_legdf | 0.229 | 0.004 | 0.233 | |
| ped_to_plotdf | 0.380 | 0.000 | 0.381 | |
| plot-Pedigree-missing-method | 0.182 | 0.004 | 0.187 | |
| plot_fromdf | 0.604 | 0.032 | 0.638 | |
| polyfun | 0.002 | 0.000 | 0.001 | |
| polygons | 0.001 | 0.004 | 0.004 | |
| rel_code_to_factor | 0.001 | 0.000 | 0.001 | |
| sampleped | 0.516 | 0.012 | 0.529 | |
| sex_to_factor | 0.001 | 0.000 | 0.001 | |
| shrink | 7.896 | 0.056 | 7.970 | |
| unrelated | 0.251 | 0.000 | 0.252 | |
| upd_famid_id | 0.443 | 0.020 | 0.465 | |
| useful_inds | 0.202 | 0.028 | 0.231 | |
| vect_to_binary | 0.001 | 0.000 | 0.001 | |