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This page was generated on 2024-05-09 11:41:14 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 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 1539/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pedixplorer 1.0.0  (landing page)
Louis Le Nézet
Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/Pedixplorer
git_branch: RELEASE_3_19
git_last_commit: 20c3c27
git_last_commit_date: 2024-04-30 11:54:20 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for Pedixplorer on kunpeng2


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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

nameusersystemelapsed
Hints-class0.0150.0000.016
Ped-class0.3380.0280.366
Pedigree-class0.6970.0240.723
Pedixplorer_package000
Rel-class0.0120.0000.012
Scales-class0.0060.0000.007
align0.9120.0000.914
alignped10.4220.0000.422
alignped20.4350.0000.436
alignped30.4100.0040.414
alignped40.4270.0240.453
ancestors0.0010.0000.001
anchor_to_factor0.0010.0000.002
auto_hint0.2190.0040.223
best_hint0.8350.0240.861
bit_size0.1820.0040.186
check_columns0.0030.0000.003
circfun0.0000.0010.001
descendants0.1880.0020.190
family_check0.2830.0240.308
find_avail_affected1.3050.0041.312
find_avail_noninform0.2710.0040.276
find_unavailable0.2560.0120.269
fix_parents0.0460.0040.051
generate_aff_inds0.0020.0020.005
generate_border0.0020.0020.003
generate_colors0.2430.0120.256
generate_fill0.010.000.01
is_disconnected0.0240.0000.024
is_founder0.0010.0000.000
is_informative0.2110.0000.212
is_parent0.1800.0000.181
kindepth0.1780.0000.179
kinship0.4690.0150.486
make_famid0.2140.0160.230
min_dist_inf0.2610.0000.261
minnbreast2.3780.0562.440
na_to_length0.0010.0000.000
norm_ped0.0030.0000.002
norm_rel0.0280.0000.028
num_child0.3320.0000.334
ped_to_legdf0.2290.0040.233
ped_to_plotdf0.3800.0000.381
plot-Pedigree-missing-method0.1820.0040.187
plot_fromdf0.6040.0320.638
polyfun0.0020.0000.001
polygons0.0010.0040.004
rel_code_to_factor0.0010.0000.001
sampleped0.5160.0120.529
sex_to_factor0.0010.0000.001
shrink7.8960.0567.970
unrelated0.2510.0000.252
upd_famid_id0.4430.0200.465
useful_inds0.2020.0280.231
vect_to_binary0.0010.0000.001