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This page was generated on 2024-05-04 11:36:57 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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 nebbiolo1


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.

raw results


Summary

Package: Pedixplorer
Version: 1.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Pedixplorer_1.0.0.tar.gz
StartedAt: 2024-05-04 02:17:43 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:20:45 -0400 (Sat, 04 May 2024)
EllapsedTime: 182.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Pedixplorer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Pedixplorer.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 5.509  0.056   5.565
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL Pedixplorer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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: x86_64-pc-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 
 32.464   0.634  33.085 
Ran 1/1 deferred expressions

Example timings

Pedixplorer.Rcheck/Pedixplorer-Ex.timings

nameusersystemelapsed
Hints-class0.0140.0000.014
Ped-class0.2440.0520.296
Pedigree-class0.5050.0720.577
Pedixplorer_package000
Rel-class0.010.000.01
Scales-class0.0050.0000.006
align0.6380.0160.654
alignped10.3130.0000.312
alignped20.3400.0080.347
alignped30.2930.0030.296
alignped40.2990.0000.299
ancestors0.0010.0000.001
anchor_to_factor0.0010.0000.001
auto_hint0.1560.0000.157
best_hint0.6150.0320.647
bit_size0.1290.0000.129
check_columns0.0000.0040.003
circfun0.0020.0000.002
descendants0.1310.0000.132
family_check0.220.000.22
find_avail_affected0.9900.0161.005
find_avail_noninform0.2060.0000.206
find_unavailable0.1890.0000.189
fix_parents0.0320.0080.040
generate_aff_inds0.0040.0000.003
generate_border0.0030.0000.002
generate_colors0.1910.0040.194
generate_fill0.0070.0000.008
is_disconnected0.0210.0000.021
is_founder0.0010.0000.000
is_informative0.1530.0000.153
is_parent0.130.000.13
kindepth0.1350.0000.134
kinship0.3390.0200.359
make_famid0.1570.0120.168
min_dist_inf0.1870.0040.190
minnbreast1.6150.0401.654
na_to_length0.0000.0000.001
norm_ped0.0020.0000.002
norm_rel0.0220.0000.021
num_child0.2290.0000.228
ped_to_legdf0.1570.0120.169
ped_to_plotdf0.2520.0000.253
plot-Pedigree-missing-method0.1270.0000.127
plot_fromdf0.4180.0120.430
polyfun0.0020.0000.001
polygons0.0000.0060.006
rel_code_to_factor0.0000.0010.001
sampleped0.4070.0200.427
sex_to_factor0.0010.0000.001
shrink5.5090.0565.565
unrelated0.1830.0000.183
upd_famid_id0.2820.0200.302
useful_inds0.1460.0080.155
vect_to_binary0.0010.0000.001