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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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Pedixplorer.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* 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 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 5.796  0.021   5.823
* 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-3.19-bioc/meat/Pedixplorer.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pedixplorer
###
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* 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)

R version 4.4.0 (2024-04-24) -- "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 
 38.265   1.680  40.216 
Ran 1/1 deferred expressions