##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BiocBook.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BiocBook_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* this is package ‘BiocBook’ version ‘1.9.0’
* 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 ‘BiocBook’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BiocBook-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocBook
> ### Title: Handling BiocBook directories
> ### Aliases: BiocBook init quick_init BiocBook-class releases chapters
> ###   path,BiocBook-method releases,BiocBook-method
> ###   chapters,BiocBook-method show,BiocBook-method
> 
> ### ** Examples
> 
> ## In practice, you should not use `.local` argument. 
> unique_id <- as.numeric(Sys.time())
> bookname <- paste(Sys.info()[['sysname']], unique_id, sep = '.')
> init(bookname, .local = TRUE)
══ Running preflight checklist ═════════════════════════════════════════════════
⠙ Checking that no folder named `Linux.1764210371.00165` already exists
⠙ Checking package name availability
Error: 
! error in pak subprocess
Caused by error in `if (x) ys else no`:
! missing value where TRUE/FALSE needed
---
Backtrace:
1. BiocBook::init(bookname, .local = TRUE)
2. BiocBook:::.preflight_checks(new_package, skip_availability, .local)
3. base::tryCatch(expr = { …
4. base::tryCatchList(expr, classes, parentenv, handlers)
5. pak::pkg_name_check(name = new_package)
6. pak:::remote(function(...) { …
7. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. asNamespace("pak")$pak_preformat(ret)
 3. base::format(x, ...)
 4. pkgdepends:::format.pkg_name_check(x, ...)
 5. base::unlist(lapply(x, format, limit = limit, ...))
 6. base::lapply(x, format, limit = limit, ...)
 7. base::FUN(X[[i]], ...)
 8. pkgdepends:::format.pkg_name_check_basics(X[[i]], ...)
 9. base::paste0(mark(!x$profanity), if (!x$profanity) "  not a" else " ", …
10. local mark(!x$profanity)
11. base::.handleSimpleError(function (e) …
12. global h(simpleError(msg, call))
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
BiocBook-editing 1.88  0.268   17.46
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BiocBook
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BiocBook’ ...
** this is package ‘BiocBook’ version ‘1.9.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BiocBook)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(BiocBook)
> 
> test_check("BiocBook")
== Running preflight checklist =================================================
\ Checking that no folder named `X9S7S7M8B2` already exists
\ Checking package name availability
v Package name `X9S7S7M8B2` is available
\ Checking package name availability
! Dummy git configured
\ Checking package name availability
* git user: `dummy`
\ Checking package name availability
* git email: `dummy@dummy.com`
\ Checking package name availability
! No GitHub configured
\ Checking package name availability
* github user: NULL
\ Checking package name availability
* PAT: NULL
\ Checking package name availability
== Initiating a new `BiocBook` =================================================
\ Creating new repository from template provided in BiocBook `inst/` directory`
v New local book `X9S7S7M8B2` successfully created
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `inst/assets/_book.yml` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `README.md` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `DESCRIPTION` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
i Please finish editing the `DESCRIPTION` fields, including:
\ Creating new repository from template provided in BiocBook `inst/` directory`
  * Title
\ Creating new repository from template provided in BiocBook `inst/` directory`
  * Description
\ Creating new repository from template provided in BiocBook `inst/` directory`
  * Authors@R
\ Creating new repository from template provided in BiocBook `inst/` directory`
v Filled out `inst/index.qmd` fields
\ Creating new repository from template provided in BiocBook `inst/` directory`
i Please finish editing the `inst/index.qmd` fields, including the `Welcome` section
\ Creating new repository from template provided in BiocBook `inst/` directory`
i The following files need to be committed: 
  * .Rbuildignore
  * .github/
  * DESCRIPTION
  * Dockerfile
  * LICENSE
  * LICENSE.md
  * NAMESPACE
  * README.md
  * inst/
  * vignettes/
v The new files have been commited to the `devel` branch.

-- NOTES -----------------------------------------------------------------------
i If you wish to change the cover picture, please replace the following file:
* inst/assets/cover.png

== Results =====================================================================
v Local `BiocBook` directory successfully created  : X9S7S7M8B2
! This book will be only available in local until a Github remote is set.

# You can connect to the local directory as follows:
  biocbook <- BiocBook('X9S7S7M8B2')

BiocBook object
- local path:
/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2
- remote url:
- Title: X9S7S7M8B2
- Releases(0):
- Chapters(1):
  * Welcome [/inst/index.qmd]
v File created @ `/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/pages/preamble.qmd`
v File created @ `/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/pages/chapter-1.qmd`
v File created @ `/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/pages/chapter1.qmd`
* Edit '/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/assets/_book.yml'
* Edit '/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/assets/book.scss'
* Edit '/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/assets/bibliography.bib'
* Edit '/home/biocbuild/bbs-3.23-bioc/meat/BiocBook.Rcheck/tests/testthat/X9S7S7M8B2/inst/requirements'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  4.742   0.419  24.071