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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) (2026-01-15 r89304)
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
BiocBook-editing 2.187  0.309  17.828
BiocBook         0.479  0.138  15.418
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4. │ └─BiocBook:::.add_page(...)
    5. │   └─BiocBook:::.find_path(file.path("pages", file), book)
    6. │     ├─rprojroot::find_root_file(...)
    7. │     │ └─rprojroot::find_root(criterion = criterion, path = path)
    8. │     │   └─rprojroot:::get_start_path(path, criterion$subdir)
    9. │     │     └─base::normalizePath(path, winslash = "/", mustWork = TRUE)
   10. │     │       └─base::path.expand(path)
   11. │     └─BiocGenerics::path(book)
   12. └─base::.handleSimpleError(...)
   13.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 `D5V2L4D1C7` already exists
\ Checking package name availability
Saving _problems/test-BiocBook-10.R
Saving _problems/test-BiocBook-11.R
Saving _problems/test-BiocBook-12.R
Saving _problems/test-BiocBook-13.R
Saving _problems/test-BiocBook-14.R
Saving _problems/test-BiocBook-15.R
Saving _problems/test-BiocBook-19.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-BiocBook.R:10:5'): init work ─────────────────────────────────
Expected `init(tmpdir, .local = TRUE)` not to throw any errors.
Actually got a <rlang_error> with message:
  Package name `D5V2L4D1C7` is considered profanity. Please pick another name for this BiocBook.
── Failure ('test-BiocBook.R:11:5'): init work ─────────────────────────────────
Expected `bb <- BiocBook(tmpdir)` not to throw any errors.
Actually got a <rlang_error> with message:
  The provided path is not a `BiocBook` repository
── Failure ('test-BiocBook.R:12:5'): init work ─────────────────────────────────
Expected `show(bb)` not to throw any errors.
Actually got a <simpleError> with message:
  error in evaluating the argument 'object' in selecting a method for function 'show': object 'bb' not found
── Failure ('test-BiocBook.R:13:5'): init work ─────────────────────────────────
Expected `path(bb)` not to throw any errors.
Actually got a <simpleError> with message:
  error in evaluating the argument 'object' in selecting a method for function 'path': object 'bb' not found
── Failure ('test-BiocBook.R:14:5'): init work ─────────────────────────────────
Expected `chapters(bb)` not to throw any errors.
Actually got a <simpleError> with message:
  error in evaluating the argument 'object' in selecting a method for function 'chapters': object 'bb' not found
── Failure ('test-BiocBook.R:15:5'): init work ─────────────────────────────────
Expected `releases(bb)` not to throw any errors.
Actually got a <simpleError> with message:
  error in evaluating the argument 'object' in selecting a method for function 'releases': object 'bb' not found
── Error ('test-BiocBook.R:19:5'): init work ───────────────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'path': object 'bb' not found
Backtrace:
     ▆
  1. ├─testthat::expect_invisible(add_preamble(bb, open = FALSE)) at test-BiocBook.R:19:5
  2. │ └─base::withVisible(call)
  3. ├─BiocBook::add_preamble(bb, open = FALSE)
  4. │ └─BiocBook:::.add_page(...)
  5. │   └─BiocBook:::.find_path(file.path("pages", file), book)
  6. │     ├─rprojroot::find_root_file(...)
  7. │     │ └─rprojroot::find_root(criterion = criterion, path = path)
  8. │     │   └─rprojroot:::get_start_path(path, criterion$subdir)
  9. │     │     └─base::normalizePath(path, winslash = "/", mustWork = TRUE)
 10. │     │       └─base::path.expand(path)
 11. │     └─BiocGenerics::path(book)
 12. └─base::.handleSimpleError(...)
 13.   └─base (local) h(simpleError(msg, call))

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted