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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocBook.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocBook_1.2.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘BiocBook/DESCRIPTION’ ... OK
* this is package ‘BiocBook’ version ‘1.2.0’
* 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 4.983  0.510  27.771
BiocBook         0.473  0.087  14.574
* 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: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BiocBook
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘BiocBook’ ...
** 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 version 4.4.0 (2024-04-24) -- "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/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 `L2Z1D0W8Y4` already exists
\ Checking package name availability
v Package name `L2Z1D0W8Y4` 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 `L2Z1D0W8Y4` 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  : L2Z1D0W8Y4
! 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('L2Z1D0W8Y4')

BiocBook object
- local path:
/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4
- remote url:
- Title: L2Z1D0W8Y4
- Releases(0):
- Chapters(1):
  * Welcome [/inst/index.qmd]
v File created @ `/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/pages/preamble.qmd`
v File created @ `/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/pages/chapter-1.qmd`
v File created @ `/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/pages/chapter1.qmd`
* Edit '/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/assets/_book.yml'
* Edit '/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/assets/book.scss'
* Edit '/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/assets/bibliography.bib'
* Edit '/home/biocbuild/bbs-3.19-bioc/meat/BiocBook.Rcheck/tests/testthat/L2Z1D0W8Y4/inst/requirements'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 10.096   0.734  35.071