##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rebook.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings rebook_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/rebook.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rebook/DESCRIPTION' ... OK
* this is package 'rebook' version '1.8.0'
* 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 whether package 'rebook' 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 R 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 ... 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 ... WARNING
Found the following significant warnings:

  Warning: 'createMakefile' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
scrapeReferences   0.47   0.23    9.02
extractCached      0.39   0.11    6.24
extractFromPackage 0.00   0.03    6.58
compileChapter     0.00   0.02    5.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'F:/biocbuild/bbs-3.16-bioc/meat/rebook.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL rebook
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'rebook' ...
** using staged installation
** R
** 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 (rebook)

R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> library(testthat)
> library(rebook)
> test_check("rebook")
<button class="rebook-collapse">View set-up code (Chapter \@ref(test-chapter))</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"
```

</div>
<button class="rebook-collapse">View set-up code (Chapter \@ref(test-chapter))</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!

#--- godzilla-1978 ---#
godzilla <- "rawr rawr"
mechagodzilla <- "beep beep"

#--- godzilla-2014 ---#
godzilla <- "I'm back."
muto <- "Hi."
```

</div>


processing file: test.Rmd
output file: test.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\file1167c519153e0" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\rmarkdown-str1167c2a0c72d1.html" 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'Test-book'


processing file: test.Rmd
output file: test.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\file1167c77952bed" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\rmarkdown-str1167c1a3a3343.html" 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'Test-book'
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS stub.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output stub.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\rmarkdown-str1167c2b9d6f06.html" 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.knit'


processing file: test.Rmd
output file: test.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\file1167c18eb4945" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.16-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\Rtmp2xr2mj\rmarkdown-str1167c48d63927.html" 
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'Test-book'
<button class="rebook-collapse">View set-up code</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!
```

</div>
<button class="rebook-collapse">View set-up code</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!
```

</div>
<button class="rebook-collapse">View set-up code</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!
```

</div>
<button class="rebook-collapse">View set-up code</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!
```

</div>
<button class="rebook-collapse">View set-up code</button>
<div class="rebook-content">

```r
#--- godzilla-1954 ---#
godzilla <- "RAWR!"

#--- ghidorah-1964 ---#
godzilla <- "GAO GAO"
ghidorah <- "pew pew"
mothra = "Oh, I'm not in this one." # WRONG!
```

</div>
[ FAIL 0 | WARN 6 | SKIP 3 | PASS 108 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (3)

[ FAIL 0 | WARN 6 | SKIP 3 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
   4.76    1.87   96.81