##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rebook.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rebook_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rebook/DESCRIPTION’ ... OK
* this is package ‘rebook’ version ‘1.15.0’
* 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 for sufficient/correct file permissions ... 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 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) extractFromPackage.Rd:37: Lost braces; missing escapes or markup?
    37 | It copies the contents of {src.name} into \code{work.dir} and calls \code{\link{extractCached}} on the \code{rmd.name} inside.
       |                           ^
* 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 ... WARNING
Undocumented arguments in Rd file 'createMakefile.Rd'
  ‘pattern’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 in createMakefile(dir) : '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   12.121  1.911  18.980
extractFromPackage  6.695  2.224  11.920
compileChapter      5.743  2.048   8.924
extractCached       5.639  2.138   9.798
chapterPreamble     3.621  1.834   6.515
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rebook
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "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.

> 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

/usr/local/bin/pandoc +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpkT1RiK/file1c745a56e270 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpkT1RiK/rmarkdown-str1c747e2c5565.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
2024-05-02 10:01:42.947 R[28036:434806279] XType: com.apple.fonts is not accessible.
2024-05-02 10:01:42.950 R[28036:434806279] XType: XTFontStaticRegistry is enabled.
output file: test.knit.md

[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

/usr/local/bin/pandoc +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpkT1RiK/file1c741b58c338 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpkT1RiK/rmarkdown-str1c7460789f8e.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'
2024-05-02 10:02:17.392 R[37186:434833300] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:17.393 R[37186:434833300] XType: XTFontStaticRegistry is enabled.
2024-05-02 10:02:24.554 R[39349:434838923] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:24.555 R[39349:434838923] XType: XTFontStaticRegistry is enabled.
2024-05-02 10:02:33.669 R[41620:434845462] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:33.671 R[41620:434845462] XType: XTFontStaticRegistry is enabled.
2024-05-02 10:02:40.718 R[43142:434850050] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:40.719 R[43142:434850050] XType: XTFontStaticRegistry is enabled.
/usr/local/bin/pandoc +RTS -K512m -RTS stub.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output stub.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /tmp/RtmpkT1RiK/rmarkdown-str1c745c626479.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'
2024-05-02 10:02:51.123 R[45470:434857069] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:51.125 R[45470:434857069] XType: XTFontStaticRegistry is enabled.
2024-05-02 10:02:58.095 R[47036:434861796] XType: com.apple.fonts is not accessible.
2024-05-02 10:02:58.097 R[47036:434861796] XType: XTFontStaticRegistry is enabled.


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

/usr/local/bin/pandoc +RTS -K512m -RTS Test-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test-book.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpkT1RiK/file1c745dd75b5 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpkT1RiK/rmarkdown-str1c74e5ac115.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>
2024-05-02 10:04:07.348 R[68053:434923569] XType: com.apple.fonts is not accessible.
2024-05-02 10:04:07.350 R[68053:434923569] XType: XTFontStaticRegistry is enabled.
2024-05-02 10:04:14.157 R[70649:434931338] XType: com.apple.fonts is not accessible.
2024-05-02 10:04:14.159 R[70649:434931338] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
 154.87   40.62  226.49