##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rebook.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rebook_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rebook.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rebook/DESCRIPTION' ... OK
* this is package 'rebook' version '1.5.0'
* 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   0.40   0.13    8.81
extractCached      0.36   0.12    5.14
extractFromPackage 0.02   0.04    7.94
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/rebook.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rebook
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rebook' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rebook'
    finding HTML links ... done
    bioc-images                             html  
    bookCache                               html  
    buildChapterGraph                       html  
    chapterPreamble                         html  
    finding level-2 HTML links ... done

    collapseStart                           html  
    compileBook                             html  
    compileChapter                          html  
    configureBook                           html  
    createMakefile                          html  
    createRedirects                         html  
    deployCustomCSS                         html  
    extractCached                           html  
    extractFromPackage                      html  
    link                                    html  
    openingDetails                          html  
    prettySessionInfo                       html  
    rmd2id                                  html  
    scrapeDependencies                      html  
    scrapeReferences                        html  
    setupHTML                               html  
    updateDependencies                      html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SPsimSeq' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 2
 $ echo   : logi FALSE
 $ results: chr "asis"

  ordinary text without R code

label: godzilla-1954
  ordinary text without R code

label: unnamed-chunk-2
  ordinary text without R code

label: unref-figure (with options) 
List of 1
 $ fig.cap: chr "BLAH BLAH BLAH"

  ordinary text without R code

label: ghidorah-1964
  ordinary text without R code

label: godzilla-1978
  ordinary text without R code

label: godzilla-2014
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 "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\filea9fc6dbc2b40" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\rmarkdown-stra9fc63ce18e2.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
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 2
 $ echo   : logi FALSE
 $ results: chr "asis"

  ordinary text without R code

label: godzilla-1954
  ordinary text without R code

label: unnamed-chunk-2
  ordinary text without R code

label: unref-figure (with options) 
List of 1
 $ fig.cap: chr "BLAH BLAH BLAH"

  ordinary text without R code

label: ghidorah-1964
  ordinary text without R code

label: godzilla-1978
  ordinary text without R code

label: godzilla-2014
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 "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\filea9fc7259fa" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\rmarkdown-stra9fc1c0b54e6.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'
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

"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 "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "D:\biocbuild\bbs-3.15-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 "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\rmarkdown-stra9fc317b6f84.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
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 2
 $ echo   : logi FALSE
 $ results: chr "asis"

  ordinary text without R code

label: godzilla-1954
  ordinary text without R code

label: unnamed-chunk-2
  ordinary text without R code

label: unref-figure (with options) 
List of 1
 $ fig.cap: chr "BLAH BLAH BLAH"

  ordinary text without R code

label: ghidorah-1964
  ordinary text without R code

label: godzilla-1978
  ordinary text without R code

label: godzilla-2014
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 "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "D:\biocbuild\bbs-3.15-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\filea9fcb9e1d15" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "D:\biocbuild\bbs-3.15-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpigqY35\rmarkdown-stra9fc42e39d7.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 
   3.84    0.85   85.96