Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:11 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rebook on tokay2


To the developers/maintainers of the rebook package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rebook.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1562/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rebook 1.4.0  (landing page)
Aaron Lun
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rebook
git_branch: RELEASE_3_14
git_last_commit: 8c4ac33
git_last_commit_date: 2021-10-26 13:01:49 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: rebook
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rebook.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rebook_1.4.0.tar.gz
StartedAt: 2022-04-13 01:22:40 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:28:27 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 347.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rebook.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rebook.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings rebook_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/rebook.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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
extractCached      0.74   0.07    6.46
scrapeReferences   0.63   0.17   11.25
extractFromPackage 0.01   0.01   11.79
compileChapter     0.00   0.00    5.69
** running examples for arch 'x64' ... 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   0.61   0.11   10.97
extractCached      0.57   0.11    5.38
extractFromPackage 0.04   0.00    5.58
compileChapter     0.00   0.00    5.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/rebook.Rcheck/00check.log'
for details.



Installation output

rebook.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/rebook_1.4.0.tar.gz && rm -rf rebook.buildbin-libdir && mkdir rebook.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rebook.buildbin-libdir rebook_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL rebook_1.4.0.zip && rm rebook_1.4.0.tar.gz rebook_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 42727  100 42727    0     0   177k      0 --:--:-- --:--:-- --:--:--  176k

install for i386

* 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

install for x64

* installing *source* package 'rebook' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rebook' as rebook_1.4.0.zip
* DONE (rebook)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'rebook' successfully unpacked and MD5 sums checked

Tests output

rebook.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\file10ebc25f26b8c" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\rmarkdown-str10ebc7bc25041.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\file10ebc73be7420" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\rmarkdown-str10ebc6a715d47.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.14-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 "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\rmarkdown-str10ebc639a5931.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\file10ebc5a8511f2" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp0a661P\rmarkdown-str10ebc66cd48c5.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 
   6.71    1.06  105.34 

rebook.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\file838873244bdf" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\rmarkdown-str83888714649.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\file8388d0f7c71" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\rmarkdown-str8388460daa3.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --template "C:\Users\biocbuild\bbs-3.14-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 "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\rmarkdown-str8388721649b1.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 "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\file838810cb5fe6" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpuidvUA\rmarkdown-str838816722a.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 
   6.95    1.00  101.61 

Example timings

rebook.Rcheck/examples_i386/rebook-Ex.timings

nameusersystemelapsed
bioc-images000
bookCache0.020.000.02
buildChapterGraph0.220.000.22
chapterPreamble2.530.874.21
collapseStart000
compileChapter0.000.005.69
createMakefile0.050.000.05
createRedirects000
deployCustomCSS0.010.000.01
extractCached0.740.076.46
extractFromPackage 0.01 0.0111.79
link000
openingDetails0.020.000.02
prettySessionInfo0.250.080.67
rmd2id000
scrapeDependencies0.370.000.38
scrapeReferences 0.63 0.1711.25
setupHTML000
updateDependencies0.010.020.03

rebook.Rcheck/examples_x64/rebook-Ex.timings

nameusersystemelapsed
bioc-images000
bookCache0.010.000.02
buildChapterGraph0.210.000.20
chapterPreamble2.590.833.98
collapseStart000
compileChapter0.00.05.3
createMakefile0.050.000.05
createRedirects0.000.020.01
deployCustomCSS000
extractCached0.570.115.38
extractFromPackage0.040.005.58
link0.010.000.01
openingDetails0.020.000.02
prettySessionInfo0.250.040.61
rmd2id000
scrapeDependencies0.280.040.31
scrapeReferences 0.61 0.1110.97
setupHTML000
updateDependencies0.040.000.05