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This page was generated on 2024-02-22 11:38:08 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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

Package 1697/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rebook 1.12.0  (landing page)
Aaron Lun
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/rebook
git_branch: RELEASE_3_18
git_last_commit: bfb9a3f
git_last_commit_date: 2023-10-24 11:24:41 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for rebook on lconway


To the developers/maintainers of the rebook package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rebook
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-02-21 22:30:13 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 22:33:34 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 200.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rebook.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/rebook.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rebook/DESCRIPTION’ ... OK
* this is package ‘rebook’ version ‘1.12.0’
* 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 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 ... WARNING
Undocumented arguments in documentation object 'createMakefile'
  ‘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: '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   7.575  1.315   9.798
extractFromPackage 4.103  1.517   5.902
extractCached      3.371  1.434   5.135
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/rebook.Rcheck/00check.log’
for details.



Installation output

rebook.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)

Tests output

rebook.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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

/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/4.3-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmpm8K9ki/file123727396ea65 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmpm8K9ki/rmarkdown-str1237238f6c82c.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

[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/4.3-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmpm8K9ki/file12372144ec373 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmpm8K9ki/rmarkdown-str123723f01bd6f.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'
/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/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.3-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/Rtmpm8K9ki/rmarkdown-str12372749cb8a7.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

/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/4.3-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmpm8K9ki/file123724e9479e9 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmpm8K9ki/rmarkdown-str1237275cfd84c.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 0 | PASS 115 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  91.36   26.47  124.23 

Example timings

rebook.Rcheck/rebook-Ex.timings

nameusersystemelapsed
bioc-images0.0010.0010.001
bookCache0.0030.0010.005
buildChapterGraph0.2060.0190.226
chapterPreamble2.1891.2173.667
collapseStart000
compileChapter3.2811.3584.831
createMakefile0.0310.0040.035
createRedirects0.0020.0010.004
deployCustomCSS0.0000.0010.002
extractCached3.3711.4345.135
extractFromPackage4.1031.5175.902
link0.0050.0020.007
openingDetails0.0070.0020.008
prettySessionInfo0.3100.0710.458
rmd2id0.0010.0020.001
scrapeDependencies0.2970.0160.316
scrapeReferences7.5751.3159.798
setupHTML000
updateDependencies0.0350.0050.045