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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1668/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rebook 1.15.0  (landing page)
Aaron Lun
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/rebook
git_branch: devel
git_last_commit: 1e4823e
git_last_commit_date: 2024-04-30 11:26:07 -0400 (Tue, 30 Apr 2024)
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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for rebook on palomino4

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: 1.15.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rebook.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rebook_1.15.0.tar.gz
StartedAt: 2024-06-10 08:01:14 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:11:12 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 597.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rebook.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rebook.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rebook_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
chapterPreamble    2.72   5.55   10.58
scrapeReferences   0.41   0.28   30.86
extractCached      0.42   0.18   16.36
extractFromPackage 0.03   0.05   17.19
compileChapter     0.00   0.01   16.34
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck/00check.log'
for details.


Installation output

rebook.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rebook
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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)

Tests output

rebook.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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-3.20-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\file2221440ed79b9" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.20-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\rmarkdown-str222146edd5103.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-3.20-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\file2221412775d70" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.20-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\rmarkdown-str2221468f46849.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-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "F:\biocbuild\bbs-3.20-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-3.20-bioc\tmpdir\RtmpYj5S9D\rmarkdown-str2221463407bd3.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-3.20-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --lua-filter "F:\biocbuild\bbs-3.20-bioc\R\library\rmarkdown\rmarkdown\lua\anchor-sections.lua" --metadata-file "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\file222145cae5d84" --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template "F:\biocbuild\bbs-3.20-bioc\R\library\bookdown\templates\gitbook.html" --highlight-style pygments --number-sections --mathjax --include-in-header "F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpYj5S9D\rmarkdown-str222147853824.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 (3) ═══════════════════════════════════════════════════════════
• On Windows (3): 'test-cache.R:77:5', 'test-compile-book.R:33:5',
  'test-extract-package.R:64:5'

[ FAIL 0 | WARN 6 | SKIP 3 | PASS 108 ]
> 
> proc.time()
   user  system elapsed 
   5.06    9.54  305.42 

Example timings

rebook.Rcheck/rebook-Ex.timings

nameusersystemelapsed
bioc-images0.000.020.02
bookCache0.000.030.03
buildChapterGraph0.170.720.92
chapterPreamble 2.72 5.5510.58
collapseStart000
compileChapter 0.00 0.0116.34
createMakefile0.030.000.06
createRedirects0.000.020.03
deployCustomCSS0.000.000.02
extractCached 0.42 0.1816.36
extractFromPackage 0.03 0.0517.19
link0.020.000.01
openingDetails0.010.000.02
prettySessionInfo0.160.811.95
rmd2id0.000.000.02
scrapeDependencies0.450.040.48
scrapeReferences 0.41 0.2830.86
setupHTML000
updateDependencies0.030.010.06