Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1702/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rebook 1.16.0  (landing page)
Aaron Lun
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/rebook
git_branch: RELEASE_3_20
git_last_commit: 4109cbb
git_last_commit_date: 2024-10-29 10:49:26 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for rebook on teran2

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: 1.16.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rebook.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rebook_1.16.0.tar.gz
StartedAt: 2024-11-20 08:11:43 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 08:13:45 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 121.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rebook.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:rebook.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings rebook_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘rebook/DESCRIPTION’ ... OK
* this is package ‘rebook’ version ‘1.16.0’
* 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 loading without being on the library search path ... 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.
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/rebook.Rcheck/00check.log’
for details.


Installation output

rebook.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rebook
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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/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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmptfe9fc/file1a0a3b60416840 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmptfe9fc/rmarkdown-str1a0a3b280c96cf.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/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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmptfe9fc/file1a0a3b6e3abe99 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmptfe9fc/rmarkdown-str1a0a3b2a85035e.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/bin/pandoc +RTS -K512m -RTS stub.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output stub.html --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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/Rtmptfe9fc/rmarkdown-str1a0a3b57f2a797.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/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 /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/Rtmptfe9fc/file1a0a3b192ff0b7 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/Rtmptfe9fc/rmarkdown-str1a0a3b4f4e92c4.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 
 37.747   6.814  63.522 

Example timings

rebook.Rcheck/rebook-Ex.timings

nameusersystemelapsed
bioc-images0.0010.0000.001
bookCache0.0020.0010.003
buildChapterGraph0.1170.0100.127
chapterPreamble0.4120.0470.677
collapseStart0.0010.0000.000
compileChapter0.9220.1721.730
createMakefile0.0180.0010.038
createRedirects0.0010.0000.005
deployCustomCSS0.0000.0000.001
extractCached0.9060.1781.998
extractFromPackage1.2110.1942.306
link0.0020.0010.008
openingDetails0.0050.0000.009
prettySessionInfo0.1670.0370.385
rmd2id0.0010.0000.000
scrapeDependencies0.1350.0330.271
scrapeReferences3.8580.6144.808
setupHTML000
updateDependencies0.0130.0020.020