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) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:38 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 1562/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rebook 1.4.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rebook |
| Version: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2022-04-12 17:25:22 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:29:13 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 231.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rebook.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/rebook.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 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 ... 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 9.985 1.178 11.344
extractFromPackage 5.499 0.974 6.608
extractCached 4.490 0.848 5.502
compileChapter 4.486 0.839 5.372
* 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
‘/Users/biocbuild/bbs-3.14-bioc/meat/rebook.Rcheck/00check.log’
for details.
rebook.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rebook ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
rebook.Rcheck/tests/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-apple-darwin17.0 (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
/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/4.1/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpSexOeF/file1561a5f79e47b --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpSexOeF/rmarkdown-str1561a3b877835.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
[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
/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/4.1/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpSexOeF/file1561a4454ecc --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpSexOeF/rmarkdown-str1561a62383544.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
/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/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/4.1/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/RtmpSexOeF/rmarkdown-str1561a7274722a.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
/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/4.1/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpSexOeF/file1561a2736e191 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.1/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpSexOeF/rmarkdown-str1561a4130ab4.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
118.8 18.7 140.0
rebook.Rcheck/rebook-Ex.timings
| name | user | system | elapsed | |
| bioc-images | 0.001 | 0.001 | 0.001 | |
| bookCache | 0.007 | 0.002 | 0.009 | |
| buildChapterGraph | 0.289 | 0.020 | 0.310 | |
| chapterPreamble | 2.626 | 0.619 | 3.370 | |
| collapseStart | 0.000 | 0.000 | 0.001 | |
| compileChapter | 4.486 | 0.839 | 5.372 | |
| createMakefile | 0.046 | 0.003 | 0.049 | |
| createRedirects | 0.003 | 0.001 | 0.004 | |
| deployCustomCSS | 0.000 | 0.001 | 0.002 | |
| extractCached | 4.490 | 0.848 | 5.502 | |
| extractFromPackage | 5.499 | 0.974 | 6.608 | |
| link | 0.004 | 0.000 | 0.005 | |
| openingDetails | 0.006 | 0.001 | 0.006 | |
| prettySessionInfo | 0.443 | 0.057 | 0.524 | |
| rmd2id | 0.001 | 0.001 | 0.003 | |
| scrapeDependencies | 0.432 | 0.013 | 0.446 | |
| scrapeReferences | 9.985 | 1.178 | 11.344 | |
| setupHTML | 0.001 | 0.000 | 0.000 | |
| updateDependencies | 0.040 | 0.003 | 0.043 | |