| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:24 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 1619/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rebook 1.9.0 (landing page) Aaron Lun
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: rebook |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rebook.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rebook_1.9.0.tar.gz |
| StartedAt: 2023-02-07 12:58:31 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 13:01:40 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 189.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rebook.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rebook.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rebook_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rebook.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘rebook/DESCRIPTION’ ... OK
* this is package ‘rebook’ version ‘1.9.0’
* 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 7.496 0.503 8.019
* 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 ...
‘userguide.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.17-bioc/meat/rebook.Rcheck/00check.log’
for details.
rebook.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rebook ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
rebook.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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/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 /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpsNWCns/file3bde616c484ff0 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpsNWCns/rmarkdown-str3bde61efae33c.html
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'Test-book' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
processing file: test.Rmd
output file: test.knit.md
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'Test-book' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
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 /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpsNWCns/file3bde611edfe83c --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpsNWCns/rmarkdown-str3bde613c464530.html
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'Test-book' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
/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 /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.17-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 /tmp/RtmpsNWCns/rmarkdown-str3bde613dc73027.html
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'stub.knit' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
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 /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpsNWCns/file3bde613a07cc5c --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpsNWCns/rmarkdown-str3bde617f938e17.html
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'Test-book' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
<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
92.766 7.753 101.491
rebook.Rcheck/rebook-Ex.timings
| name | user | system | elapsed | |
| bioc-images | 0.001 | 0.000 | 0.001 | |
| bookCache | 0.005 | 0.000 | 0.006 | |
| buildChapterGraph | 0.184 | 0.004 | 0.190 | |
| chapterPreamble | 1.965 | 0.231 | 2.334 | |
| collapseStart | 0 | 0 | 0 | |
| compileChapter | 3.233 | 0.277 | 3.529 | |
| createMakefile | 0.030 | 0.004 | 0.034 | |
| createRedirects | 0.002 | 0.000 | 0.002 | |
| deployCustomCSS | 0.001 | 0.000 | 0.000 | |
| extractCached | 3.229 | 0.364 | 3.634 | |
| extractFromPackage | 4.061 | 0.336 | 4.422 | |
| link | 0.004 | 0.000 | 0.004 | |
| openingDetails | 0.007 | 0.000 | 0.006 | |
| prettySessionInfo | 0.360 | 0.022 | 0.384 | |
| rmd2id | 0.001 | 0.000 | 0.001 | |
| scrapeDependencies | 0.267 | 0.008 | 0.276 | |
| scrapeReferences | 7.496 | 0.503 | 8.019 | |
| setupHTML | 0 | 0 | 0 | |
| updateDependencies | 0.031 | 0.000 | 0.031 | |