| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:39 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1636/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rebook 1.11.0 (landing page) Aaron Lun
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: rebook |
| Version: 1.11.0 |
| 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/site-library --timings rebook_1.11.0.tar.gz |
| StartedAt: 2023-05-10 01:48:56 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 01:51:58 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 182.2 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/site-library --timings rebook_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rebook.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘rebook/DESCRIPTION’ ... OK
* this is package ‘rebook’ version ‘1.11.0’
* 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 7.274 0.642 7.915
* 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-devel_2023-03-12_r83975-bin/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)
rebook.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "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-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpOAGCzI/file1a7c75628a69ba --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpOAGCzI/rmarkdown-str1a7c75ea02cd.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-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpOAGCzI/file1a7c75670a7557 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpOAGCzI/rmarkdown-str1a7c7555d123a6.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-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/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/RtmpOAGCzI/rmarkdown-str1a7c75596a15a7.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-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpOAGCzI/file1a7c7565afaf78 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --mathjax --include-in-header /tmp/RtmpOAGCzI/rmarkdown-str1a7c751f84d5c2.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
88.734 8.839 97.641
rebook.Rcheck/rebook-Ex.timings
| name | user | system | elapsed | |
| bioc-images | 0.002 | 0.000 | 0.001 | |
| bookCache | 0.005 | 0.000 | 0.004 | |
| buildChapterGraph | 0.166 | 0.012 | 0.178 | |
| chapterPreamble | 1.835 | 0.182 | 2.177 | |
| collapseStart | 0 | 0 | 0 | |
| compileChapter | 2.999 | 0.302 | 3.307 | |
| createMakefile | 0.029 | 0.001 | 0.030 | |
| createRedirects | 0.003 | 0.000 | 0.002 | |
| deployCustomCSS | 0.001 | 0.000 | 0.001 | |
| extractCached | 2.979 | 0.334 | 3.309 | |
| extractFromPackage | 3.831 | 0.389 | 4.233 | |
| link | 0.006 | 0.000 | 0.005 | |
| openingDetails | 0.007 | 0.001 | 0.008 | |
| prettySessionInfo | 0.304 | 0.048 | 0.356 | |
| rmd2id | 0.001 | 0.000 | 0.001 | |
| scrapeDependencies | 0.267 | 0.152 | 0.419 | |
| scrapeReferences | 7.274 | 0.642 | 7.915 | |
| setupHTML | 0 | 0 | 0 | |
| updateDependencies | 0.03 | 0.00 | 0.03 | |