Back to Books build report for BioC 3.17

This page was generated on 2023-10-16 14:00:06 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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 8/8HostnameOS / ArchINSTALLBUILD
SingleRBook 1.10.0  (landing page)
Aaron Lun
Snapshot Date: 2023-10-16 06:45:01 -0400 (Mon, 16 Oct 2023)
git_url: https://git.bioconductor.org/packages/SingleRBook
git_branch: RELEASE_3_17
git_last_commit: 03c23c7
git_last_commit_date: 2023-04-25 09:40:40 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  

BUILD results for SingleRBook on nebbiolo1


To the developers/maintainers of the SingleRBook package:
- 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: SingleRBook
Version: 1.10.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingleRBook
StartedAt: 2023-10-16 07:01:56 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:34:02 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 1926.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingleRBook
###
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* checking for file ‘SingleRBook/DESCRIPTION’ ... OK
* preparing ‘SingleRBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[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'
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.17-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('SingleRBook'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

  Natural language support but running in an English locale

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.

> work.dir <- rebook::bookCache('SingleRBook'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
# 
# 
# processing file: ontology.Rmd
# 1/20                   
# 2/20 [unnamed-chunk-1] 
# 3/20                   
# 4/20 [unnamed-chunk-2] 
# 
# Quitting from lines 25-29 [unnamed-chunk-2] (ontology.Rmd)
# Error in `getCellOnto()`:
# ! could not find function "getCellOnto"
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/SingleRBook/1.10.0/ontology.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted