Back to Books build report for BioC 3.21

This page was generated on 2024-11-25 14:30 -0500 (Mon, 25 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
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 1/10HostnameOS / ArchINSTALLBUILDCHECK
BiocBookDemo 1.5.0  (landing page)
Jacques Serizay
Snapshot Date: 2024-11-25 10:00 -0500 (Mon, 25 Nov 2024)
git_url: https://git.bioconductor.org/packages/BiocBookDemo
git_branch: devel
git_last_commit: 0ee60f5
git_last_commit_date: 2024-10-29 10:08:05 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped

BUILD results for BiocBookDemo on nebbiolo1

To the developers/maintainers of the BiocBookDemo 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: BiocBookDemo
Version: 1.5.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBookDemo
StartedAt: 2024-11-25 10:17:01 -0500 (Mon, 25 Nov 2024)
EndedAt: 2024-11-25 10:18:22 -0500 (Mon, 25 Nov 2024)
EllapsedTime: 81.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBookDemo
###
##############################################################################
##############################################################################


* checking for file ‘BiocBookDemo/DESCRIPTION’ ... OK
* preparing ‘BiocBookDemo’:
* 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.
  Defaulting to 'stub.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[1/6] index.qmd


processing file: index.qmd
1/9               
2/9 [intro]       
3/9               
4/9 [docker]      
5/9               
6/9 [rstudio]     
7/9               
8/9 [session info]
9/9               
output file: index.knit.md



processing file: index.qmd
1/9               
2/9 [intro]       
3/9               
4/9 [docker]      
5/9               
6/9 [rstudio]     
7/9               
8/9 [session info]
9/9               
output file: index.knit.md


[2/6] pages/preamble.qmd

[3/6] pages/Chapter-1.qmd


processing file: Chapter-1.qmd
1/7                  
2/7 [unnamed-chunk-1]
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4/7 [unnamed-chunk-2]
5/7                  
6/7 [unnamed-chunk-3]
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output file: Chapter-1.knit.md



processing file: Chapter-1.qmd
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2/7 [unnamed-chunk-1]
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4/7 [unnamed-chunk-2]
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6/7 [unnamed-chunk-3]
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output file: Chapter-1.knit.md


[4/6] pages/Chapter-2.qmd


processing file: Chapter-2.qmd
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2/31 [unnamed-chunk-1] 
3/31                   
4/31 [unnamed-chunk-2] 
5/31                   
6/31 [unnamed-chunk-3] 
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8/31 [unnamed-chunk-4] 
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12/31 [unnamed-chunk-6] 
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14/31 [unnamed-chunk-7] 
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20/31 [unnamed-chunk-10]
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22/31 [unnamed-chunk-11]
23/31                   
24/31 [unnamed-chunk-12]
running: sh  -c 'find ../ -name "*.qmd"'
25/31                   
26/31 [unnamed-chunk-13]
27/31                   
28/31 [unnamed-chunk-14]
29/31                   
30/31 [unnamed-chunk-15]
31/31                   
output file: Chapter-2.knit.md

Warning messages:
1: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).
2: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).


processing file: Chapter-2.qmd
1/31                   
2/31 [unnamed-chunk-1] 
3/31                   
4/31 [unnamed-chunk-2] 
5/31                   
6/31 [unnamed-chunk-3] 
7/31                   
8/31 [unnamed-chunk-4] 
9/31                   
10/31 [unnamed-chunk-5] 
11/31                   
12/31 [unnamed-chunk-6] 
13/31                   
14/31 [unnamed-chunk-7] 
15/31                   
16/31 [unnamed-chunk-8] 
17/31                   
18/31 [unnamed-chunk-9] 
19/31                   
20/31 [unnamed-chunk-10]
21/31                   
22/31 [unnamed-chunk-11]
23/31                   
24/31 [unnamed-chunk-12]
running: sh  -c 'find ../ -name "*.qmd"'
25/31                   
26/31 [unnamed-chunk-13]
27/31                   
28/31 [unnamed-chunk-14]
29/31                   
30/31 [unnamed-chunk-15]
31/31                   
output file: Chapter-2.knit.md

Warning messages:
1: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).
2: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).

[5/6] pages/Chapter-3.qmd


processing file: Chapter-3.qmd
1/15                  
2/15 [unnamed-chunk-1]
3/15                  
4/15 [unnamed-chunk-2]
5/15                  
6/15 [unnamed-chunk-3]
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8/15 [unnamed-chunk-4]
9/15                  
10/15 [unnamed-chunk-5]
11/15                  
12/15 [unnamed-chunk-6]
13/15                  
14/15 [unnamed-chunk-7]
15/15                  
output file: Chapter-3.knit.md



processing file: Chapter-3.qmd
1/15                  
2/15 [unnamed-chunk-1]
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6/15 [unnamed-chunk-3]
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10/15 [unnamed-chunk-5]
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12/15 [unnamed-chunk-6]
13/15                  
14/15 [unnamed-chunk-7]
15/15                  
output file: Chapter-3.knit.md


[6/6] pages/biocbook-vs-rebook.qmd


processing file: biocbook-vs-rebook.qmd
1/7                  
2/7 [unnamed-chunk-1]
3/7                  
4/7 [unnamed-chunk-2]
5/7                  
6/7 [unnamed-chunk-3]
7/7                  
output file: biocbook-vs-rebook.knit.md



processing file: biocbook-vs-rebook.qmd
1/7                  
2/7 [unnamed-chunk-1]
3/7                  
4/7 [unnamed-chunk-2]
5/7                  
6/7 [unnamed-chunk-3]
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output file: biocbook-vs-rebook.knit.md


pandoc 
  to: latex
  output-file: index.tex
  standalone: true
  toc: true
  number-sections: true
  top-level-division: chapter
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  
metadata
  crossref:
    chapters: true
  documentclass: scrreprt
  papersize: letter
  classoption:
    - DIV=11
    - numbers=noendperiod
  header-includes:
    - '\KOMAoption{captions}{tableheading}'
  block-headings: true
  knitr:
    opts_chunk:
      collapse: true
      comment: '## '
      cache: false
      fig.align: center
      python.reticulate: false
      R.options:
        dplyr.print_min: 6
        dplyr.print_max: 6
        pillar.max_footer_lines: 2
        pillar.min_chars: 15
        stringr.view_n: 6
        pillar.bold: true
        width: 77
  title: Write Quarto books with Bioconductor
  

Rendering PDF
running xelatex - 1
command xelatex not found, attempting install
finding package for xelatex
> 1 package to install
> installing xelatex (1 of 1)
ERROR: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/biocbuild/texmf
tlmgr: user mode not initialized, please read the documentation!


Stack trace:
TLPDB: not a directory, not loading: /home/biocbuild/texmf
tlmgr: user mode not initialized, please read the documentation!

    at Object.onComplete (file:///opt/quarto/bin/quarto.js:92847:64)
    at eventLoopTick (ext:core/01_core.js:153:7)
    at async renderFiles (file:///opt/quarto/bin/quarto.js:78077:16)
    at async renderProject (file:///opt/quarto/bin/quarto.js:78479:25)
    at async Command.actionHandler (file:///opt/quarto/bin/quarto.js:83077:32)
    at async Command.execute (file:///opt/quarto/bin/quarto.js:8017:13)
    at async Command.parseCommand (file:///opt/quarto/bin/quarto.js:7907:20)
    at async quarto (file:///opt/quarto/bin/quarto.js:118224:9)
    at async file:///opt/quarto/bin/quarto.js:118244:9
    at async mainRunner (file:///opt/quarto/bin/quarto.js:118128:9)
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted