search

ropensci / babette

babette is an R package to work with BEAST2
https://docs.ropensci.org/babette
GNU General Public License v3.0
44 stars 6 forks source link

Vignette build errro #77

Closed jeroen closed 5 years ago

jeroen commented 5 years ago

Any idea what could cause this?

[command]/bin/bash --noprofile --norc /__w/_temp/68fb0547-66bb-40d8-9bc3-636321dc5e04.sh
* checking for file ‘babette/DESCRIPTION’ ... OK
* preparing ‘babette’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘article.Rmd’ using rmarkdown
--- finished re-building ‘article.Rmd’

--- re-building ‘demo.Rmd’ using rmarkdown
Quitting from lines 96-97 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
'phylos' must be of class 'multiPhylo'
--- failed re-building ‘demo.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
--- finished re-building ‘examples.Rmd’

--- re-building ‘nested_sampling.Rmd’ using rmarkdown
--- finished re-building ‘nested_sampling.Rmd’

--- re-building ‘step_by_step.Rmd’ using rmarkdown
--- finished re-building ‘step_by_step.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
--- finished re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘demo.Rmd’

Error: Vignette re-building failed.
Execution halted

On the docs server this vignette also fails:

Reading 'man/plot_densitree.Rd'
Writing 'reference/plot_densitree.html'
Reading 'man/prepare_file_creation.Rd'
Writing 'reference/prepare_file_creation.html'
Reading 'man/update_babette.Rd'
Writing 'reference/update_babette.html'
── Building articles ───────────────────────────────────────────────────────────
Writing 'articles/index.html'
Reading 'vignettes/article.Rmd'
Writing 'articles/article.html'
Reading 'vignettes/demo.Rmd'
Error : callr subprocess failed: object 'out' not found
Error: callr subprocess failed: callr subprocess failed: object 'out' not found
Execution halted
richelbilderbeek commented 5 years ago

@jeroen:weird! Thanks for letting me know! Will take a look today, before 21:00 (Dutch time) :+1:

richelbilderbeek commented 5 years ago

Note to self: I predict it is because the ropensci build server does not install BEAST2. Will prepare babette (again) to take this into account (as is also needed for CRAN).

richelbilderbeek commented 5 years ago

@jeroen: I think I fixed it. Travis CI is stalling for already quite some time, so I just merged to master in the blind. If the build fails tomorrow, will fix it then :+1: