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documents fail on bookdown 0.23 #380
Description
Summary:
After upgrading the R package bookdown to the 0.23 (the latest), our documents fail to build. I know it builds in 0.18 as that's the previous version I had. See below for the gory details.
This might be an issue with bookdown, but I don't see that anywhere.
Description:
~/github/stan-dev/docs (feature/issue-375-complex-numbers)$ python build.py 2 28 reference-manual html
processing file: _main.Rmd
|......................................................................| 100%
inline R code fragments
output file: _main.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS _main.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output _main.html --email-obfuscation none --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/3.6/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css ../stan-manual.css --include-in-header /var/folders/b3/6h4t41094vz281j7nn48ws900001jv/T//RtmpRHfYjh/rmarkdown-strd100676522e8.html --mathjax --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/latex-div.lua --filter /usr/local/bin/pandoc-citeproc
Output created: _book/index.html
[1] "/Users/bcarpenter/github/stan-dev/docs/src/reference-manual/_book/index.html"
and then
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bookdown_0.18
loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2 knitr_1.28 xfun_0.12
but then after updating:
> install.packages('bookdown')
--- Please select a CRAN mirror for use in this session ---
...
I get this
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bookdown_0.23
loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2 knitr_1.33 xfun_0.25
but the docs fail to build with this error:
~/github/stan-dev/docs (feature/issue-375-complex-numbers)$ python build.py 2 28 reference-manual html
Error: $ operator is invalid for atomic vectors
Execution halted
Command Rscript -e "bookdown::render_book('index.Rmd', output_format='bookdown::gitbook')" failed
Traceback (most recent call last):
File "build.py", line 113, in <module>
main()
File "build.py", line 109, in main
make_docs(docspath, stan_version, doc, formats)
File "build.py", line 54, in make_docs
shexec(command)
File "build.py", line 35, in shexec
raise Exception(returncode)
Exception: 1
Nothing informative in the error other than the line I spaced out. Is there a way to figure out what's going wrong here?
Additional Information:
Provide any additional information here.
Current Version:
v2.18.0
Activity
mitzimorris commentedon Aug 23, 2021
https://stackoverflow.com/questions/68806645/bookdown-0-22-0-23-error-operator-is-invalid-for-atomic-vectors
problem is a bookdown problem. we could pin the version to 0.22. or follow other suggestions in the SO discussion.
bob-carpenter commentedon Aug 23, 2021
@mitzimorris: How do we pin a version of an R package? If the last suggestion in the StackOverflow discussion works for the latest bookdown, I think we should go with that. My reasoning is that it's easier to keep an R package upgraded than downgraded.
mitzimorris commentedon Aug 23, 2021
global namespace of R will make pinning version difficult.
the problem is that the devs at RStudio introduced a breaking change to the yaml config ("_output.yml").
we need to change the header from:
to
(or search engine fuse - they're saying go with fuse).
WardBrian commentedon Oct 26, 2021
Closed by #390