blogdown problem with Hugo update

blazingarrow · June 20, 2019, 2:46am

I previous used Hugo 0.38.2 with R 3.4.0 to build my website. Everything worked fine until I accidentally updated to Hugo 0.55.6 in R 3.6.0 and updated several packages. So I downgraded my Hugo version to 0.38.2 and ran into the following error while trying to build the same website (exactly the same project) in R 3.4.0. My Rstudio version is 1.2.1335.

I guess the problem might be the update of several packages. Does anyone know what the following error message mean? Thanks a lot!

==> rmarkdown::render_site(encoding = 'UTF-8')

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'sans_ext' not found
Calls: ... build_site -> build_rmds -> by_products -> ::: -> get
Execution halted

Exited with status 1.

jrlewi · June 20, 2019, 4:06am

Hi @blazingarrow - maybe checkout:

github.com/hadley/ggplot2-book

sans_ext error

opened 05:15AM - 25 Jan 19 UTC

closed 04:04PM - 15 Jun 19 UTC

thatchermo

Hi. In attempting to build the book, I ran into this error: object 'sans_ext' n…ot found that occurred in common.R associated to the line that reads "{", knitr:::sans_ext(x), "}", (about line 92, I believe) With the caveat that I know very little, it looks like it's trying to use a private function from the knitr package that would remove a file name extension, but that function doesn't seem to exist? I got a lot farther in building by loading the package xfun and using its version of sans_ext in common.R. Or maybe I totally misunderstand the situation...

and

github.com/hadley/ggplot2-book

Minimal changes to produce passing travis build

hadley:master ← djnavarro:clean_build

opened 10:42PM - 14 Jun 19 UTC

djnavarro

+48 -15850

This aim here is to allow the ggplot2 book to build cleanly on travis. It still …uses `oldbookdown` and makes almost no changes to any R code shown in the book (the only exceptions being those caused by changes to the `USAboundaries` and `scales` packages since publication of the 2nd edition). ### changes that alter the code (or output) shown to reader - The back transformation example in position.rmd produces several pages of warnings about `NaN` values. These are now suppressed in the knitr chunk on line 446 - In scales.Rmd there are a couple of cases where the interface to `scales::unit_format()` etc has changed, so the arguments to `scales::unit_format()` and `scales::dollar_format()` are now named explicitly (I think the dollar one may be unnecessary) - palette names in the `wesanderson` package have changes since second edition to the book. These are all updated now (e.g. Zissou is now Zissou1). - The `USAboundaries` package has changed in two respects since ggplot2 2nd ed: it now generates an sf object, and the underlying data is in the `USAboundariesData` package on ropensci. Lines 685-687 of toolbox.rmd make minimal changes to the R code in the book. ### changes that manage dependencies etc - The DESCRIPTION file lists new package dependencies (mostly linked to the dependency on the `sf` package), and travis.yml includes lines for sources, repos and packages needed to build sf on travis. - The existing source produces odd method dispatch for `select`. Rather than edit the code in the book, I've used `conflicted::conflict_prefer()` to manage this in the common.R script, explicitly preferring `dplyr::select()`. (Ditto for `tidyr::extract()`) - In the render-tex.R file, I've added a dummy version of the `tex_chapter()` function that mirrors `oldbookdown::tex_chapter()` but now uses `"--top-level-division=chapter"` as an argument to pandoc. (Presumably this will be irrelevant when moving to new bookdown) - In ggplot2-book.tex, I've defined commands for `OperatorTok` and `ControlFlowTok`. The inserted commands don't do anything, but the .tex files generated by current version of pandoc now include those - The common.R script now calls `tools::file_path_sans_ext()` in place of the (now deleted) internal `knitr:::sans_ext()` function. ### miscellaneous - for no particularly good reason the repository is reset to the "clean" state so the generated tex files for each chapter are deleted. - travis log for the current build: https://travis-ci.org/djnavarro/ggplot2-book/jobs/545943102 - I'm still learning the etiquette of making a PR. My apologies in advance if something is awry! - just in case :-) "I assign the copyright of this contribution to Hadley Wickham"

From these - my guess in that the function knitr:::sans_ext is no longer available. Maybe run sessionInfo() in the console to find out what version on knitr you have. My guess is your version no longer has it. Not sure what the best fix is at this point... you could revert back to an older version of knitr or get the xfun package as the post suggests and then see if you can build your site. The knitr version I currently have is 1.20 and it still has the sans_ext function.

apreshill · June 20, 2019, 4:40am

Hi there,

To be clear, you show yourself using rmarkdown::render_site() on a blogdown site? With a blogdown site, you cannot use that function. You'll need to use the serve site function, described in the book:

blazingarrow · June 20, 2019, 2:36pm

@jrlewi Thank you so much for pointing me to this direction! The function 'sans_ext' was indeed removed from the 'knitr' package. I downgraded both 'knitr' and 'rmarkdown' packages, and it worked!

I have one error message but it does not seem to affect the website. The error message is:

Error in as.vector(x, "character") :
cannot coerce type 'environment' to vector of type 'character'

I tried old version of 'xfun' but it didn't solve the above problem. I cannot use old versions of 'later' and 'httpuv' because serve_site seems to force me to use the latest 'httpuv' and 'later' packages.

Your advice saved me lots of time.

blazingarrow · June 20, 2019, 2:41pm

Hi Alison,
Use serve site function gave the following error message:

blogdown:::serve_site()
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'loadable' not found

I downgraded the knitr and rmarkdown packages to make it work.

BTW, most of my knowledge about blogdown and netlify comes from your blog post. Thank you for sharing the knowledge!

blazingarrow · June 22, 2019, 1:43am

I also replaced Rstudio with an old version 1.1.463. The error message about "as.vector()" is gone. Looks like everything is fixed.

system · July 13, 2019, 1:43am

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