bookdown でのビルド時エラー

ysaito8015 commented 1 year ago

bookdown でビルドしているときに、下記のエラーに遭遇しますこのエラーは、すべての Rmd ファイルをビルドする際に発生し、gis.Rmd のみを bookdown ビルドするときは発生しません gis.Rmd のみを knit する場合もこのエラーは発生しません。

実行コマンド

bookdown::render_book(input = '.', output_format = 'bookdown::bs4_book', clean = TRUE, config_file = '_bookdown.yml')

label: unnamed-chunk-943
Quitting from lines 20951-20955 (_main.Rmd) 
Error: A data frame is not a valid object for this function.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Registered S3 method overwritten by 'ape':
  method   from 
  plot.mst spdep

もしくは

label: unnamed-chunk-944
Quitting from lines 20962-20966 (_main.Rmd) 
Error in find_formula.data.frame(x, verbose = FALSE) : 
  A data frame is not a valid object for this function.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

該当 chunk ./new_pages/gis.Rmd

# ADM3 level clean
sle_adm3 <- sle_adm3_raw %>%
  clean_names() %>% # 列名の標準化
  filter(admin2name %in% c("Western Area Urban", "Western Area Rural")) # 特定の地域を残してフィルター

環境１ version R version 4.2.1 (2022-06-23 ucrt) os Windows 10 x64 (build 19044) system x86_64, mingw32 ui RStudio language (EN) collate English_United Kingdom.utf8 ctype English_United Kingdom.utf8 tz Asia/Tokyo date 2022-09-21 rstudio 2022.07.1+554 Spotted Wakerobin (desktop) pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)

環境２ -> docker image version R version 4.2.1 (2022-06-23) os Ubuntu 20.04.5 LTS system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Etc/UTC date 2022-09-22 pandoc 2.18 @ /usr/local/bin/pandoc

ysaito8015 commented 1 year ago

Fix it with using package_name::function in gis.Rmd

ironwest commented 1 year ago

There is no problem in Netlify page. Merge.

appliedepi / epiRhandbook_jp

bookdown でのビルド時エラー #91