Unexplainable error

[xiaodaigh]

Below are the content in my rmarkdown file.

---
title: "Test"
output: rmarkdown::html_vignette
---

` ` ` {r setup, include = FALSE}
remotes::install_github("xiaodaigh/disk.frame", ref="development")
suppressPackageStartupMessages(library(disk.frame))
library(fst)
library(magrittr)
library(nycflights13)
library(dplyr)
library(data.table)

# you need to run this for multi-worker support
# limit to 2 cores if not running interactively; most likely on CRAN
# set-up disk.frame to use multiple workers
if(interactive()) {
  setup_disk.frame()
  # highly recommended, however it is pun into interactive() for CRAN because
  # change user options are not allowed on CRAN
  options(future.globals.maxSize = Inf)  
} else {
  setup_disk.frame(2)
}


knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
` ` `

` ` `{r asdiskframe, cache=TRUE}
library(nycflights13)
library(dplyr)
library(disk.frame)
library(data.table)

# convert the flights data to a disk.frame and store the disk.frame in the folder
# "tmp_flights" and overwrite any content if needed
flights.df <- as.disk.frame(
  flights, 
  outdir = file.path(tempdir(), "tmp_flights.df"),
  overwrite = TRUE)

flights.df
` ` `

` ` `{r, dependson='asdiskframe'}
library(disk.frame)
flights.df %>%
  group_by(carrier) %>% # notice that hard_group_by needs to be set
  summarize(count = n(), mean_dep_delay = mean(dep_delay, na.rm=T)) %>%  # mean follows normal R rules
  collect %>% 
  arrange(carrier)
` ` `

When I Knit it in RStudio I get this error

However, when I run it cell by cell I don't get any error.

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[cderv]

Hello,

It does not seems like a rmarkdown issue. This seems to be an error that comes from one of your chunk. For this kind of general question, you should ask on https://community.rstudio.com or SO as suggested on the issue guide you read https://yihui.org/issue/#got-a-question
There is a broad community there to help you with your questions. It could help find what is going on faster I think.

Hope it helps

[xiaodaigh]

Ok

[cderv]

Hi, I did not meant that you should close... sorry if it felt that way.
I just wanted to advice to ask this question also on a place like community.rstudio.com because there is a much broader audience of helpers there that could contribute to solve this with you.
It seems like an issue at the interaction of rmarkdown, knitr, dplyr, disk.frame and RStudio IDE.

[xiaodaigh]

For reference this is the SO post https://stackoverflow.com/questions/59341040/is-it-possible-to-disable-callr-for-rmarkdown

[xiaodaigh]

Here's the RStudio community post https://community.rstudio.com/t/error-with-callr-not-doing-nse-the-way-disk-frame-does-causing-issue-with-knitting-in-rmarkdown/47401

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