My Rmarkdowns will no longer knit, every file give the same error.
Under the Render window, it says:
Error in library(emo) : there is no package called ‘emo’
Execution halted
However, I have never used a package called emo and that package is certainly not in this empty .Rmd file
I've tried updating R and RStudio, I'm just quite lost. Any guidance would help!
Here is my code, I haven't changed a single thing after opening the new .Rmd. has
---
title: "knitting_test"
author: "XXXXX"
date: "1/20/2022"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
Related
When starting RStudio, this error appears. I can run several commands, but I can't compile anything in Rmarkdown. Does anyone know how I can fix it?
The error does not appear when typing a path to read from the file. It even appears when I try to compile an empty file in RMarkdown.
The error even appears with the default example script in RMarkdown.
---
title: "Untitled"
author: "Autor"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
As the example, if you create a new R markdown file and save it as 'test'. Can one then run or deploy this test.Rmd file from within a normal R script. The purpose being to generate the output in HTML, without having to open the .Rmd file.
I'm hoping to create one master file to do this for many markdown files in one go; which would save considerable time as you then don't have to open many markdown files and wait for each one to complete.
You are looking for rmarkdown::render().
Contents of "test.Rmd"
---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
Contents of script.R
# provided test.Rmd is in the working directory
rmarkdown::render("test.Rmd")
A Way to Render Multiple Rmd
cwd_rmd_files <- list.files(pattern = ".Rmd$")
lapply(cwd_rmd_files, rmarkdown::render)
Thanks the-mad-statter, your answer was very helpful. The issue I faced, required me to prepare markdown dynamically. By adapting your code, that's easily possible:
Contents of "test_dyn.rmd"
---
title: "Untitled"
output: html_document
---
The chunk below adds formatted text, based on your inputs.
```{r text, echo=FALSE, results="asis"}
cat(text)
```
The chunk below uses your input in as code.
```{r results}
y
```
Contents of "script_dyn.r"
in_text <- c("**Test 1**", "*Test 2*")
in_y <- 1:2
lapply(1:2, function(x) {
text <- in_text[[x]]
y <- in_y[[x]]
rmarkdown::render(input = "test_dyn.rmd", output_file = paste0("test", x))
})
Like this you can create files with different text and different variables values in your code.
Here's a reproducible example of PDF Rmarkdown:
---
title: "Untitled"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
I need "This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com."
to be in Calibri font than the default one.
If you are okay with setting the latex engine to xelatex, you can use \fontspec{Calibri} to set the font to Calibri and then \normalfont to return to the default font.
---
title: "Untitled"
output:
pdf_document:
latex_engine: xelatex
---
## R Markdown
\fontspec{Calibri}
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
\normalfont
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
Trying to knit a doc into html, RStudio would hang on the conversion to html part. I looked around and it looked like this happened to other folks when they were using an out of date pandoc version. I updated pandoc to 2.8. I received the error in the title. Looking around again, it appeared that v 2.5 seemed stable. I installed that, restarted my computer, and still get the same error.
repex is the default example when you create an RMarkdown file in RStudio: file -> New file -> R Markdown -> html.
---
title: "repexpandocerror23"
author: "Adam Korejwa"
date: "11/22/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for
authoring HTML, PDF, and MS Word documents. For more details on using R
Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that
includes both content as well as the output of any embedded R code chunks
within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to
prevent printing of the R code that generated the plot.
I have fixed this issue two months ago. Please make sure your rmarkdown version is at least v1.16. Once again, when in doubt, consider updating your packages:
update.packages(ask = FALSE, checkBuilt = TRUE)
I'm getting started with rmarkdown and knitr. In the sample document provided by RStudio, I can successfully use render() to generate an HTML file that views fine in Chrome. However, when I click on the knit button, it generates a .markdown file and then returns the following error without rendering the preview:
Error generating HTML preview for ~/path/to/file/report.rmarkdown system error 2 (The system cannot find the file specified)
I think it's getting hung up at the pandoc stage. Is it possible that RStudio is looking for pandoc in the wrong place? Pandoc was already installed at C:\Program Files (x86)\Pandoc\pandoc.exe, but RStudio installed its own instance at C:\Program Files\RStudio\bin\pandoc\pandoc.exe, so maybe it's looking in the wrong place and/or confusing settings from one with the other?
Any help would be greatly appreciated. Thanks!
And just in case, here's the RMarkdown template I'm starting with:
---
title: "Monthly Report"
author: "Kris Shaffer"
date: "February 17, 2017"
output: html_document
---
```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
R version 3.3.2
RStudio 1.0.136
rmarkdown 1.3
knitr 1.15.1
pandoc 1.17.2 (both installations)
Turns out it was as simple as a file extension. I changed the filename from report.rmarkdown to report.Rmd. Knit works fine now.