So I am creating a html document with html_document in the yalm header with Rmarkdown. I push "knit" in Rstudio and the document gets created, but I get the following message at the end (in the Rmarkdown tab next to the Console and Terminal tabs):
Output created: version2_rapport.html
There were 14 warnings (use warnings() to see them)
But I don't know how to see the warnings... Where and how should I use warnings()? I have tried to type warnings() in the console but nothing happens.
My setup chunk is:
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
```
I don't want messages in my output and I just want to see them i.e. they should not be included in my html file with my graphs etc.
Related
When starting RStudio, this error appears. I can run several commands, but I can't compile anything in Rmarkdown. Does anyone know how I can fix it?
The error does not appear when typing a path to read from the file. It even appears when I try to compile an empty file in RMarkdown.
The error even appears with the default example script in RMarkdown.
---
title: "Untitled"
author: "Autor"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$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.
I have created a word file from an rmarkdown file using redoc output directly in RStudio and clicking "knit". This works fine.
---
title: "Untitled"
output:
redoc::redoc
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## GitHub Documents
This is an R Markdown format used for publishing markdown documents to GitHub. When you click the **Knit** button all R code chunks are run and a markdown file (.md) suitable for publishing to GitHub is generated.
## Including Code
You can include R code in the document as follows:
```{r cars}
summary(cars)
```
but trying to convert it back to Rmd it throws an error. Has anyone else had that?
redoc::dedoc(docx = "test.docx",overwrite = TRUE)
Error in convert_docx_to_md(docx, track_changes, wrap, verbose, md_only) :
lazy-load database '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/R/rmarkdown.rdb' is corrupt
In addition: Warning messages:
1: In convert_docx_to_md(docx, track_changes, wrap, verbose, md_only) :
restarting interrupted promise evaluation
2: In convert_docx_to_md(docx, track_changes, wrap, verbose, md_only) :
internal error -3 in R_decompress1
I am able to knit the following code to PDF. However, it always fails when trying to knit the output to Word (win 10, Rstudio 1.2.5033, R 3.6.2, papaja 0.1.0.9942). I had to delete the papaja header for posting (too much code).
```{r setup, include = FALSE}
library("papaja")
```
# Methods
```{r figure}
plot(cars)
```
The error message reads
Error running filter D:/Boelte/R_library/papaja/rmd/docx_fixes.lua:
[string "--[[..."]:227: Constructor for Emph failed: [string
"--[[..."]:258: attempt to index a nil value (local 'x')
stack traceback: [C]: in function 'error'
..."]:227: in field 'Emph' D:/Boelte/R_library/papaja/rmd/docx_fixes.lua:14: in function 'Image'
Fehler: pandoc document conversion failed with error 83
Is there any way to correct this error? It is a papaja or a pandoc error?
This is a papaja error related to post-processing of the document (in this case styling figure captions) via the docx_fixes.lua-filter. I will try to fix this as soon as possible. For the time being, you should be able to resolve this problem by specifying a figure caption in the chunk options.
```{r setup, include = FALSE}
library("papaja")
```
# Methods
(ref:fig-cap) This is the figure caption.
```{r figure, fig.cap = "(ref:fig-cap)"}
plot(cars)
```
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)
Why in Rmarkdown, if the expression inside try fails, the error message is not printed, even though in chunk error = TRUE. Code is below, which does not print anything:
```{r, error = TRUE}
try(log("a"), silent = FALSE)
```
Use the below code to get the printed output
```{r}
try(log("a"))[1]
```
It will look like this in pdf
Paste the below code in your .rmd file at the start to get the errors and warnings generated in the r chunks to html output or pdf.
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, error = TRUE, warning = TRUE)
```
This is not chunk specific its for all chunks inside .rmd file, this will print all the errors or warnings if any any at all in the r chunks written.
After adding the above chunk, you can knit html or pdf that will also show you the errors and/or warnings if any at all in r chunk.