After I have created a revealjs-presentation in my Rstudio-project, i proceed to open it. This works fine except that I get an error in my browser (Chrome) that pdf.css doesn't exist. Which it doesn't, because the presentation is looking for it in a sub-folder in my project directory. Now, I can add pdf.css according to the path that fails and the presentation works...until I re-run it and the added directory is deleted (I guess the knit process delete the aformentioned sub-folder?)
This is a minor problem but there seems to be something buggy going on here, anyone got any idea what I could do (besides re-installing everything)?
Example at the bottom
---
title: "Untitled"
output: revealjs::revealjs_presentation
---
## R Markdown
This is an R Markdown presentation. 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.
## Slide with Bullets
- Bullet 1
- Bullet 2
- Bullet 3
## Slide with R Code and Output
```{r}
summary(cars)
```
## Slide with Plot
```{r, echo=FALSE}
plot(cars)
```
And this is the folder-tree that's missing (relpath from a given Rstudio project):
Failed to load resource: net::ERR_FILE_NOT_FOUND
/TestRevealJs_files/reveal.js-3.3.0/css/print/paper.css
Where TestRevealJs is the name of the project.
Related
I've been trying to solve some HTML knitting issues. My HTML does not currently allow me to use HTML in the code, and thus I am unable to create tabsets.
However, while trying to solve that issue a new issue occured: My HTML output adds a clickable # behind each # Header.
I use the basic Rmarkdown format:
---
title: "Try"
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:
## Including Plots
And then the output shows me this:
Anyway have any idea how to solve this?
This is a new feature introduced in the current development version of rmarkdown. See the NEWS file for more info. To disable this feature, you may use:
output:
html_document:
anchor_sections: false
I have an R markdown file which I'd like to be available on my corporate Shiny Server.
According to R Markdown: The Definitive Guide I can add runtime: shiny to the YAML metadata at the top of the Rmd file to turn it into a Shiny document. I have done this and it works. If I click "Run Document" in RStudio it will run the Rmd and I will see the report with no problems.
My project is located in the ShinyApps directory where the Shiny Server is looking for apps to serve. When I hit the URL for this project I get the report without any charts. I just get broken image icons where the charts should be. (I am using RStudio Server so it is the exact same files being accessed by RStudio and Shiny Server).
R version 3.4.3, Shiny Server version 1.5.6.875
UPDATE: I have reproduced the behaviour with the simplest possible example. I created a new RStudio project - just a plain project - called TEST located in my ShinyApps directory. Then I created a new R Markdown file, which I called TEST.Rmd. This file is pre-populated with example RMarkdown using the cars and pressure built-in datasets. I changed the YAML header to include runtime: shiny. The RStudio "knit" button is replaced by the "Run Document" button, as expected, and clicking this runs the document and works as expected. Attempting to view the page via the Shiny Server has the same issue whereby the plot is not included; a broken image icon takes its place.
UPDATE 2: As requested, here is the Markdown file. It is literally the sample file generated by RStudio with the addition of runtime: shiny in the YAML header.
---
title: "Test RMarkdown"
author: "Michael Henry"
date: "4/6/2020"
output: html_document
runtime: shiny
---
```{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.
UPDATE 3: So I went hunting around the server looking for a log file for Shiny Server. I do not have any administrator privileges so I've never looked for this before, but I found a log file which included this: /lib64/libpango-1.0.so.0: undefined symbol: g_log_structured_standard. It turns out there is a bug in RHEL which has a fix available so I have put a request in with my administrator to apply the fix. I will report back after this has been applied as to whether it resolved my issue.
UPDATE 4: It turns out my RHEL server is up-to-date; it already has the version of glib2 suggested by the bugfix. The fact that I am still getting this error is therefore something that my administrator is going to escalate to Red Hat.
UPDATE 5: The Red Hat support suggested there was another glib2 so file lying around and it turned out that this was the case. Removing this file resolved the issue!
So, I think you might need to add some extra code to make the markdown application run as you expect in the Shiny Server environment
try wrapping the charts and plots with the following:
renderPlot({})
This gives the server an order to both run the plot and then make it available to the Shiny document. Shiny is a weird thing to straight up R programmers.
You are basically computing and creating things in an R environment and handing them off to a Javascript/HTML one which needs to know in its own language what to do. That renderPlot({}) tells the JS component how to promote the R output to your page.
You can see from this section of the reference document you linked to what the format is and how it is promoted to the page by Shiny.
If you are still stuck after doing this, reach back out and I will try to help trouble shoot!
Searching for the error message: /lib64/libpango-1.0.so.0: undefined symbol: g_log_structured_standard led to a known issue with RHEL whereby there was an older version of glib2 on the system that did not contain the symbol g_log_structured_standard. In my case the server was up-to-date and had the correct version of glib2, but there was another version of this library lying around which was causing the issue.
The moral of the story: search for the log files early and follow the leads contained therein!
I am working within RStudio 1.1.383 using rmarkdown. I am trying to render to Latex a string that is created within a knitr chunk so that it appears as latex code within the document.
So far I have experimented with the 'results=' options in the chunk header and find that results='asis' enables it to be rendered once the document is knitted, but I have not been able to find a way to enable the result to be rendered using the preview feature that allows you to run a single chunk and see the results within the .Rmd editor.
Any help on this matter would be appreciated.
A minimal example is included below that should be copied into a .Rmd file before rendering.
Thanks in advance,
Michael
---
title: "Minimal Example"
output: html_document
---
```{r}
str <- "$$\\alpha \\cdot \\beta = \\delta$$"
# this doesn't show in the preview 'run chunk feature'
cat(str, "\n")
# neither does this
writeLines(str)
```
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.
I opened a new R Markdown file in R studio and got the default small working example.
---
title: "test"
author: "Katharina Zweig"
date: "30. Januar 2016"
output: html_document
---
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}
summary(cars)
```
You can also embed plots, for example:
```{r, echo=FALSE}
plot(cars)
```
Note that the `echo = FALSE` parameter was added to the code chunk to
prevent printing of the R code that generated the plot.
It says, you only need to press the knit button to create an HTML
containg the text, the code and the results of the code. I got some long
error logs that were hardly helpful. Neither did changing the output to
PDF and Word - same result: text was there, code was there, no results of
running the code. By producing the output, the original file vanished.
What is wrong?
When the knit button is used on a file not yet saved, it asks you under which name to save it. The file needs to be saved as an Rmd file - just give no extension and R-Studio will do it right. Then, the file does not vanish and the resulting document contains the results of the r commands. I thought it asked where to save the output and gave it the extension of the output file, i.e., either myfile.html / myfile.pdf / myfile.doc.
In the chunk option try this:
{r, results='asis'}
summary(cars)
You can also embed plots, for example:
{r, echo=FALSE, results='asis'}
plot(cars)
The results = 'asis' command should output the tables and graphs if not please let me know.