I'm working on a document with Rmarkdown on RStudio. In that rmd I use shiny runtime and my question is if I could generate some file with that document to open it outside RStudio, just like rmd without shiny runtime which generates an .html.
I was searching but I found nothing, does anyone know some tool to do that?
Many thanks!
Xevi
Related
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!
Hi knitr experts: I cannot for the life of me figure out how to compile the knitr Miminal Demo .Rnw document correctly. When I download and run Yihui's Minimal Demo of knitr .Rnw file (link), the document compiles but incorrectly handles the R chunks:
I changed nothing, just opened and compiled. Help welcome. As an aside, would very much appreciate tips on whether this is how I should be going about adding R code into a latex template that UT-Austin requires for dissertation publication. Thanks.
I can reproduce your PDF file when using Sweave instead of knitr for translating the .Rnw file. When switching to knitr via the RStudio options (c.f. https://support.rstudio.com/hc/en-us/articles/200532247), I get an error message and no PDF, which probably reproduces #r2evans' results in the comments. I also get a warning message that line 19 is Sweave specific (\SweaveOpts{concordance=TRUE}). Removing that line, the file processes with knitr correctly producing
All my codes developed in base R and I don't want to use RStudio, however I want to use rmarkdown feature in base R which is available in Rstudio.
I have downloaded rmarkdown package in base r, but not able to derive a code to publish my work
All the output of my codes written in R should be view able through web browser.
First make sure you're using .Rmd as your file extension. If not, rename it to a .Rmd extension. Make sure you have Pandoc installed on your OS.
Next, add the following to the top of the file:
---
title: "Your notebook title"
output: html_document
---
output: could take any value. You can pass in the value of ioslides_presentation for example if you want but it looks like html_document fits the criteria of what you want pretty well.
Once you have that, write your code in any editor (or the R console if you prefer). Use the code chunks and markdown text formatting as you normally would:
```{r}
plot(1:10)
```
In my base R Console, this is how mynotebook.Rmd looks like:
Finally, use the render() function from rmarkdown. You can either attach it and run render():
library(rmarkdown)
render("mynotebook.Rmd")
Or, run rmarkdown::render("mynotebook.Rmd").
Notice that the use of RStudio is not required at all since Pandoc is the document converter performing this task. For the so inclined, this is what its documentation has to say:
When you run render, R Markdown feeds the .Rmd file to knitr,
which executes all of the code chunks and creates a new markdown (.md)
document which includes the code and it's output.
The markdown file generated by knitr is then processed by pandoc
which is responsible for creating the finished format.
This may sound complicated, but R Markdown makes it extremely simple
by encapsulating all of the above processing into a single render
function.
Once again I am in the situation that I want to replicate what is happening when I press the Compile PDF button on an .Rnw file in RStudio with my own R script.
For example I create a new .Rnw file in RStudio with File > New File > R Sweave. It looks like this:
\documentclass{article}
\begin{document}
\SweaveOpts{concordance=TRUE}
<<echo=F, results=tex>>=
library(xtable)
xtable(mtcars)
#
\end{document}
I inserted a chunk with alt+cmd+i and used the autocompletion to set the chunk options. Hence I assume I did everything with the default settings as RStudio assumes it to be. When I press Compile PDF everything works without problems. But when I execute:
knitr::knit2pdf("Sweave-test.Rnw")
I get an Error "It seems you are using the Sweave-specific syntax". Hence there are additional steps needed.
What I came up with so far is the following:
library(knitr)
tempfile1 <- tempfile(fileext=".Rnw")
Sweave2knitr(file = "input.Rnw", output = tempfile1)
tempfile2 <- tempfile(fileext=".tex")
knit(tempfile1, output=tempfile2)
tools::texi2pdf(tempfile2, clean=T)
system(paste("open", sub(".tex", ".pdf", basename(tempfile2))))
(The last line is OSX specific I think).
But I am curious to know what RStudio is doing exactly. I looked into the RStudio github page but am not sure where to find the command. Other Stackoverlow questions show that there are slight differences between what the button does and knit2pdf. It seems the question has been asked over and over again, also in relation to the Knit Html button. It might use functions from the knitr package, the markdown, the rmarkdown package, texi2pdf from the tools package, Sweave from the utils package or pandoc. I have no Idea...
Related question (that all got some rather vague answers):
Difference: "Compile PDF" button in RStudio vs. knit() and knit2pdf()
Difference between "Compile PDF" and knit2pdf
How to convert R Markdown to HTML? I.e., What does "Knit HTML" do in Rstudio 0.96?
What does “Knit HTML” do in Rstudio 0.98?
Compile .Rnw file with command
How to build Knitr document from the command line
Currently I am using RStudio 1.0.136.
I suspect it is just Sweave to turn a Rnw file into tex file and then calling pdflatex.exe to turn it from a tex file into a pdf file.
Sweave("Sweave-test.Rnw")
system("pdflatex.exe Sweave-test.tex")
And if you encountered a File Sweave.sty not found, you will need to add a path this file in your MiKTeX Options, please see here.
The new version of Rstudio (0.98.932) has many new options including knit to PDF. An article describing the new version has a comment from Dave that says:
...after installing rstudio 0.98.932 I don’t get the little dropdown menu
for knit-pdf or word when editing a .Rmd file.
I'm having the same issue. A helpful response was posted:
It might be that either:
a) You are not running R 3.0 (which is required for RMarkdown v2); or
b) You have a custom markdown renderer defined (markdownToHTML
option). You can check for this by executing:
getOption(“rstudio.markdownToHTML”)
That solved Dave's problem (b), but when I run that command I get NULL
> getOption("rstudio.markdownToHTML")
NULL
Which I assume means I don't have a custom markdown renderer defined. (Previously I did in a cusomized .Rprofile, but I removed that.) My R version is 3.1.0.
Am I misunderstanding the getOption command? Could something else be tripping up my Rstudio?
I have just installed the new version of RStudio (0.98.932), which prompted me to upgrade a couple of packages (I can't remember which, although I see I have knitr 1.6, markdown 0.7 and rmarkdown 0.2.46). At first I had the same problem; there was only a single 'knit' option on the tool bar. I managed to get the ability to knit to .pdf by adding the following to the head of my .Rmd file.
---
title: "Sample Document"
output: pdf_document
---
Having done that, I now find I do have a drop down menu with options to knit to HTML, PDF and word. There's also a little gear icon that provides access to the R Markdown document options that wasn't there before. I have no idea what the problem was but it seems OK now!
Adding on #nicholas response
This is also why I create new .Rmd documents through the RStudio gui
File > New File > R markdown.
This way the YAML header is populated correctly.