When I run my Rmarkdown program interactively chunk-by-chunk, the program runs successfully without errors, however, when I try to knit it, I get this error message:
Error in dirname(name) : path too long
Any ideas what could be causing this?
If you get this error message, check the length of your code chunks in your Rmarkdown code. I was getting the above error because one of my chunks were named as follows:
```{r additional descriptives and other statistical tests tests,echo=FALSE,message=FALSE,warning=FALSE}
Through trial and error, I found out the maximum length for the code chunk description is 48 characters. As long as the description has 48 or fewer characters, this error will not get triggered.
Related
I am getting an error message while running knit to HTML. But If I run chunk individually, it draws plot as expected.
What would be a problem? The error message is below:
Quitting from lines 270-274 (HC_FC_indivisual_cellline_fdr_1%.Rmd)
Error in png(..., res = dpi, units = "in") : invalid 'filename' Calls:
... in_dir -> plot2dev -> do.call -> -> png
Execution halted
The described error also occurs, when you are knitting plots within named code chunks, and the name of the chunk does not lead to a valid path name during knitting process.
That is, during the knitting process the plots are written into a temporary path which contains the name of the code chunk, ergo this name should contain only characters that are valid for path names. One should avoid to use white characters for chunk names as well.
I ran into the same issue. I ran this right before my first plot in the chunk and it solved it for me
dev.off()
hope this helps.
I had the same problem. I updated R to the latest version and also RStudio. Install the required packages for the knit and then everything became fine.
Adding 'dev.off()' can solve the problem for knitting but will cause another problem and does not show the plots in the HTML file.
I am testing RMarkdown for the first time and am running into an issue when trying to knit anything to HTML. For example: I attempt to knit the following to HTML
# Say Hello to markdown
Markdown is an **easy to use** format for writing reports. It resembles what you naturally write every time you compose an email. In fact, you may have already used markdown *without realizing it*. These websites all rely on markdown formatting
* [Github](www.github.com)
* [StackOverflow](www.stackoverflow.com)
* [Reddit](www.reddit.com)
The above is taken directly from an example on this page: http://rmarkdown.rstudio.com/articles_intro.html
However, when I use the Knit to HTML button I receive this error:
Error: object 'a' not found
Execution halted
Maybe this is a simple question that I am not seeing the answer to, but I do not know how to interpret and correct this error message, as nowhere in my Markdown file am I calling any sort of object 'a'. Thank you for your assistance!
I'm new to Shiny and I was just trying to see what's the result gonna look like and test out different data sets. I entered the code provided by Diego Lescano, you can find the full script here, http://datascienceplus.com/how-to-create-a-twitter-sentiment-analysis-using-r-and-shiny/
Everything ran through smoothly, however I wasn't able to see the final graph when I tried to knit. Instead, I received the following warning
output file: Final_Project.knit.md
Error: path for html_dependency not provided
Execution halted
I tried to knit to pdf and word as well, it all failed. Here's what my output looked like
output:
html_document: default
I get an error message when running the code below which is expected - I would like this to be ran and displayed in the pdf, however the error is returned in r and the code doesn't run.
{r, warning=TRUE}
library(survey)
debug(withReplicates.svyrep.design)
I have tried warning=TRUE but this doesn't work.
How can I get the error displayed in the document?
Add error=TRUE to the chunk options. That will result in the script running to completion with the error appearing in the output.
I ran Compile PDF using RStudio with knitr on my document. I then received the error
Line 2333 Error in FUN(left, right) : non-numeric argument to binary operator
I understand where this error can normally occur. However, in this instance I cannot.
Running the purled version of the knitr script produces no errors. That is, there are no problems with the R chunks.
There is no R code on line 2333 of the .Rnw file. Only pure LaTeX. Replacing the LaTeX code with a % produces the same error (and on the same line).
When I comment out the previous lines, I get the same error, always on the line just before the commented-out line.
What should I do to diagnose this problem?
The error was in an inline (\Sexpr) function in a subsequent line of the knitr file.