There are some things that I run into fairly frequently (and some not so much) when I’m rendering my R Markdown documents. This section details some the common problems, and the solution that I have found works for me.
If you want to practice on fixing broken rmarkdown documents, check out some pathologically broken examples on GitHub at njtierney/rmd-errors.
To avoid problems in the first place, I try and do the following:
Then, if there is an error:
What follows from here are all the errors you might in an R Markdown document, with the following structure:
What it might look like
Chunks like this:
```{r title-one}
```
```{r title-one}
```
The error message
This is caught before the document compiles with a warning like:
processing file: common-problems.Rmd
Error in parse_block(g[-1], g[1], params.src) :
duplicate label 'title-one'
Calls: local ... process_file -> split_file -> lapply -> FUN -> parse_block
Execution halted
Error in Rscript_render(f, render_args, render_meta) :
Failed to compile common-problems.Rmd
Calls: <Anonymous> ... render_book -> render_new_session -> Rscript_render
Execution halted
The important part to note is the start:
.
.
.
Error in parse_block(g[-1], g[1], params.src) :
duplicate label 'title-one'
.
.
.
How to solve
What it might look like
plot(my_table)
my_table <- table(mtcars$cyl)
The error message
How to solve
What it might look like
The error message
How to solve
What it might look like
The error message
processing file: rstudio.Rmd
(*) NOTE: I saw chunk options "fig-rstudio-workspace-options, fig.cap = "Setting the options right for rstudio, so you don't restore previous sessions work, and don't save it either."
please go to https://yihui.name/knitr/options
(it is likely that you forgot to quote "character" options)
Error in parse(text = code, keep.source = FALSE) :
<text>:1:51: unexpected INCOMPLETE_STRING
1: alist( 'fig-rstudio-workspace-options', fig.cap = "Setting the options right for rstudio, so you don't restore previous sessions work, and don't save it either. )
How to solve it?
"fig.cap = "Setting the options right for rstudio, so you don't restore previous sessions work, and. I search for the partial string because there might be parts at the end of the error message that aren’t in the text.What it might look like
The error message
processing file: figures-tables-captions.Rmd
(*) NOTE: I saw chunk options "read-gapminder include = FALSE, echo = FALSe"
please go to https://yihui.name/knitr/options
(it is likely that you forgot to quote "character" options)
Error in parse(text = code, keep.source = FALSE) :
<text>:1:23: unexpected symbol
1: alist( read-gapminder include
^
How to solve
This error message is pretty good, I needed to add a comma after my chunk name.
So, go from:
``{r read-gapminder include = FALSE, echo = FALSE}
gapminder <- readr::read_csv(here::here("data", "gapminder.csv"))
```
to
``{r read-gapminder, include = FALSE, echo = FALSE}
gapminder <- readr::read_csv(here::here("data", "gapminder.csv"))
```
What it might look like
The error message
How to solve
These are often not an error, but you just won’t get the behaviour that you expect.
What it might look like
fig.caption instead of fig.cap. This once caused me to rewrite a lot of code and an entire section of a paper until I realised the problem.The error message
How to solve
knitr to solveSo this is when you provide the wrong input to your chunk options. Like something that requires TRUE gets “yes”, or something that needs "100%" instead gets 100
What it might look like
The error message
Quitting from lines 31-32 (figures-tables-captions.Rmd)
Error in eval(x, envir = envir) : object 'FALSe' not found
Calls: local ... process_group.block -> call_block -> eval_lang -> eval -> eval
Execution halted
Error in Rscript_render(f, render_args, render_meta) :
Failed to compile figures-tables-captions.Rmd
Calls: <Anonymous> ... render_book -> render_new_session -> Rscript_render
Execution halted
How to solve
What was the problem? Turns out I provided the option FALSe instead of FALSE.
Go from:
``{r read-gapminder include = FALSE, echo = FALSe}
gapminder <- readr::read_csv(here::here("data", "gapminder.csv"))
```
to
``{r read-gapminder, include = FALSE, echo = FALSE}
gapminder <- readr::read_csv(here::here("data", "gapminder.csv"))
```
![]() don’t work.I often forget that it is , and not ![]("path/to/image"). There are no quote marks!
There is no panacea for LaTeX errors, but if you aren’t familiar with “what that error message” might look like, here are some details.
What it might look like
The error message
How to solve
… Like for a book on using R Markdown or something.
Check out this great blog post by T. Hovorka from R Views
It boils down to this:
`` `r "\u0060r expression\u0060"` ``.
What it might look like
You create a figure,
The error message
There isn’t one - you just get \@ref(fig:figure-chunk-name) printed.
How to solve
You need to make sure that you actually print the table or plot. If you create the plot and save it, but do not print it in the document, then you will not be able to reference the plot or table.