[Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

Witold Wolski wew @end|ng |rom |gcz@ethz@ch
Mon Nov 22 11:16:33 CET 2021

Dear Andrew,

Thanks for your suggestion.
Loading the data explicitly in the markdown instead of the YAML section 
- appeals to me. It is desirable to show the code in the vignette if the 
vignette loads it.

However, I would like not to display the code if I pass the data using 
the params argument of the `render` function.

Therefore, I thought about the following code, which unfortunately 
Errors with BiocCheck.

```{r data-fonfig, include=FALSE}
evalAll <- is.null(params$data)
if(!evalAll ){
	data <- params$data

```{r eval = evalAll}
data(data_ionstar, package = "prolfqua")
data <- data_ionstar$data

Running BiocCheck produces:
* Checking library calls...
Error in eval(x, envir = envir) : object 'evalAll' not found

Best regards

On 19/11/2021 17:00, McDavid, Andrew wrote:
> How about in the YAML:
> params:
>    configuration: NULL
>    project_conf: NULL
>    data: NULL
> Then in the first chunk something like:
> ```{r data-config}
> if(is.null(params$data)){
> data(data_ionstar, package = "prolfqua")
>   data =  data_ionstar
> configuration = data$filtered()$config
> }
> ```
> You can use a more ornate expression for these parameters when rendering 
> otherwise `rmarkdown::render()`, which I suppose you could call from a 
> Makefile if needed when rendering package the vignettes.
> Andrew McDavid
> Biostatistics and Computational Biology
> University of Rochester Medical Center
>> On Nov 19, 2021, at 6:00 AM, bioc-devel-request using r-project.org 
>> <mailto:bioc-devel-request using r-project.org> wrote:
>> If anyone wonders, why do I need it. By this I can reuse the vignette
>> with a different dataset.

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