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

[Marcel Ramos]

Hi Witold,

I am not sure what the use case is for loading data in the yaml header.
If you're swapping out data for your vignettes, perhaps your introduction
chunks could contain the code to load the data.

In any case, I recommend that you use `data("dataset", package = "package")`
to load the data with LazyData turned off.

Best regards,

Marcel

On 11/18/21 9:51 AM, Witold Wolski wrote:
> Hi,
>
> I with BiocCheck I am getting a warning that my packages uses 
> LazyData: true.
>
> So far some of the package vignettes loaded the data in the params 
> section of the Rmd file e.g.,
>
> ---
> title:
> ...
> ...
> params:
>   configuration:  !r data(prolfqua::data_ionstar); 
> quote(prolfqua::data_ionstar$filtered()$config )
>   project_conf: NULL
>   data: !r quote( prolfqua::data_ionstar$filtered()$data )
> ...
> ---
>
>
> However, this will not work with LazyData false. What is the 
> bioconductor way of loading the data in the Rmd file Yaml section?
>
> If anyone wonders, why do I need it. By this I can reuse the vignette 
> with a different dataset.
>
> Best Witold
>
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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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