I guess I failed to explain:
In the yaml section of the rmarkdown I can only use a single R expression;
i.e., I can not write:
```
configuration: !r data('somedata', package="xyz"); somedata$uvw
```
because these are two expressions.
I could write:
xyz::somedata$uvw
So to rephrase my question. What would be your recommendation to convert
these two expressions:
data('somedata', package="xyz"); somedata$uvw
into one?
Hope this clarifies my question.
Best regards
Witek
On 18/11/2021 16:44, Marcel Ramos wrote:
Hi Witold,
I am not sure what the use case is for loading data in the yaml header.
If you're swapping out data for your vignettes, perhaps your introduction
chunks could contain the code to load the data.
In any case, I recommend that you use `data("dataset", package = "package")`
to load the data with LazyData turned off.
Best regards,
Marcel
On 11/18/21 9:51 AM, Witold Wolski wrote:
Hi,
I with BiocCheck I am getting a warning that my packages uses
LazyData: true.
So far some of the package vignettes loaded the data in the params
section of the Rmd file e.g.,
---
title:
...
...
params:
configuration: !r data(prolfqua::data_ionstar);
quote(prolfqua::data_ionstar$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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