R Package Dependencies
The MDI apps framework loads and attaches a set of commonly used R packages that you may use when writing your app code, listed here:
App-specific R package declarations
The suite-level packages.yml file and all app and module configuration files can declare additional R package dependencies required for an app to function, as follows:
# suite-level: shiny/shared/global/packages/config.yml
# app and module level: various config.yml or module.yml files
packages:
R:
- <packageName>
# etc.
Bioconductor: null # or a list of packages as for "R"
The R key lists general R packages, e.g., those on CRAN. Bioconductor is self-evident.
It is not harmful to re-declare R packages already listed elsewhere, they will only be installed once.
Installing vs. attaching
R packages listed in the the mdi-apps-framework package.yml file are attached and their functions can be called directly, e.g., Shiny’s observeEvent().
In contrast, packages declared in a tool suite are installed but are never attached using the library() function. Thus, you must either:
- call functions in full syntax, e.g.,
package::function()(preferred) - call
library(package)yourself (discouraged, you could break the framework)