Introduction
mauricer is an R package to handle BEAST2 package
management from R, similar to the BEAST2 package manager.
In this vignette, we will:
- List all BEAST2 packages
- Install the first non-installed BEAST2 package
- Verify the BEAST2 package is indeed installed
- Uninstall the BEAST2 package
To do so, we’ll need to load mauricer. We’ll also load
testthat for testing:
To install BEAST2 packages, one needs
- an internet connection
- BEAST2 must be installed
If there is no internet connection, or if BEAST2 is not installed, this vignette will be close to empty.
if (!curl::has_internet()) {
print("No internet connection")
}
if (!beastier::is_beast2_installed()) {
print("No BEAST2 installed")
}
#> [1] "No BEAST2 installed"List all BEAST2 packages
Use get_beast2_pkg_names to get a data frame with the
name, version and install status of all BEAST2 packages:
if (curl::has_internet() && beastier::is_beast2_installed()) {
beast2_packages <- get_beast2_pkg_names()
knitr::kable(head(beast2_packages))
}Install the first non-installed BEAST2 package
Find a package that is not installed:
if (curl::has_internet() && beastier::is_beast2_installed()) {
package_name <- beast2_packages[
beast2_packages$installed_version == "NA",
]$name[1]
print(package_name)
}Install that package:
if (curl::has_internet() && beastier::is_beast2_installed()) {
mauricerinstall::install_beast2_pkg(package_name)
}Note that this installation uses a non-CRAN package, called
mauricerinstall, as installing software is against CRAN
policy.
Uninstall the BEAST2 package
Use uninstall_beast2_pkg:
if (curl::has_internet() && beastier::is_beast2_installed()) {
mauricerinstall::uninstall_beast2_pkg(package_name)
}Also this code uses a non-CRAN package, called
mauricerinstall, as installing software is against CRAN
policy.