installMiniconda {basilisk.utils}R Documentation

Install Miniconda

Description

Install Miniconda (version 3, 2019.10) to a destination path that depends on the operating system. This skips the installation if said path already exists.

Usage

installMiniconda(installed = TRUE)

Arguments

installed

Logical scalar indicating whether basilisk is already installed. Should only be set to FALSE in basilisk configure scripts.

Details

This function was originally created from code in https://github.com/hafen/rminiconda, also borrowing code from reticulate's install_miniconda for correct Windows installation. We use BiocFileCache if available to avoid redownloading the Miniconda installer upon basilisk re-installation.

Whenever installMiniconda is re-run (and BASILISK_USE_SYSTEM_DIR is not set, see ?getBasiliskDir), the previous Miniconda installation and its various basilisk environments are destroyed. This avoids duplication of Miniconda instances that would otherwise chew up disk space at 3 GB a pop.

After the destruction of the previous instance, we rely on the client packages to recreate their required environments. They should do this automatically if they are using basilisk correctly.

Users can disable this destruction by setting the BASILISK_NO_DESTROY environment variable to "1". This may be necessary on rare occasions when running multiple R instances on the same Bioconductor release. (Setting this variable is not required for instances using different Bioconductor releases.)

Value

An Miniconda instance is created at the location specified by getBasiliskDir. Nothing is performed if the instance already exists. A logical scalar is returned indicating whether a new instance was created.

Author(s)

Aaron Lun

Examples

# We can't actually run installMiniconda() here, as it 
# either relies on basilisk already being installed or
# it has a hard-coded path to the basilisk system dir.
print("dummy test to pass BiocCheck")


[Package basilisk.utils version 1.0.4 Index]