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Set up of the Julia environment needed for DataAxesFormats and TanayLabUtilities

Source: R/setup.R
setup_daf.Rd

This will set up a new Julia environment in the current working directory or another folder if provided. This environment will then be set with all Julia dependencies needed.

Usage

setup_daf(
  pkg_check = TRUE,
  seed = NULL,
  env_path = getwd(),
  installJulia = FALSE,
  force_dev = getOption("dafr.force_dev", FALSE),
  level = "Warn",
  show_time = TRUE,
  show_module = TRUE,
  show_location = FALSE,
  julia_environment = getOption("dafr.julia_environment", "default"),
  JULIA_HOME = getOption("dafr.JULIA_HOME", NULL),
  ...
)

Arguments

pkg_check

(Default=TRUE) Check whether needed Julia packages are installed.

seed

Seed to be used.

env_path

The path to were the Julia environment should be created. By default, this is the current working directory.

installJulia

(Default=TRUE) Whether to install Julia

force_dev

(Default=FALSE) Whether to force dev versions of packages, default value comes from getOption("dafr.force_dev")

level

Log level, one of "Debug", "Info", "Warn", "Error", or an integer (default: "Warn")

show_time

Whether to show timestamp (default: TRUE)

show_module

Whether to show module name (default: TRUE)

show_location

Whether to show source location (default: FALSE)

julia_environment

Specify which Julia environment to use: "custom" creates a new environment (default if option not set), "default" uses the default Julia environment, any other value can be the path to a custom environment. Default value comes from getOption("dafr.julia_environment")

JULIA_HOME

The path to the Julia installation. Default value comes from getOption("dafr.JULIA_HOME"). See julia_setup for more details.

...

Other parameters passed on to julia_setup

Value

No return value, called for side effects.

Examples

if (FALSE) { # \dontrun{
# Install from default URLs
setup_daf()

# Time consuming and requires Julia
setup_daf(installJulia = TRUE, seed = 60427)

# Install from latest github versions
setup_daf(
    installJulia = TRUE,
    custom_urls = c(
        "https://github.com/tanaylab/DataAxesFormats.jl",
        "https://github.com/tanaylab/TanayLabUtilities.jl"
    )
)

# Use default Julia environment instead of creating a new one
setup_daf(julia_environment = "default")

# Only load packages without installation
setup_daf(pkg_check = FALSE)

# Set global option
options(dafr.julia_environment = "default")
setup_daf() # Will use the default Julia environment
} # }