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Install Packages in a Existing Conda Environment

Source: R/install_packages.R
install_packages.Rd

Install Packages in a Existing Conda Environment

Usage

install_packages(
  packages,
  env_name = "condathis-env",
  channels = c("conda-forge"),
  channel_priority = c("disabled", "strict", "flexible"),
  additional_channels = NULL,
  verbose = c("output", "silent", "cmd", "spinner", "full")
)

Arguments

packages

Character vector with the names of the packages and version strings if necessary.

env_name

Name of the Conda environment where the packages are going to be installed. Defaults to 'condathis-env'.

channels

Character vector. Names of the channels to be included. By default 'c("conda-forge", "bioconda")' are used for solving dependencies.

channel_priority

Character. Set the channel priority. Can be "disabled", "strict", or "flexible". Defaults to "disabled".

Note: This is different from the default Conda behavior. Where "flexible" is the default.

  • "disabled": The package dependency solver will search for packages across all channels without prioritizing any channel.

  • "strict": Packages and dependencies for those packages will be installed from the highest priority channel that contains them and fail if dependencies cannot be satisfied from that channel.

  • "flexible": The solver will prefer packages from higher priority channels but will fall back to lower priority channels if necessary.

additional_channels

Character. Additional Channels to be added to the default ones.

verbose

Character string specifying the verbosity level of the function's output. Acceptable values are:

  • "output": Print the standard output and error from the command-line tool to the screen. Note that the order of the standard output and error lines may not be correct, as standard output is typically buffered.

  • "silent": Suppress all output from internal command-line tools. Equivalent to FALSE.

  • "cmd": Print the internal command(s) passed to the command-line tool. If the standard output and/or error is redirected to a file or they are ignored, they will not be echoed. Equivalent to TRUE.

  • "full": Print both the internal command(s) ("cmd") and their standard output and error ("output").

  • Logical values FALSE and TRUE are also accepted for backward compatibility but are soft-deprecated. Please use "silent" or "output" instead.

Value

An object of class list representing the result of the command execution. Contains information about the standard output, standard error, and exit status of the command.

Examples

if (FALSE) { # \dontrun{
condathis::with_sandbox_dir({
  condathis::create_env(
    packages = "fastqc",
    env_name = "fastqc-env"
  )
  # Install the package `python` in the `fastqc-env` environment.
  # It is not recommended to install multiple packages in the same environment,
  #  # as it defeats the purpose of isolation provided by separate environments.
  condathis::install_packages(packages = "python", env_name = "fastqc-env")
})
} # }