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Install micromamba

Source: R/install_micromamba.R
install_micromamba.Rd

Downloads the micromamba binary that condathis uses and installs it in the condathis data directory, at the path that micromamba_bin_path() returns. The functions that need micromamba call it when no usable binary is found (see micromamba discovery in condathis-options). You need to call it only to choose the version, or to install micromamba ahead of time.

Usage

install_micromamba(
  micromamba_version = "2.10.0-0",
  timeout = 3600,
  download_method = "auto",
  force = FALSE,
  verbose = c("output", "silent", "cmd", "spinner", "full"),
  timeout_limit = NULL
)

Arguments

micromamba_version

Character string with the micromamba version, in the format "X.Y.Z-N" (version and build number), for example "2.10.0-0", the default. Another format aborts with class condathis_install_micromamba_invalid_micromamba_version. Versions older than 2.8.1 abort with class condathis_install_micromamba_unsupported_version, because condathis does not use them. When you pass micromamba_version and a binary is already installed, install_micromamba() keeps the binary only when its version (X.Y.Z) is the requested one. When it reports another version, or its version cannot be read, install_micromamba() installs the requested version. Without micromamba_version, it always keeps an installed binary, unless force = TRUE.

timeout

Numeric download timeout in seconds, a single non-negative number. Inf means no limit. Defaults to 3600. Each download uses the larger of this value and getOption("timeout"), so 0 means no limit only when getOption("timeout") is 0 too. The function lowers values above 2147483 seconds (about 24.8 days) to 2147483. Other values abort with class condathis_install_micromamba_invalid_timeout.

download_method

Character string with the download method of utils::download.file(): one of "auto" (the default), "internal", "libcurl", "wget", "curl" or "wininet". It is ignored when the curl package 5.0.0 or later is installed, because then curl::curl_download() is used. Other values abort with class condathis_install_micromamba_invalid_download_method.

force

Logical value. TRUE downloads micromamba also when a binary is already installed. Defaults to FALSE. A value that is not TRUE or FALSE aborts with class condathis_install_micromamba_invalid_force.

verbose

Character string that controls the console output. One of:

  • "output": show the output of the command and the messages of condathis.

  • "silent": show nothing.

  • "cmd": show the command line.

  • "spinner": show only a spinner.

  • "full": show the command line, the output, and the backend's own log.

TRUE means "output" and FALSE means "silent". Every level except "silent" shows a spinner in interactive sessions. Invalid values abort with class condathis_invalid_verbose (see condathis-conditions). The default is shown in Usage.

The command line shown, the cmd of a result and the messages of condathis show the password and the token of a URL as *****. micromamba does the same (https://user:*****@host/channel, https://host/t/*****/channel). The command still gets them.

timeout_limit

Deprecated. Use timeout. A value warns with class condathis_deprecated_arg and is used as timeout. Passing both aborts with class condathis_install_micromamba_conflicting_args.

Value

The path of the micromamba binary, an fs_path, invisibly: the path that micromamba_bin_path() returns. A failed download aborts with class condathis_install_micromamba_download_failed.

Details

The binary is the build for the platform of the running R (see get_sys_arch()): linux-64, linux-aarch64, linux-ppc64le, osx-64, osx-arm64, win-64 or win-arm64. A native ARM64 R on Windows gets win-arm64. An x64 R on an ARM64 PC gets win-64, which runs through x64 emulation. Every R of a user shares the installed binary. So on an ARM64 PC, the binary installed first stays until you replace it, for example with force = TRUE. Either binary works with both builds of R: micromamba builds environments for its own platform.

install_micromamba() tries the compressed archive first, from the micromamba releases on GitHub, then from the conda-forge channel on anaconda.org and prefix.dev. It extracts the archive with R's internal tar, so no system tar or bzip2 is needed. When every archive fails, it downloads the standalone binary from GitHub. A mirror fails when the download fails, or when the file does not extract, does not run, or does not match the SHA256 checksum published with the release. Then it tries the next mirror. It replaces an installed binary only with a download that passed these checks, also with force = TRUE.

When no published checksum can be read, install_micromamba() installs the binary. It warns with class condathis_install_micromamba_checksum_unavailable when verbose is "output" or "full". A checksum that does not match warns with class condathis_install_micromamba_checksum_mismatch, and that binary is not installed.

See also

Other setup: clean_cache(), get_install_dir(), get_sys_arch(), micromamba_bin_path(), with_sandbox_dir()

Examples

if (FALSE) { # \dontrun{
condathis::with_sandbox_dir({
  # Install the default version of micromamba
  condathis::install_micromamba()

  # Install a specific version (2.8.1 or newer): it replaces a binary of
  # another version
  condathis::install_micromamba(micromamba_version = "2.9.0-0")

  # Without `micromamba_version`, the installed binary is kept unless
  # `force = TRUE`
  condathis::install_micromamba(force = TRUE)
})
} # }