R/mdrb.R

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

# Public #####

#' @export
#'
#' @title Check Rust Backend Requirements
#'
#' @description
#' `check_mdrb()` returns a boolean indicating whether a suitable version of the
#' metabodecon Rust backend [mdrb](https://github.com/spang-lab/mdrb) is
#' currently installed.
#'
#' `check_mdrb_deps()` returns a list with information about the
#' installation status of mdrb system dependencies.
#'
#' @param stop_on_fail
#' If TRUE, an error is thrown if the check fails, providing instructions on how
#' to install or upgrade mdrb.
#'
#' @param verbose
#' If TRUE, additional information is printed during the check process.
#'
#' @author 2024-2025 Tobias Schmidt: initial version.
#'
#' @return
#' `check_mdrb()` returns TRUE if a suitable version of mdrb is installed,
#' else FALSE.
#'
#' `check_mdrb_deps()` returns a data.frame as follows:
#'
#' ```R
#'             check           passed  comment
#'     r       R >= 4.2        TRUE    Current: R 4.4.2
#'     rtools  Rtools exist    TRUE    Tested with: pkgbuild::has_build_tools()
#'     cargo   cargo >= 1.80   TRUE    Current: cargo 1.84.1 (66221abde 2024-11-19)
#'     rustc   rustc >= 1.80   TRUE    Current: rustc 1.84.1 (e71f9a9a9 2025-01-27)
#' ```
#'
#' Column `check` is a string describing the performed check.\cr
#' Column `passed` is a boolean indicating whether the check passed.\cr
#' Column `comment` is a string string describing the check result.
#'
#' The rownames of the dataframe one-word descriptions of the performed checks.
#'
#' @examples
#' check_mdrb()
#'
#' \donttest{
#' # Checking dependencies might take more than 5 seconds, as it
#' # requires the compilation of a small test program as well as
#' # running `cargo --version` and `rustc --version`, which,
#' # depending on your system, might involve updating or installing
#' # Rust toolchain components.
#' check_mdrb_deps(verbose = TRUE)
#' }
check_mdrb <- function(stop_on_fail = FALSE) {
    stopifnot(is_bool(stop_on_fail, 1))
    mdrb_version <- get_mdrb_version()
    req_version <- package_version("0.0.1")
    mdrb_is_ok <- mdrb_version >= req_version
    if (mdrb_is_ok || !stop_on_fail) return(mdrb_is_ok)
    err_msg <- paste(sep = "\n",
        "Using the Rust backend requires mdrb >= 0.0.1.\n",
        "To install or upgrade mdrb run: install_mdrb()",
        "To check system requirements run: check_mdrb_deps()\n",
        "For more information see: https://github.com/spang-lab/mdrb"
    )
    stop(err_msg, call. = FALSE)
}

#' @export
#' @rdname check_mdrb
check_mdrb_deps <- function(verbose = FALSE) {

    check <- c("R >= 4.2", "Rtools exist", "cargo >= 1.80", "rustc >= 1.80")
    df <- data.frame(check, passed = NA, comment = NA)
    rownames(df) <- c("r", "rtools", "cargo", "rustc")

    # Check R version
    if (verbose) logf("Checking R version...")
    r_cur <- package_version(getRversion())
    r_req <- package_version("4.2.0")
    df["r", "passed"] <- r_cur >= r_req
    df["r", "comment"] <- paste("Current: R", r_cur)

    # Check buildtools exist
    if (verbose) logf("Checking if buildtools exist...")
    df["rtools", "passed"] <- pkgbuild::has_build_tools(debug = verbose)
    df["rtools", "comment"] <- "Testcall: pkgbuild::has_build_tools()"

    # Add $HOME/.cargo/bin to PATH before checking cargo and rustc
    win <- .Platform$OS.type == "windows"
    home_cargo_bin <- paste(home(), ".cargo", "bin", sep = .Platform$file.sep)
    PATH <- Sys.getenv("PATH")
    PATH <- paste(PATH, home_cargo_bin, sep = if (win) ";" else ":")
    Sys.setenv(PATH = PATH)

    # Check cargo version
    if (verbose) logf("Checking cargo version...")
    cargo_out <- "not found in PATH"
    cargo_str <- "0.0.0"
    try(silent = TRUE, {
        local_options(warn = -1)
        cargo_out <- system2("cargo", args = "--version", stdout = TRUE, stderr = FALSE)
        cargo_str <- strsplit(cargo_out, " ")[[1]][2] # cargo_out == 'cargo x.y.z (commitsha yyyy-mm-dd)'
    })
    cargo_cur <- package_version(cargo_str)
    cargo_req <- package_version("1.80.0")
    df["cargo", "passed"] <- cargo_cur >= cargo_req
    df["cargo", "comment"] <- paste("Current:", cargo_out)

    # Check rustc version
    if (verbose) logf("Checking rustc version...")
    rustc_out <- "not found in PATH"
    rustc_str <- "0.0.0"
    try(silent = TRUE, {
        local_options(warn = -1)
        rustc_out <- system2("rustc", args = "--version", stdout = TRUE, stderr = FALSE)
        rustc_str <- strsplit(rustc_out, " ")[[1]][2] # rustc_out == 'rustc x.y.z (commitsha yyyy-mm-dd)'
    })
    rustc_cur <- package_version(rustc_str)
    rustc_req <- package_version("1.80.0")
    df["rustc", "passed"] <- rustc_cur >= rustc_req
    df["rustc", "comment"] <- paste("Current:", rustc_out)

    if (verbose) logf("Done")
    df
}

#' @export
#'
#' @title Install Rust Backend
#'
#' @description
#' Installs metabodecon's Rust backend [mdrb](https://github.com/spang-lab/mdrb)
#' from [R-Universe](https://spang-lab.r-universe.dev/mdrb).
#'
#' lifecycle::badge("experimental")
#'
#' @param ask
#' Whether to ask for confirmation before attempting installation. Default is
#' TRUE.
#'
#' @param ...
#' Additional arguments to pass to [utils::install.packages()] when attempting
#' installation of mdrb.
#'
#' @return NULL. Called for side effect of installing the Rust backend.
#'
#' @author 2024-2025 Tobias Schmidt: initial version.
#'
#' @examples
#' if (interactive()) try(install_mdrb())
install_mdrb <- function(ask = TRUE, ...) {
    if (getRversion() < numeric_version("4.2")) {
        stop("installation of mdrb requires R version 4.2 or greater", call. = FALSE)
    }
    msg <- "Proceeding will install package 'mdrb'. Continue?"
    if (isTRUE(ask) && isFALSE(get_yn_input(msg))) return()
    invisible(install.packages("mdrb", repos = "https://spang-lab.r-universe.dev", ...))
}

# Internal #####

#' @noRd
#' @author 2024-2025 Tobias Schmidt: initial version.
get_mdrb_version <- function() {
    tryCatch(
        packageVersion("mdrb"),
        error = function(e) package_version("0.0.0")
    )
}