Require: Installing and Loading R Packages for Reproducible Workflows

A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.

This is an "all in one" function that will run install.packages for CRAN and GitHub https://github.com/ packages and will install specific versions of each package if versions are specified either via an (in)equality (e.g., "glue (>=1.6.2)" or "glue (==1.6.2)" for an exact version) or with a packageVersionFile. If require = TRUE, the default, the function will then run require on all named packages that satisfy their version requirements. If packages are already installed (packages supplied), and their optional version numbers are satisfied, then the "install" component will be skipped.

Usage

Require(
  packages,
  packageVersionFile,
  libPaths,
  install_githubArgs = list(),
  install.packagesArgs = list(INSTALL_opts = "--no-multiarch"),
  standAlone = getOption("Require.standAlone", FALSE),
  install = getOption("Require.install", TRUE),
  require = getOption("Require.require", TRUE),
  repos = getOption("repos"),
  purge = getOption("Require.purge", FALSE),
  verbose = getOption("Require.verbose", FALSE),
  type = getOption("pkgType"),
  upgrade = FALSE,
  returnDetails = FALSE,
  ...
)

Install(
  packages,
  packageVersionFile,
  libPaths,
  install_githubArgs = list(),
  install.packagesArgs = list(INSTALL_opts = "--no-multiarch"),
  standAlone = getOption("Require.standAlone", FALSE),
  install = TRUE,
  repos = getOption("repos"),
  purge = getOption("Require.purge", FALSE),
  verbose = getOption("Require.verbose", FALSE),
  type = getOption("pkgType"),
  upgrade = FALSE,
  ...
)

Arguments

packages

Either a character vector of packages to install via install.packages, then load (i.e., with library), or, for convenience, a vector or list (using c or list) of unquoted package names to install and/or load (as in require, but vectorized). Passing vectors of names may not work in all cases, so user should confirm before relying on this behaviour in operational code. In the case of a GitHub package, it will be assumed that the name of the repository is the name of the package. If this is not the case, then pass a named character vector here, where the names are the package names that could be different than the GitHub repository name.

packageVersionFile

Character string of a file name or logical. If TRUE, then this function will load the default file, getOption("Require.packageVersionFile"). If this argument is provided, then this will override any packages passed to packages. By default, Require will attempt to resolve dependency violations (i.e., if this packageVersionFile specifies a version of a package that violates the dependency specification of another package). If a user wishes to attempt to install the packageVersionFile without assessing the dependencies, set dependencies = FALSE.

libPaths

The library path (or libraries) where all packages should be installed, and looked for to load (i.e., call library). This can be used to create isolated, stand alone package installations, if used with standAlone = TRUE. Currently, the path supplied here will be prepended to .libPaths() (temporarily during this call) to Require if standAlone = FALSE or will set (temporarily) .libPaths() to c(libPaths, tail(libPaths(), 1) to keep base packages.

install_githubArgs

Deprecated. Values passed here are merged with install.packagesArgs, with the install.packagesArgs taking precedence if conflicting.

install.packagesArgs

List of optional named arguments, passed to install.packages. Default is only --no-multi-arch, meaning that only the current architecture will be built and installed (e.g., 64 bit, not 32 bit, in many cases).

standAlone

Logical. If TRUE, all packages will be installed to and loaded from the libPaths only. NOTE: If TRUE, THIS WILL CHANGE THE USER'S .libPaths(), similar to e.g., the checkpoint package. If FALSE, then libPath will be prepended to .libPaths() during the Require call, resulting in shared packages, i.e., it will include the user's default package folder(s). This can be create dramatically faster installs if the user has a substantial number of the packages already in their personal library. Default FALSE to minimize package installing.

install

Logical or "force". If FALSE, this will not try to install anything. If "force", then it will force installation of requested packages, mimicking a call to e.g., install.packages. If TRUE, the default, then this function will try to install any missing packages or dependencies.

require

Logical or character string. If TRUE, the default, then the function will attempt to call require on all requested packages, possibly after they are installed. If a character string, then it will only call require on those specific packages (i.e., it will install the ones listed in packages, but load the packages listed in require)

repos

The remote repository (e.g., a CRAN mirror), passed to either install.packages, install_github or installVersions.

purge

Logical. Should all caches be purged? Default is getOption("Require.purge", FALSE). There is a lot of internal caching of results throughout the Require package. These help with speed and reduce calls to internet sources. However, sometimes these caches must be purged. The cached values are renewed when found to be too old, with the age limit. This maximum age can be set in seconds with the environment variable R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE, or if unset, defaults to 3600 (one hour – see utils::available.packages).

Internally, there are calls to available.packages.

verbose

Numeric or logical indicating how verbose should the function be. If -1 or -2, then as little verbosity as possible. If 0 or FALSE, then minimal outputs; if 1 or TRUE, more outputs; 2 even more. NOTE: in Require function, when verbose >= 2, also returns details as if returnDetails = TRUE (for backwards compatibility).

type

See utils::install.packages

upgrade

When FALSE, the default, will only upgrade a package when the version on in the local library is not adequate for the version requirements of the packages. Note: for convenience, update can be used for this argument.

returnDetails

Logical. If TRUE the return object will have an attribute: attr(.., "Require") which has lots of information about the processes of the installs.

...

Passed to install.packages. Good candidates are e.g., type or dependencies. This can be used with install_githubArgs or install.packageArgs which give individual options for those 2 internal function calls.

Value

Require is intended to replace base::require, thus it returns a logical, named vector indicating whether the named packages have been loaded. Because Require also has the ability to install packages, a return value of FALSE does not mean that it did not install correctly; rather, it means it did not attach with require, which could be because it did not install correctly, or also because e.g., require = FALSE.

standAlone will either put the Required packages and their dependencies all within the libPaths (if TRUE) or if FALSE will only install packages and their dependencies that are otherwise not installed in .libPaths()[1], i.e., the current active R package directory. Any packages or dependencies that are not yet installed will be installed in libPaths.

Details

Install is the same as Require(..., require = FALSE), for convenience.

Note

For advanced use and diagnosis, the user can set verbose = TRUE or 1 or 2 (or via options("Require.verbose")). This will attach an attribute attr(obj, "Require") to the output of this function.

GitHub Package

Follows remotes::install_github standard. As with remotes::install_github, it is not possible to specify a past version of a GitHub package unless that version is a tag or the user passes the SHA that had that package version. Similarly, if a developer does a local install e.g., via pkgload::install, of an active project, this package will not be able know of the GitHub state, and thus pkgSnapshot will not be able to recover this state as there is no SHA associated with a local installation. Use Require (or remotes::install_github) to create a record of the GitHub state.

Package Snapshots

To build a snapshot of the desired packages and their versions, first run Require with all packages, then pkgSnapshot. If a libPaths is used, it must be used in both functions.

Mutual Dependencies

This function works best if all required packages are called within one Require call, as all dependencies can be identified together, and all package versions will be addressed (if there are no conflicts), allowing a call to pkgSnapshot() to take a snapshot or "record" of the current collection of packages and versions.

Local Cache of Packages

When installing new packages, Require will put all source and binary files in an R-version specific subfolder of getOption("Require.cachePkgDir") whose default is RPackageCache(), meaning cache packages locally in a project-independent location, and will reuse them if needed. To turn off this feature, set options("Require.cachePkgDir" = FALSE).

See also

Useful links:

• https://Require.predictiveecology.org

• https://github.com/PredictiveEcology/Require

• Report bugs at https://github.com/PredictiveEcology/Require/issues

Author

Maintainer: Eliot J B McIntire eliot.mcintire@canada.ca (ORCID)

Other contributors:

• Alex M Chubaty achubaty@for-cast.ca (ORCID) [contributor]

• Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [copyright holder]

Examples

if (FALSE) { # \dontrun{
opts <- Require:::.setupExample()

library(Require)
getCRANrepos(ind = 1)
Require("utils") # analogous to require(stats), but it checks for
#   pkg dependencies, and installs them, if missing

# unquoted version
Require(c(tools, utils))

if (Require:::.runLongExamples()) {
  # Install in a new local library (libPaths)
  tempPkgFolder <- file.path(tempdir(), "Require/Packages")
  # use standAlone, means it will put it in libPaths, even if it already exists
  #   in another local library (e.g., personal library)
  Install("crayon", libPaths = tempPkgFolder, standAlone = TRUE)

  # Mutual dependencies, only installs once -- e.g., cli
  tempPkgFolder <- file.path(tempdir(), "Require/Packages")
  Install(c("cli", "R6"), libPaths = tempPkgFolder, standAlone = TRUE)

  # Mutual dependencies, only installs once -- e.g., rlang
  tempPkgFolder <- file.path(tempdir(), "Require/Packages")
  Install(c("rlang", "ellipsis"), libPaths = tempPkgFolder, standAlone = TRUE)

  #####################################################################################
  # Isolated projects -- Use a project folder and pass to libPaths or set .libPaths() #
  #####################################################################################
  # GitHub packages
  if (requireNamespace("gitcreds", quietly = TRUE)) {
    #if (is(try(gitcreds::gitcreds_get(), silent = TRUE), "gitcreds")) {
      ProjectPackageFolder <- file.path(tempdir(), "Require/ProjectA")
      if (requireNamespace("curl")) {
        Require("PredictiveEcology/fpCompare@development",
          libPaths = ProjectPackageFolder,
        )
      }

      # No install because it is there already
      Install("PredictiveEcology/fpCompare@development",
        libPaths = ProjectPackageFolder,
      ) # the latest version on GitHub

      ############################################################################
      # Mixing and matching GitHub, CRAN, with and without version numbering
      ############################################################################
      pkgs <- c(
        "remotes (<=2.4.1)", # old version
        "digest (>= 0.6.28)", # recent version
        "PredictiveEcology/fpCompare@a0260b8476b06628bba0ae73af3430cce9620ca0" # exact version
      )
      Require::Require(pkgs, libPaths = ProjectPackageFolder)
    #}
  }
  Require:::.cleanup(opts)
}
} # }