Evaluate function in R or shell command via nix-shell environment

This function needs an installation of Nix. with_nix() has two effects to run code in isolated and reproducible environments.

1. Evaluate a function in R or a shell command via the nix-shell environment (Nix expression for custom software libraries; involving pinned versions of R and R packages via Nixpkgs)

2. If no error, return the result object of expr in with_nix() into the current R session.

Usage

with_nix(
  expr,
  program = c("R", "shell"),
  project_path = ".",
  message_type = c("simple", "quiet", "verbose")
)

Arguments

expr

Single R function or call, or character vector of length one with shell command and possibly options (flags) of the command to be invoked. For program = R, you can both use a named or an anonymous function. The function provided in expr should not evaluate when you pass arguments, hence you need to wrap your function call like function() your_fun(arg_a = "a", arg_b = "b"), to avoid evaluation and make sure expr is a function (see details and examples).

program

String stating where to evaluate the expression. Either "R", the default, or "shell". where = "R" will evaluate the expression via RScript and where = "shell" will run the system command in nix-shell.

project_path

Path to the folder where the default.nix file resides. The default is ".", which is the working directory in the current R session. This approach also useful when you have different subfolders with separate software environments defined in different default.nix files.

message_type

String how detailed output is. Currently, there is either "simple" (default), "quiet or "verbose", which shows the script that runs via nix-shell.

Value

• if program = "R", R object returned by function given in expr when evaluated via the R environment in nix-shell defined by Nix expression.

• if program = "shell", list with the following elements:

  • status: exit code

  • stdout: character vector with standard output

  • stderr: character vector with standard error of expr command sent to a command line interface provided by a Nix package.

Details

with_nix() gives you the power of evaluating a main function expr and its function call stack that are defined in the current R session in an encapsulated nix-R session defined by Nix expression (default.nix), which is located in at a distinct project path (project_path).

with_nix() is very convenient because it gives direct code feedback in read-eval-print-loop style, which gives a direct interface to the very reproducible infrastructure-as-code approach offered by Nix and Nixpkgs. You don't need extra efforts such as setting up DevOps tooling like Docker and domain specific tools like {renv} to control complex software environments in R and any other language. It is for example useful for the following purposes.

1. test compatibility of custom R code and software/package dependencies in development and production environments

2. directly stream outputs (returned objects), messages and errors from any command line tool offered in Nixpkgs into an R session.

3. Test if evolving R packages change their behavior for given unchanged R code, and whether they give identical results or not.

with_nix() can evaluate both R code from a nix-R session within another nix-R session, and also from a host R session (i.e., on macOS or Linux) within a specific nix-R session. This feature is useful for testing the reproducibility and compatibility of given code across different software environments. If testing of different sets of environments is necessary, you can easily do so by providing Nix expressions in custom .nix or default.nix files in different subfolders of the project.

rix_init() is run automatically to generate a custom .Rprofile file for the subshell in project_dir. The defaults in that file ensure that only R packages from the Nix store, that are defined in the subshell .nix file are loaded and system's libraries are excluded.

To do its job, with_nix() heavily relies on patterns that manipulate language expressions (aka computing on the language) offered in base R as well as the {codetools} package by Luke Tierney.

Some of the key steps that are done behind the scene:

1. recursively find, classify, and export global objects (globals) in the call stack of expr as well as propagate R package environments found.

2. Serialize (save to disk) and deserialize (read from disk) dependent data structures as .Rds with necessary function arguments provided, any relevant globals in the call stack, packages, and expr outputs returned in a temporary directory.

3. Use pure nix-shell environments to execute a R code script reconstructed catching expressions with quoting; it is launched by commands like this via {sys} by Jeroen Ooms: nix-shell --pure --run "Rscript --vanilla".

Examples

if (FALSE) { # \dontrun{
# create an isolated, runtime-pure R setup via Nix
project_path <- "./sub_shell"
rix_init(
  project_path = project_path,
  rprofile_action = "create_missing"
)
# generate nix environment in `default.nix`
rix(
  r_ver = "4.2.0",
  project_path = project_path
)
# evaluate function in Nix-R environment via `nix-shell` and `Rscript`,
# stream messages, and bring output back to current R session
out <- with_nix(
  expr = function(mtcars) nrow(mtcars),
  program = "R", project_path = project_path,
  message_type = "simple"
)

# There no limit in the complexity of function call stacks that `with_nix()`
# can possibly handle; however, `expr` should not evaluate and
# needs to be a function for `program = "R"`. If you want to pass the
# a function with arguments, you can do like this
get_sample <- function(seed, n) {
  set.seed(seed)
  out <- sample(seq(1, 10), n)
  return(out)
}

out <- with_nix(
  expr = function() get_sample(seed = 1234, n = 5),
  program = "R",
  project_path = ".",
  message_type = "simple"
)

## You can also attach packages with `library()` calls in the current R
## session, which will be exported to the nix-R session.
## Other option: running system commands through `nix-shell` environment.
} # }