evalwith: Evaluate an expression with predefined global state

In metabodecon: Deconvolution and Alignment of 1d NMR Spectra

Evaluate an expression with predefined global state

Description

Evaluates an expression with a predefined global state, including the:

• working directory (set via setwd())

• global options (set via options())

• graphical parameters (set via par())

In addition to that, evalwith allows to:

• Redirect or capture the output and/or message stream via sink()

• Measure the runtime of the evaluated expression via system.time()

• Creating a temporary test directory (inside tmpdir()) and populating it with input files according to inputs

• Predefine answers for calls to readline() happening during evaluation of expr

• Caching the result of the expression

All changes to the global state are reverted after the expression has been evaluated.

Usage

evalwith(
  expr,
  testdir = NULL,
  answers = NULL,
  output = NULL,
  message = NULL,
  plot = NULL,
  datadir_temp = c("default", "missing", "empty", "filled")[1],
  datadir_persistent = c("default", "missing", "empty", "filled")[1],
  inputs = character(),
  opts = NULL,
  pars = NULL,
  cache = FALSE,
  overwrite = FALSE
)

Arguments

expr	Expression to be evaluated.
testdir	ID of the test directory. E.g. "xyz/2". Will be created and populated with inputs. To clear, use clear(testdir("xyz/2")).
answers	Answers to be returned by readline().
output	Path to the file where output stream should be redirected to. Use "captured" to capture the output.
message	Path to the file where message stream be redirected to. Use "captured" to capture the messages.
plot	An expression opening a device, the string "captured" or a path ending in ".pdf", ".svg", or ".png". Examples: svg("tmp.svg"), quote(pdf("tmp.pdf")), "captured", "tmp.png". Passing "captured" is equivalent to passing tempfile(fileext = ".png").
datadir_temp	State of the mocked temporary data directory. See details section.
datadir_persistent	State of the mocked persistent data directory. See details section.
inputs	Paths to be copied to the test directory before evaluating expr.
opts	Named list of options to be set. See options().
pars	Named list of parameters to be set. See par().
cache	Logical indicating whether to cache the result of the expression.
overwrite	Logical indicating whether to overwrite the cache file if it already exists.

Details

The datadir_temp and datadir_persistent arguments accept values "missing", "filled" and "empty". Setting a value unequal NULL causes the functions datadir_temp() and/or datadir_persistent() to be replaced with mock functions pointing to fake directories. Functions depending on these functions will then use the fake directories instead of the real ones. When set to "missing" the returned mock directory does not exist. When set to "empty" it exists and is guaranteed to be empty. When set to "filled", it is populated with example datasets.

Attention: the mocked functions, i.e. datadir_temp() and datadir_persistent() cannot be used directly inside expr when called via devtools::test(). I'm not sure why, but it seems as if devtools and/or testthat have their own copies of the functions which are used when the expression is evaluated.

Value

A list containing with following elements:

• rv: The return value of the expression.

• runtime: The "elapsed" runtime of the expression in seconds. Measured with system.time().

• output: The captured output.

• message: The captured messages.

• plot: The path to the saved plot.

• testdir: The path to the test directory.

• inputs: The paths to the copied input files.

Author(s)

2024-2025 Tobias Schmidt: initial version.

Examples

x1 <- evalwith(output = "captured", cat("Helloworld\n"))
str(x1)

x2 <- evalwith(datadir_persistent = "missing", message = "captured", datadir())
str(x2)

x3 <- evalwith(testdir = "dummy", inputs = "bruker/urine/urine_1", dir())
str(x3)

x4 <- evalwith(Sys.sleep(0.02))
str(x4)

metabodecon documentation built on Nov. 5, 2025, 7:12 p.m.