linkOrCopy: Hardlink, symlink, or copy a file

In PredictiveEcology/reproducible: Enhance Reproducibility of R Code

Hardlink, symlink, or copy a file

Description

Attempt first to make a hardlink. If that fails, try to make a symlink (on non-windows systems and symlink = TRUE). If that fails, copy the file.

Usage

linkOrCopy(
  from,
  to,
  symlink = TRUE,
  overwrite = TRUE,
  verbose = getOption("reproducible.verbose", 1)
)

Arguments

from, to	Character vectors, containing file names or paths. to can alternatively be the path to a single existing directory.
symlink	Logical indicating whether to use symlink (instead of hardlink). Default FALSE.
overwrite	Logical. Should downloading and all the other actions occur even if they pass the checksums or the files are all there.
verbose	Numeric, -1 silent (where possible), 0 being very quiet, 1 showing more messaging, 2 being more messaging, etc. Default is 1. Above 3 will output much more information about the internals of Caching, which may help diagnose Caching challenges. Can set globally with an option, e.g., ⁠options('reproducible.verbose' = 0) to reduce to minimal⁠

Value

This function is called for its side effects, which will be a file.link is that is available or file.copy if not (e.g., the two directories are not on the same physical disk).

Note

Use caution with files-backed objects (e.g., rasters). See examples.

Author(s)

Alex Chubaty and Eliot McIntire

See Also

file.link(), file.symlink(), file.copy().

Examples

tmpDir <- file.path(tempdir(), "symlink-test")
tmpDir <- normalizePath(tmpDir, winslash = "/", mustWork = FALSE)
dir.create(tmpDir)

f0 <- file.path(tmpDir, "file0.csv")
write.csv(iris, f0)

d1 <- file.path(tmpDir, "dir1")
dir.create(d1)
write.csv(iris, file.path(d1, "file1.csv"))

d2 <- file.path(tmpDir, "dir2")
dir.create(d2)
f2 <- file.path(tmpDir, "file2.csv")

## create link to a file
linkOrCopy(f0, f2)
file.exists(f2) ## TRUE
identical(read.table(f0), read.table(f2)) ## TRUE

## deleting the link shouldn't delete the original file
unlink(f0)
file.exists(f0) ## FALSE
file.exists(f2) ## TRUE

if (requireNamespace("terra", quietly = TRUE)) {
  ## using spatRasters and other file-backed objects
  f3a <- system.file("ex/test.grd", package = "terra")
  f3b <- system.file("ex/test.gri", package = "terra")
  r3a <- terra::rast(f3a)
  f4a <- file.path(tmpDir, "raster4.grd")
  f4b <- file.path(tmpDir, "raster4.gri")
  linkOrCopy(f3a, f4a) ## hardlink
  linkOrCopy(f3b, f4b) ## hardlink
  r4a <- terra::rast(f4a)

  isTRUE(all.equal(r3a, r4a)) # TRUE

  ## cleanup
  unlink(tmpDir, recursive = TRUE)
}

PredictiveEcology/reproducible documentation built on April 19, 2024, 7:23 p.m.