robustDigest: Create reproducible digests of objects in R

In reproducible: Enhance Reproducibility of R Code

Create reproducible digests of objects in R

Description

Not all aspects of R objects are captured by current hashing tools in R (e.g. digest::digest, knitr caching, archivist::cache). This is mostly because many objects have "transient" (e.g., functions have environments), or "disk-backed" features. Since the goal of using reproducibility is to have tools that are not session specific, this function attempts to strip all session specific information so that the digest works between sessions and operating systems. It is tested under many conditions and object types, there are bound to be others that don't work correctly.

Usage

.robustDigest(
  object,
  .objects = NULL,
  length = getOption("reproducible.length", Inf),
  algo = "xxhash64",
  quick = getOption("reproducible.quick", FALSE),
  classOptions = list(),
  ...
)

## S4 method for signature 'ANY'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'function'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'expression'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'language'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'character'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'Path'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'environment'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'list'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'data.frame'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'numeric'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'matrix'
.robustDigest(object, .objects, length, algo, quick, classOptions)

## S4 method for signature 'integer'
.robustDigest(object, .objects, length, algo, quick, classOptions)

Arguments

object	an object to digest.
.objects	Character vector of objects to be digested. This is only applicable if there is a list, environment (or similar) with named objects within it. Only this/these objects will be considered for caching, i.e., only use a subset of the list, environment or similar objects. In the case of nested list-type objects, this will only be applied outermost first.
length	Numeric. If the element passed to Cache is a Path class object (from e.g., asPath(filename)) or it is a Raster with file-backing, then this will be passed to digest::digest, essentially limiting the number of bytes to digest (for speed). This will only be used if quick = FALSE. Default is getOption("reproducible.length"), which is set to Inf.
algo	The algorithms to be used; currently available choices are md5, which is also the default, sha1, crc32, sha256, sha512, xxhash32, xxhash64, murmur32, spookyhash, blake3, crc32c, xxh3_64, and xxh3_128.
quick	Logical or character. If TRUE, no disk-based information will be assessed, i.e., only memory content. See Details section about quick in Cache().
classOptions	Optional list. This will pass into .robustDigest for specific classes. Should be options that the .robustDigest knows what to do with.
...	Arguments passed to FUN, if FUN is not an expression.
objects	Optional character vector indicating which objects are to be considered while making digestible. This argument is not used in the default cases; the only known method that uses this in the default cases; the only known method that uses this argument is the simList class from SpaDES.core.

Value

A hash i.e., digest of the object passed in.

Classes

⁠Raster*⁠ objects have the potential for disk-backed storage, thus, require more work. Also, because ⁠Raster*⁠ can have a built-in representation for having their data content located on disk, this format will be maintained if the raster already is file-backed, i.e., to create .tif or .grd backed rasters, use writeRaster first, then Cache. The ‘.tif’ or ‘.grd’ will be copied to the ‘raster/’ subdirectory of the cachePath. Their RAM representation (as an R object) will still be in the usual ‘cacheOutputs/’ (or formerly ‘gallery/’) directory. For inMemory raster objects, they will remain as binary .RData files.

Functions (which are contained within environments) are converted to a text representation via a call to format(FUN).

Objects contained within a list or environment are recursively hashed using digest::digest(), while removing all references to environments.

Character strings are first assessed with dir.exists and file.exists to check for paths. If they are found to be paths, then the path is hashed with only its filename via basename(filename). If it is actually a path, we suggest using asPath(thePath)

Author(s)

Eliot McIntire

Examples

a <- 2
tmpfile1 <- tempfile()
tmpfile2 <- tempfile()
tmpfile3 <- tempfile(fileext = ".grd")
tmpfile4 <- tempfile(fileext = ".grd")
save(a, file = tmpfile1)
save(a, file = tmpfile2)

# treats as character string, so 2 filenames are different
digest::digest(tmpfile1)
digest::digest(tmpfile2)

# tests to see whether character string is representing a file
.robustDigest(tmpfile1)
.robustDigest(tmpfile2) # same

# if you tell it that it is a path, then you can decide if you want it to be
#  treated as a character string or as a file path
.robustDigest(asPath(tmpfile1), quick = TRUE)
.robustDigest(asPath(tmpfile2), quick = TRUE) # different because using file info

.robustDigest(asPath(tmpfile1), quick = FALSE)
.robustDigest(asPath(tmpfile2), quick = FALSE) # same because using file content

# SpatRasters are have pointers
if (requireNamespace("terra", quietly = TRUE)) {
  r <- terra::rast(system.file("ex/elev.tif", package = "terra"))
  r3 <- terra::deepcopy(r)
  r1 <- terra::writeRaster(r, filename = tmpfile3)

  digest::digest(r)
  digest::digest(r3) # different but should be same
  .robustDigest(r1)
  .robustDigest(r3) # same... data & metadata are the same

  # note, this is not true for comparing memory and file-backed rasters
  .robustDigest(r)
  .robustDigest(r1) # different
}

reproducible documentation built on June 22, 2024, 10:18 a.m.