Checksums {reproducible}

Calculate checksum

Description

Verify (and optionally write) checksums. Checksums are computed using .digest(), which is simply a wrapper around digest::digest.

Usage

Checksums(
  path,
  write,
  quickCheck = getOption("reproducible.quickCheck", FALSE),
  checksumFile = identifyCHECKSUMStxtFile(path),
  files = NULL,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

## S4 method for signature 'character,logical'
Checksums(
  path,
  write,
  quickCheck = getOption("reproducible.quickCheck", FALSE),
  checksumFile = identifyCHECKSUMStxtFile(path),
  files = NULL,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

## S4 method for signature 'character,missing'
Checksums(
  path,
  write,
  quickCheck = getOption("reproducible.quickCheck", FALSE),
  checksumFile = identifyCHECKSUMStxtFile(path),
  files = NULL,
  verbose = getOption("reproducible.verbose", 1),
  ...
)

Arguments

path

Character string giving the directory path containing CHECKSUMS.txt file, or where it will be written if checksumFile = TRUE.

write

Logical indicating whether to overwrite CHECKSUMS.txt. Default is FALSE, as users should not change this file. Module developers should write this file prior to distributing their module code, and update accordingly when the data change.

quickCheck

Logical. If TRUE, then this will only use file sizes, rather than a digest::digest hash. This is generally faster, but will be much less robust.

checksumFile

The filename of the checksums file to read or write to. The default is ‘CHECKSUMS.txt’ located at file.path(path, module, "data", checksumFile). It is likely not a good idea to change this, and should only be used in cases such as Cache, which can evaluate if the checksumFile has changed.

files

An optional character string or vector of specific files to checksum. This may be very important if there are many files listed in a CHECKSUMS.txt file, but only a few are to be checksummed.

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

...

Passed to digest::digest() and utils::write.table(). For digest, the notable argument is algo. For write.table, the notable argument is append.

Value

A data.table with columns: result, expectedFile, actualFile, checksum.x, checksum.y, algorithm.x, algorithm.y, filesize.x, filesize.y indicating the result of comparison between local file (x) and expectation based on the CHECKSUMS.txt file.

Note

In version 1.2.0 and earlier, two checksums per file were required because of differences in the checksum hash values on Windows and Unix-like platforms. Recent versions use a different (faster) algorithm and only require one checksum value per file. To update your ‘CHECKSUMS.txt’ files using the new algorithm, see https://github.com/PredictiveEcology/SpaDES/issues/295#issuecomment-246513405.

Author(s)

Alex Chubaty

Examples

## Not run: 
modulePath <- file.path(tempdir(), "myModulePath")
dir.create(modulePath, recursive = TRUE, showWarnings = FALSE)
moduleName <- "myModule"
cat("hi", file = file.path(modulePath, moduleName)) # put something there for this example

## verify checksums of all data files
Checksums(modulePath, files = moduleName)

## write new CHECKSUMS.txt file
Checksums(files = moduleName, modulePath, write = TRUE)

## End(Not run)