R: Create hash function digests for arbitrary R objects or files

digest {digest}

R Documentation

Create hash function digests for arbitrary R objects or files

Description

The digest function applies one of several cryptographic or non-cryptographics hash function to arbitrary R objects or files. By default, the objects are internally serialized, and the selected hash functions algorithms can be used to compute a compact digest of the serialized object.

In order to compare this implementation with others, serialization of the input argument can also be turned off in which the input argument must be a character string for which its digest is returned.

Usage

digest(object, algo=c("md5", "sha1", "crc32", "sha256", "sha512",
                      "xxhash32", "xxhash64", "murmur32", "spookyhash",
                      "blake3", "crc32c", "xxh3_64", "xxh3_128"),
       serialize=TRUE, file=FALSE,
       length=Inf, skip="auto", ascii=FALSE, raw=FALSE, seed=0,
       errormode=c("stop","warn","silent"),
       serializeVersion=.getSerializeVersion())

Arguments

`object`	An arbitrary R object which will then be passed to the `serialize` function, unless the `serialize` argument is set to `FALSE`.
`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`.
`serialize`	A logical variable indicating whether the object should be serialized using `serialize` (in ASCII form). Setting this to `FALSE` allows to compare the digest output of given character strings to known control output. It also allows the use of raw vectors such as the output of non-ASCII serialization.
`file`	A logical variable indicating whether the object is a file name or a file name if `object` is not specified.
`length`	Number of characters to process. By default, when `length` is set to `Inf`, the whole string or file is processed.
`skip`	Number of input bytes to skip before calculating the digest. Negative values are invalid and currently treated as zero. Special value `"auto"` will cause serialization header to be skipped if `serialize` is set to `TRUE` (the serialization header contains the R version number thus skipping it allows the comparison of hashes across platforms and some R versions).
`ascii`	This flag is passed to the `serialize` function if `serialize` is set to `TRUE`, determining whether the hash is computed on the ASCII or binary representation.
`raw`	A logical variable with a default value of FALSE, implying `digest` returns digest output as ASCII hex values. Set to TRUE to return `digest` output in raw (binary) form. Note that this option is supported by most but not all of the implemented hashing algorithms
`seed`	an integer to seed the random number generator. This is only used in the `xxhash32`, `xxhash64` and `murmur32` functions and can be used to generate additional hashes for the same input if desired.
`errormode`	A character value denoting a choice for the behaviour in the case of error: ‘stop’ aborts (and is the default value), ‘warn’ emits a warning and returns `NULL` and ‘silent’ suppresses the error and returns an empty string.
`serializeVersion`	An integer value specifying the internal version of the serialization format, with 2 being the default; see `serialize` for details. The `serializeVersion` field of `option` can also be used to set a different value.

Details

Cryptographic hash functions are well researched and documented. The MD5 algorithm by Ron Rivest is specified in RFC 1321. The SHA-1 algorithm is specified in FIPS-180-1, SHA-2 is described in FIPS-180-2.

For md5, sha-1 and sha-256, this R implementation relies on standalone implementations in C by Christophe Devine. For crc32, code from the zlib library by Jean-loup Gailly and Mark Adler is used.

For sha-512, a standalone implementation from Aaron Gifford is used.

For xxhash32, xxhash64, xxh3_64 and xxh3_128 the reference implementation by Yann Collet is used.

For murmur32, the progressive implementation by Shane Day is used.

For spookyhash, the original source code by Bob Jenkins is used. The R implementation that integrates R's serialization directly with the algorithm allowing for memory-efficient incremental calculation of the hash is by Gabe Becker.

For blake3, the C implementation by Samuel Neves and Jack O'Connor is used.

For crc32c, the portable (i.e. non-hardware accelerated) version from Google is used.

Please note that this package is not meant to be used for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used. Also, it is known that crc32 is not collision-proof. For sha-1, recent results indicate certain cryptographic weaknesses as well. For more details, see for example https://www.schneier.com/blog/archives/2005/02/cryptanalysis_o.html.

Value

The digest function returns a character string of a fixed length containing the requested digest of the supplied R object. This string is of length 32 for MD5; of length 40 for SHA-1; of length 8 for CRC32 a string; of length 8 for for xxhash32; of length 16 for xxhash64; and of length 8 for murmur32.

Change Management

Version 0.6.16 of digest corrects an error in which crc32 was not guaranteeing an eight-character return. We now pad with zero to always return eight characters. Should the previous behaviour be required, set option("digestOldCRC32Format"=TRUE) and the output will be consistent with prior version (but not be consistentnly eight characters).

Author(s)

Dirk Eddelbuettel edd@debian.org for the R interface; Antoine Lucas for the integration of crc32; Jarek Tuszynski for the file-based operations; Henrik Bengtsson and Simon Urbanek for improved serialization patches; Christophe Devine for the hash function implementations for sha-1, sha-256 and md5; Jean-Loup Gailly and Mark Adler for crc32; Hannes Muehleisen for the integration of sha-512; Jim Hester for the integration of xxhash32, xxhash64 and murmur32; Kendon Bell for the integration of spookyhash using Gabe Becker's R package fastdigest.

References

MD5: https://www.ietf.org/rfc/rfc1321.txt.

SHA-1: https://en.wikipedia.org/wiki/SHA-1. SHA-256: https://csrc.nist.gov/publications/fips/fips180-2/fips180-2withchangenotice.pdf. CRC32: The original reference webpage at rocksoft.com has vanished from the web; see https://en.wikipedia.org/wiki/Cyclic_redundancy_check for general information on CRC algorithms.

https://aarongifford.com/computers/sha.html for the integrated C implementation of sha-512.

The page for the code underlying the C functions used here for sha-1 and md5, and further references, is no longer accessible. Please see https://en.wikipedia.org/wiki/SHA-1 and https://en.wikipedia.org/wiki/MD5.

https://zlib.net for documentation on the zlib library which supplied the code for crc32.

https://en.wikipedia.org/wiki/SHA_hash_functions for documentation on the sha functions.

https://github.com/Cyan4973/xxHash for documentation on the xxHash functions.

https://github.com/aappleby/smhasher for documentation on MurmurHash.

https://burtleburtle.net/bob/hash/spooky.html for the original source code of SpookyHash.

https://github.com/BLAKE3-team/BLAKE3/ for the original source code of blake3.

https://github.com/google/crc32c for the (non-hardware-accelerated) crc32c code.

Examples


## Standard RFC 1321 test vectors
md5Input <-
  c("",
    "a",
    "abc",
    "message digest",
    "abcdefghijklmnopqrstuvwxyz",
    "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789",
    paste("12345678901234567890123456789012345678901234567890123456789012",
          "345678901234567890", sep=""))
md5Output <-
  c("d41d8cd98f00b204e9800998ecf8427e",
    "0cc175b9c0f1b6a831c399e269772661",
    "900150983cd24fb0d6963f7d28e17f72",
    "f96b697d7cb7938d525a2f31aaf161d0",
    "c3fcd3d76192e4007dfb496cca67e13b",
    "d174ab98d277d9f5a5611c2c9f419d9f",
    "57edf4a22be3c955ac49da2e2107b67a")

for (i in seq(along=md5Input)) {
  md5 <- digest(md5Input[i], serialize=FALSE)
  stopifnot(identical(md5, md5Output[i]))
}

sha1Input <-
  c("abc", "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq")
sha1Output <-
  c("a9993e364706816aba3e25717850c26c9cd0d89d",
    "84983e441c3bd26ebaae4aa1f95129e5e54670f1")

for (i in seq(along=sha1Input)) {
  sha1 <- digest(sha1Input[i], algo="sha1", serialize=FALSE)
  stopifnot(identical(sha1, sha1Output[i]))
}

crc32Input <-
  c("abc",
    "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq")
crc32Output <-
  c("352441c2",
    "171a3f5f")

for (i in seq(along=crc32Input)) {
  crc32 <- digest(crc32Input[i], algo="crc32", serialize=FALSE)
  stopifnot(identical(crc32, crc32Output[i]))
}


sha256Input <-
  c("abc",
    "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq")
sha256Output <-
  c("ba7816bf8f01cfea414140de5dae2223b00361a396177a9cb410ff61f20015ad",
    "248d6a61d20638b8e5c026930c3e6039a33ce45964ff2167f6ecedd419db06c1")

for (i in seq(along=sha256Input)) {
  sha256 <- digest(sha256Input[i], algo="sha256", serialize=FALSE)
  stopifnot(identical(sha256, sha256Output[i]))
}

# SHA 512 example
sha512Input <-
  c("abc",
    "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq")
sha512Output <-
  c(paste("ddaf35a193617abacc417349ae20413112e6fa4e89a97ea20a9eeee64b55d39a",
          "2192992a274fc1a836ba3c23a3feebbd454d4423643ce80e2a9ac94fa54ca49f",
          sep=""),
    paste("204a8fc6dda82f0a0ced7beb8e08a41657c16ef468b228a8279be331a703c335",
          "96fd15c13b1b07f9aa1d3bea57789ca031ad85c7a71dd70354ec631238ca3445",
          sep=""))

for (i in seq(along=sha512Input)) {
  sha512 <- digest(sha512Input[i], algo="sha512", serialize=FALSE)
  stopifnot(identical(sha512, sha512Output[i]))
}

## xxhash32 example
xxhash32Input <-
    c("abc",
      "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq",
      "")
xxhash32Output <-
    c("32d153ff",
      "89ea60c3",
      "02cc5d05")

for (i in seq(along=xxhash32Input)) {
    xxhash32 <- digest(xxhash32Input[i], algo="xxhash32", serialize=FALSE)
    cat(xxhash32, "\n")
    stopifnot(identical(xxhash32, xxhash32Output[i]))
}

## xxhash64 example
xxhash64Input <-
    c("abc",
      "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq",
      "")
xxhash64Output <-
    c("44bc2cf5ad770999",
      "f06103773e8585df",
      "ef46db3751d8e999")

for (i in seq(along=xxhash64Input)) {
    xxhash64 <- digest(xxhash64Input[i], algo="xxhash64", serialize=FALSE)
    cat(xxhash64, "\n")
    stopifnot(identical(xxhash64, xxhash64Output[i]))
}

## these outputs were calculated using mmh3 python package
murmur32Input <-
    c("abc",
      "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq",
      "")
murmur32Output <-
    c("b3dd93fa",
      "ee925b90",
      "00000000")

for (i in seq(along=murmur32Input)) {
    murmur32 <- digest(murmur32Input[i], algo="murmur32", serialize=FALSE)
    cat(murmur32, "\n")
    stopifnot(identical(murmur32, murmur32Output[i]))
}

## these outputs were calculated using spooky python package
spookyInput <-
    c("a",
      "abc",
      "message digest")
spookyOutput <-
    c("bdc9bba09181101a922a4161f0584275",
      "67c93775f715ab8ab01178caf86713c6",
      "9630c2a55c0987a0db44434f9d67a192")

for (i in seq(along=spookyInput)) {
    # skip = 30 skips the serialization header and just hashes the strings
    spooky <- digest(spookyInput[i], algo="spookyhash", skip = 30)
    cat(spooky, "\n")
    ## we can only compare to reference output on little-endian systems
    if (isTRUE(.Call(digest:::is_little_endian)))
        stopifnot(identical(spooky, spookyOutput[i]))
}

## blake3 example
blake3Input <-
    c("abc",
      "abcdbcdecdefdefgefghfghighijhijkijkljklmklmnlmnomnopnopq",
      "")
blake3Output <-
    c("6437b3ac38465133ffb63b75273a8db548c558465d79db03fd359c6cd5bd9d85",
      "c19012cc2aaf0dc3d8e5c45a1b79114d2df42abb2a410bf54be09e891af06ff8",
      "af1349b9f5f9a1a6a0404dea36dcc9499bcb25c9adc112b7cc9a93cae41f3262")

for (i in seq(along=blake3Input)) {
    blake3 <- digest(blake3Input[i], algo="blake3", serialize=FALSE)
    cat(blake3, "\n")
    stopifnot(identical(blake3, blake3Output[i]))
}

## crc32c
crc32cInput <- c("123456789", "The quick brown fox jumps over the lazy dog")
crc32cOutput <- c("e3069283", "22620404")
for (i in seq_along(crc32cInput)) {
    crc32c <- digest(crc32cInput[i], algo="crc32c", serialize=FALSE)
    cat(crc32c, "\n")
    stopifnot(identical(crc32c, crc32cOutput[i]))
}

# example of a digest of a standard R list structure
digest(list(LETTERS, data.frame(a=letters[1:5], b=matrix(1:10,ncol=2))))

# test 'length' parameter and file input
fname <- file.path(R.home(),"COPYING")
x <- readChar(fname, file.info(fname)$size) # read file
for (alg in c("sha1", "md5", "crc32")) {
  # partial file
  h1 <- digest(x    , length=18000, algo=alg, serialize=FALSE)
  h2 <- digest(fname, length=18000, algo=alg, serialize=FALSE, file=TRUE)
  h3 <- digest( substr(x,1,18000) , algo=alg, serialize=FALSE)
  stopifnot( identical(h1,h2), identical(h1,h3) )
  # whole file
  h1 <- digest(x    , algo=alg, serialize=FALSE)
  h2 <- digest(fname, algo=alg, serialize=FALSE, file=TRUE)
  stopifnot( identical(h1,h2) )
}

# compare md5 algorithm to other tools
library(tools)
fname <- file.path(R.home(),"COPYING")
h1 <- as.character(md5sum(fname))
h2 <- digest(fname, algo="md5", file=TRUE)
stopifnot( identical(h1,h2) )

## digest is _designed_ to return one has summary per object to for a desired
## For vectorised output see digest::getVDigest() which provides
## better performance than base::Vectorize()

md5 <- getVDigest()
v <- md5(1:5)     			# digest integers 1 to 5
stopifnot(identical(v[1], digest(1L)),	# check first and third result
          identical(v[3], digest(3L)))

[Package digest version 0.6.36 Index]