Create hash function digests for arbitrary R objects
The digest function applies a cryptographical hash function to
arbitrary R objects. By default, the objects are internally
serialized, and either one of the currently implemented MD5 and SHA-1
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.
digest(object, algo=c("md5", "sha1", "crc32", "sha256", "sha512",
"xxhash32", "xxhash64", "murmur32", "spookyhash",
"blake3"), serialize=TRUE, file=FALSE,
length=Inf, skip="auto", ascii=FALSE, raw=FALSE, seed=0,
errormode=c("stop","warn","silent"),
serializeVersion=.getSerializeVersion())object |
An arbitrary R object which will then be passed to the
|
algo |
The algorithms to be used; currently available choices are
|
serialize |
A logical variable indicating whether the object
should be serialized using |
file |
A logical variable indicating whether the object is a file
name or a file name if |
length |
Number of characters to process. By default, when
|
skip |
Number of input bytes to skip before calculating the
digest. Negative values are invalid and currently treated as zero.
Special value |
ascii |
This flag is passed to the |
raw |
A logical variable with a default value of FALSE, implying
|
seed |
an integer to seed the random number generator. This is only
used in the |
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 |
serializeVersion |
An integer value specifying the internal
version of the serialization format, with 2 being the default;
see |
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 and xxhash64, 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.
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.
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.
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).
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.
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.
## 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")
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]))
}
# 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)))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.