dev/makeMD5.R
In hyginn/rptPlus: R Package Template - Enhanced
# makeMD5.R
#
#
# A sample script that produces or updates an MD5 file for a package and checks
# an existing MD5 file against the package files.
#
# Author: Boris Steipe (ORCID: 0000-0002-1134-6758)
# License: (c) Author (2019) + MIT
# Date: 2019-01-17
#
# ToDo:
# Notes:
#
# ==============================================================================
# NO SIDE EFFECTS:
# This script can be safely source()'d to define the functions it contains.
# All other code will not be executed unless this is done interactively.
# ==== FUNCTIONS =============================================================
makeMD5 <- function(myDir = getwd(), ignoreFiles, ignorePatternsIn) {
# Purpose:
# produce a file that is valid input for tools::checkMD5sums()
# Parameters:
# myDir: The directory in which the resulting MD5 file will be placed.
# All files that are returned by a call to
# dir(myDir, recursive = TRUE) will be processed unless they are
# listed in the "ignore" parameter (see below).
# Defaults to the outout of getwd(). Will be used to construct
# fully qualified paths via file.path(), so do not add a trailing
# path-separator character.
# ignoreFiles: a vector of regular expressions. Files matching any of these
# expressions will not be processed. Defaults to "^MD5$". Set this
# parameter to "" to process all files.
# ignorePatternsIn: a vector of filenames. Regular expressions contained
# in these files will be added to the ignoreFiles list.
# Defaults to ".Rbuildignore". Set this parameter
# to "" to add no patterns to the ignoreFiles list.
# Filenames are expected relative to myDir and fully
# qualified paths are constructed from file.path(), i.e.
# in a platform independent way.
# Details: The default values are appropriate to create an MD5 file in an R
# package development workflow. In this scenario, files will be
# mentioned in .Rbuildignore that should not appear in the
# package MD5 file since they will not be bundled with the package.
# Those files will not be processed into the MD5 output file.
#
# Comment- or empty lines contained in files mentioned in
# "ignorePatternsIn" will be skipped.
# Value:
# NULL (invisible). The function is executed for its side effect of
# creating a new MD5 file in the myDir directory or updating an
# existing one. This file is suitable input for
# tools::checkMD5sums("", myDir)).
# define regex patterns, which files to ignore
if (missing(ignoreFiles)) {
ignoreFiles <- c("^MD5$") # default: ignore MD5 file itself
} else if (all(ignoreFiles == "")) {
ignoreFiles <- character()
}
# define files containing additional regexes
if (missing(ignorePatternsIn)) {
ignorePatternsIn <- c(".Rbuildignore") # default
} else if (all(ignorePatternsIn == "")) {
ignorePatternsIn <- character()
}
# process all files containing additional regexes
for (fN in ignorePatternsIn) {
fN <- file.path(myDir, fN)
x <- readLines(fN)
x <- x[! grepl("(^\\s*#)|(^\\s*$)", x)] # remove comment- or empty lines
ignoreFiles <- c(ignoreFiles, x) # add regex patterns to list
}
# make initial list of filenames
fileNames <- dir(myDir, recursive = TRUE)
# also make list of directory names - some regexes may exclude
# directories, not files
dirNames <- list.dirs(path = myDir, full.names = FALSE)
dirNames <- dirNames[! grepl("(^\\.)|(^$)", dirNames)] # not empty or hidden
# remove all files that need to be ignored
for (patt in ignoreFiles) {
if (sum(grepl(patt, dirNames)) > 0) { # note: pattern matches directories!
# change pattern to match filepaths and remove all matching files
# note: must terminate with .Platform$file.sep, otherwise filenames
# starting with the directory string will be targeted!
p2 <- gsub("(\\$)*$", .Platform$file.sep, patt)
fileNames <- fileNames[! grepl(p2, fileNames)]
}
fileNames <- fileNames[! grepl(patt, fileNames)]
}
# done creating list of files to process
# md5-process all files
md5 <- tools::md5sum(file.path(myDir, fileNames))
if (length(md5) > 0) {
# filenames are fully qualified. Remove myDir to get relative
# path, and remove first character, which must be either "\" or "/"
md5 <- paste0(md5, " *", gsub(paste0(myDir, "."), "", names(md5)))
}
# output MD5 file
writeLines(md5, con = file.path(myDir, "MD5"))
return(invisible(NULL))
}
# ==== PROCESS ===============================================================
if (FALSE) {
makeMD5()
tools::checkMD5sums("", getwd())
}
# ==== TESTS =================================================================
# Enter your function tests here...
if (FALSE) {
library(testthat)
myPath <- paste0(tempdir(), "/testMD5")
dir.create(myPath)
myMD5 <- file.path(myPath, "MD5")
# list.dirs(myPath)
# list.files(myPath, recursive = TRUE)
test_that("an empty directory creates an empty MD5", {
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
unlink(myMD5)
})
dir.create(paste0(myPath, "/skip/skip"), recursive = TRUE)
dir.create(paste0(myPath, "/do/do"), recursive = TRUE)
dir.create(paste0(myPath, "/.hidden"), recursive = TRUE)
testFN <- sprintf("test%02d.txt", 1:7)
testFN[1] <- file.path(myPath, "", testFN[1])
testFN[2] <- file.path(myPath, ".hidden", testFN[2])
testFN[3] <- file.path(myPath, "skip", testFN[3])
testFN[4] <- file.path(myPath, "skip/skip", testFN[4])
testFN[5] <- file.path(myPath, "do", testFN[5])
testFN[6] <- file.path(myPath, "do", testFN[6])
testFN[7] <- file.path(myPath, "do/do", testFN[7])
txt <- "Test string"
test_that("an empty file tree creates an empty MD5", {
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(0, length(x)) # empty
expect_true(tools::checkMD5sums("", myPath)) # should skip "MD5"
unlink(myMD5)
})
test_that("a single file in myPath creates the right MD5", {
writeLines(txt, con = testFN[1])
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(1, length(x))
expect_true(grepl(paste0("\\*", gsub("^.+/","", testFN[1])), x))
expect_true(tools::checkMD5sums("", myPath))
unlink(testFN[1]) # note: we are keeping MD5
})
test_that("ignoring the MD5 file works", {
writeLines(txt, con = testFN[1])
# MD5 is not used per function default
makeMD5(myDir = myPath, ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(1, length(x)) # 1, not 2
expect_true(grepl(paste0("\\*", gsub("^.+/","", testFN[1])), x))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, testFN[1]))
})
test_that("several files in the tree create the right MD5", {
for (i in 1:7) {
writeLines(txt, con = testFN[i])
}
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(6, length(x))
expect_equal(6, sum(grepl("\\*.*test0[1-7]\\.txt", x)))
expect_false(any(grepl("\\*.*test02\\.txt", x))) # in .hidden directory
expect_true(tools::checkMD5sums("", myPath))
unlink(myMD5) # keep test files in place
})
test_that("one or more regular expressions work in the ignoreFiles parameter", {
makeMD5(myDir = myPath,
ignoreFiles = c("^MD5$", "[567]"),
ignorePatternsIn = "")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(3, length(x))
expect_equal(3, sum(grepl("\\*.*test0[1-7]\\.txt", x)))
expect_false(any(grepl("[567]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(myMD5) # keep test files in place
})
test_that("the default .Rbuildignore file works with one regex", {
writeLines("test0[13]\\.txt$", con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[4-7]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("the default .Rbuildignore file works with two regexes", {
writeLines(c("test07\\.txt$",
"test05\\.txt$"),
con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[1346]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("the default .Rbuildignore file works with two directories", {
writeLines(c("^skip$",
"^do/do$"),
con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(3, length(x))
expect_equal(3, sum(grepl("\\*.*test0[156]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("a file .Rtestignore file works with two regexes", {
writeLines(c("test01\\.txt$",
"test06\\.txt$"),
con = file.path(myPath, ".Rtestignore"))
makeMD5(myDir = myPath, ignorePatternsIn = ".Rtestignore")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[3457]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rtestignore")))
})
test_that("two ignore files with two regexes each work", {
writeLines(c("^skip$",
"test01\\.txt$"),
con = file.path(myPath, ".Rbuildignore"))
writeLines(c("test05\\.txt$",
"^do/do$"),
con = file.path(myPath, ".Rtestignore"))
makeMD5(myDir = myPath, ignorePatternsIn = c(".Rbuildignore",
".Rtestignore"))
x <- readLines(file.path(myPath, "MD5"))
expect_equal(1, length(x))
expect_equal(1, sum(grepl("\\*.*test06\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5,
file.path(myPath, ".Rtestignore"),
file.path(myPath, ".Rbuildignore")))
})
# Cleanup:
# unlink(testFN)
# unlink(myPath, recursive = TRUE)
# list.dirs(myPath)
# list.files(myPath, recursive = TRUE)
}
# [END]
hyginn/rptPlus documentation built on May 30, 2019, 2:11 p.m.
R Package Documentation
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# makeMD5.R
#
#
# A sample script that produces or updates an MD5 file for a package and checks
# an existing MD5 file against the package files.
#
# Author: Boris Steipe (ORCID: 0000-0002-1134-6758)
# License: (c) Author (2019) + MIT
# Date: 2019-01-17
#
# ToDo:
# Notes:
#
# ==============================================================================
# NO SIDE EFFECTS:
# This script can be safely source()'d to define the functions it contains.
# All other code will not be executed unless this is done interactively.
# ==== FUNCTIONS =============================================================
makeMD5 <- function(myDir = getwd(), ignoreFiles, ignorePatternsIn) {
# Purpose:
# produce a file that is valid input for tools::checkMD5sums()
# Parameters:
# myDir: The directory in which the resulting MD5 file will be placed.
# All files that are returned by a call to
# dir(myDir, recursive = TRUE) will be processed unless they are
# listed in the "ignore" parameter (see below).
# Defaults to the outout of getwd(). Will be used to construct
# fully qualified paths via file.path(), so do not add a trailing
# path-separator character.
# ignoreFiles: a vector of regular expressions. Files matching any of these
# expressions will not be processed. Defaults to "^MD5$". Set this
# parameter to "" to process all files.
# ignorePatternsIn: a vector of filenames. Regular expressions contained
# in these files will be added to the ignoreFiles list.
# Defaults to ".Rbuildignore". Set this parameter
# to "" to add no patterns to the ignoreFiles list.
# Filenames are expected relative to myDir and fully
# qualified paths are constructed from file.path(), i.e.
# in a platform independent way.
# Details: The default values are appropriate to create an MD5 file in an R
# package development workflow. In this scenario, files will be
# mentioned in .Rbuildignore that should not appear in the
# package MD5 file since they will not be bundled with the package.
# Those files will not be processed into the MD5 output file.
#
# Comment- or empty lines contained in files mentioned in
# "ignorePatternsIn" will be skipped.
# Value:
# NULL (invisible). The function is executed for its side effect of
# creating a new MD5 file in the myDir directory or updating an
# existing one. This file is suitable input for
# tools::checkMD5sums("", myDir)).
# define regex patterns, which files to ignore
if (missing(ignoreFiles)) {
ignoreFiles <- c("^MD5$") # default: ignore MD5 file itself
} else if (all(ignoreFiles == "")) {
ignoreFiles <- character()
}
# define files containing additional regexes
if (missing(ignorePatternsIn)) {
ignorePatternsIn <- c(".Rbuildignore") # default
} else if (all(ignorePatternsIn == "")) {
ignorePatternsIn <- character()
}
# process all files containing additional regexes
for (fN in ignorePatternsIn) {
fN <- file.path(myDir, fN)
x <- readLines(fN)
x <- x[! grepl("(^\\s*#)|(^\\s*$)", x)] # remove comment- or empty lines
ignoreFiles <- c(ignoreFiles, x) # add regex patterns to list
}
# make initial list of filenames
fileNames <- dir(myDir, recursive = TRUE)
# also make list of directory names - some regexes may exclude
# directories, not files
dirNames <- list.dirs(path = myDir, full.names = FALSE)
dirNames <- dirNames[! grepl("(^\\.)|(^$)", dirNames)] # not empty or hidden
# remove all files that need to be ignored
for (patt in ignoreFiles) {
if (sum(grepl(patt, dirNames)) > 0) { # note: pattern matches directories!
# change pattern to match filepaths and remove all matching files
# note: must terminate with .Platform$file.sep, otherwise filenames
# starting with the directory string will be targeted!
p2 <- gsub("(\\$)*$", .Platform$file.sep, patt)
fileNames <- fileNames[! grepl(p2, fileNames)]
}
fileNames <- fileNames[! grepl(patt, fileNames)]
}
# done creating list of files to process
# md5-process all files
md5 <- tools::md5sum(file.path(myDir, fileNames))
if (length(md5) > 0) {
# filenames are fully qualified. Remove myDir to get relative
# path, and remove first character, which must be either "\" or "/"
md5 <- paste0(md5, " *", gsub(paste0(myDir, "."), "", names(md5)))
}
# output MD5 file
writeLines(md5, con = file.path(myDir, "MD5"))
return(invisible(NULL))
}
# ==== PROCESS ===============================================================
if (FALSE) {
makeMD5()
tools::checkMD5sums("", getwd())
}
# ==== TESTS =================================================================
# Enter your function tests here...
if (FALSE) {
library(testthat)
myPath <- paste0(tempdir(), "/testMD5")
dir.create(myPath)
myMD5 <- file.path(myPath, "MD5")
# list.dirs(myPath)
# list.files(myPath, recursive = TRUE)
test_that("an empty directory creates an empty MD5", {
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
unlink(myMD5)
})
dir.create(paste0(myPath, "/skip/skip"), recursive = TRUE)
dir.create(paste0(myPath, "/do/do"), recursive = TRUE)
dir.create(paste0(myPath, "/.hidden"), recursive = TRUE)
testFN <- sprintf("test%02d.txt", 1:7)
testFN[1] <- file.path(myPath, "", testFN[1])
testFN[2] <- file.path(myPath, ".hidden", testFN[2])
testFN[3] <- file.path(myPath, "skip", testFN[3])
testFN[4] <- file.path(myPath, "skip/skip", testFN[4])
testFN[5] <- file.path(myPath, "do", testFN[5])
testFN[6] <- file.path(myPath, "do", testFN[6])
testFN[7] <- file.path(myPath, "do/do", testFN[7])
txt <- "Test string"
test_that("an empty file tree creates an empty MD5", {
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(0, length(x)) # empty
expect_true(tools::checkMD5sums("", myPath)) # should skip "MD5"
unlink(myMD5)
})
test_that("a single file in myPath creates the right MD5", {
writeLines(txt, con = testFN[1])
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(1, length(x))
expect_true(grepl(paste0("\\*", gsub("^.+/","", testFN[1])), x))
expect_true(tools::checkMD5sums("", myPath))
unlink(testFN[1]) # note: we are keeping MD5
})
test_that("ignoring the MD5 file works", {
writeLines(txt, con = testFN[1])
# MD5 is not used per function default
makeMD5(myDir = myPath, ignorePatternsIn = "")
x <- readLines(myMD5)
expect_equal(1, length(x)) # 1, not 2
expect_true(grepl(paste0("\\*", gsub("^.+/","", testFN[1])), x))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, testFN[1]))
})
test_that("several files in the tree create the right MD5", {
for (i in 1:7) {
writeLines(txt, con = testFN[i])
}
makeMD5(myDir = myPath, ignoreFiles = "", ignorePatternsIn = "")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(6, length(x))
expect_equal(6, sum(grepl("\\*.*test0[1-7]\\.txt", x)))
expect_false(any(grepl("\\*.*test02\\.txt", x))) # in .hidden directory
expect_true(tools::checkMD5sums("", myPath))
unlink(myMD5) # keep test files in place
})
test_that("one or more regular expressions work in the ignoreFiles parameter", {
makeMD5(myDir = myPath,
ignoreFiles = c("^MD5$", "[567]"),
ignorePatternsIn = "")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(3, length(x))
expect_equal(3, sum(grepl("\\*.*test0[1-7]\\.txt", x)))
expect_false(any(grepl("[567]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(myMD5) # keep test files in place
})
test_that("the default .Rbuildignore file works with one regex", {
writeLines("test0[13]\\.txt$", con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[4-7]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("the default .Rbuildignore file works with two regexes", {
writeLines(c("test07\\.txt$",
"test05\\.txt$"),
con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[1346]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("the default .Rbuildignore file works with two directories", {
writeLines(c("^skip$",
"^do/do$"),
con = file.path(myPath, ".Rbuildignore"))
makeMD5(myDir = myPath)
x <- readLines(file.path(myPath, "MD5"))
expect_equal(3, length(x))
expect_equal(3, sum(grepl("\\*.*test0[156]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rbuildignore")))
})
test_that("a file .Rtestignore file works with two regexes", {
writeLines(c("test01\\.txt$",
"test06\\.txt$"),
con = file.path(myPath, ".Rtestignore"))
makeMD5(myDir = myPath, ignorePatternsIn = ".Rtestignore")
x <- readLines(file.path(myPath, "MD5"))
expect_equal(4, length(x))
expect_equal(4, sum(grepl("\\*.*test0[3457]\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5, file.path(myPath, ".Rtestignore")))
})
test_that("two ignore files with two regexes each work", {
writeLines(c("^skip$",
"test01\\.txt$"),
con = file.path(myPath, ".Rbuildignore"))
writeLines(c("test05\\.txt$",
"^do/do$"),
con = file.path(myPath, ".Rtestignore"))
makeMD5(myDir = myPath, ignorePatternsIn = c(".Rbuildignore",
".Rtestignore"))
x <- readLines(file.path(myPath, "MD5"))
expect_equal(1, length(x))
expect_equal(1, sum(grepl("\\*.*test06\\.txt", x)))
expect_true(tools::checkMD5sums("", myPath))
unlink(c(myMD5,
file.path(myPath, ".Rtestignore"),
file.path(myPath, ".Rbuildignore")))
})
# Cleanup:
# unlink(testFN)
# unlink(myPath, recursive = TRUE)
# list.dirs(myPath)
# list.files(myPath, recursive = TRUE)
}
# [END]
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