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R.utils (version 2.1.0)

Various Programming Utilities

Description

Utility functions useful when programming and developing R packages.

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install.packages('R.utils')

Monthly Downloads

192,589

Version

2.1.0

License

LGPL (>= 2.1)

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Repository

https://github.com/HenrikBengtsson/R.utils

Maintainer

Henrik Bengtsson

Last Published

May 28th, 2015

Functions in R.utils (2.1.0)

R.utils-package

Package R.utils

Sys.readlink2

Read File Symbolic Links (also on Windows)

Non-documented objects

as.character.Options

Returns a character string version of this object

FileProgressBar

A progress bar that sets the size of a file accordingly

enter.Verbose

Writes a message and indents the following output

ProgressBar

Provides text based counting progress bar

TimeoutException

TimeoutException represents timeout errors

Java$asLong

Converts a numeric to a Java long

SmartComments

Abstract class SmartComments

Arguments$getNumerics

Coerces to a numeric vector and validates

Arguments$getIndices

Coerces to a integer vector and validates

getRaw.GString

Gets the unprocessed GString

getRelativePath

Gets the relative pathname relative to a directory

Java$readShort

Reads a Java formatted short (16 bits) from a connection

as.double.Verbose

Gets a numeric value of this object

cmdArgsCall

Calls an R function passing command-line arguments

compile.SmartComments

Preprocess a vector of code lines

compressPDF

Compresses a PDF (into a new PDF)

GString$getBuiltinRversion

Gets the current R version

dimNA< -

Sets the dimension of an object with the option to infer one dimension autmatically

Verbose

Class to writing verbose messages to a connection or file

Java$asByte

Converts a numeric to a Java byte

PERCENT< -PERCENT

Assignment operator for delayed assignments ('lazy future')

VComments

The VComments class

Settings$findSettings

Searches for the settings file in one or several directories

egsub

Global substitute of expression using regular expressions

Options

The Options class

callHooks

Call hook functions by hook name

as.character.GString

Gets the processed character string

System$getHostname

Retrieves the computer name of the current host

colClasses

Creates a vector of column classes used for tabular reading

NullVerbose

A Verbose class ignoring everything

Arguments

Static class to validate and process arguments

attachLocally.list

Assigns an objects elements locally

System$currentTimeMillis

Get the current time in milliseconds

evaluate.GString

Parses and evaluates a GString

getAbsolutePath

Gets the absolute pathname string

hasOption.Options

Checks if an option exists

commandArgs

Extract command-line arguments

getLoadedPathname.Settings

Gets the pathname of the settings file loaded

isVisible.Verbose

Checks if a certain verbose level will be shown or not

cat.Verbose

Concatenates and prints objects if above threshold

cmdArgs

Simple access to parsed command-line arguments

timestamp.Verbose

Writes a timestamp

MultiVerbose

A Verbose class ignoring everything

swapXY.density

Swaps x and y coordinates of a density object

callHooks.function

Call hook functions

Java$asInt

Converts an numeric to a Java integer

Arguments$getVector

Validates a vector

update.TextStatusBar

Updates the status bar (visually)

TextStatusBar

A status bar at the R prompt that can be updated

downloadFile.character

Downloads a file

capitalize

Capitalizes/decapitalizes each character string in a vector

extract.array

Extract a subset of an array, matrix or a vector with unknown dimensions

Assert$inherits

Static method asserting that an object inherits from of a certain class

Arguments$getVerbose

Coerces to Verbose object

isDirectory

Checks if the file specification is a directory

Assert$check

Static method asserting that a generic condition is true

GString$getBuiltinDate

Gets the current date

less.Verbose

Creates a cloned instance with a higher threshold

convertComment.SmartComments

Converts a single smart comment to R code

gcat

Parses, evaluates and outputs a GString

countLines

Counts the number of lines in a text file

env

Creates a new environment, evaluates an expression therein, and returns the environment

System

Static class to query information about the system

as.logical.Verbose

Gets a logical value of this object

GString$getBuiltinTime

Gets the current time

LComments

The LComments class

exit.Verbose

Writes a message and unindents the following output

createFileAtomically

Creates a file atomically

Assert$isMatrix

Static method asserting thatan object is a matrix

readTable

Reads a file in table format

Arguments$getFilename

Gets and validates a filename

GString

Character string with advanced substitutions

isFile

Checks if the file specification is a file

System$getUsername

Retrieves the name of the user running R

GString$getBuiltinRhome

Gets the path where R is installed

on.Verbose

Turn on the output

System$parseDebian

Parses a string, file or connection for Debian formatted parameters

print.GString

Prints the processed GString

GString$getVariableValue

Gets a variable value given a name and attributes

getLabel.TextStatusBar

Gets the current value of a label

as.character.ProgressBar

Gets a string description of the progress bar

getOption.Options

Gets an option

printf

C-style formatted output

isVisible.NullVerbose

Checks if a certain verbose level will be shown or not

lastModified

Gets the time when the file was last modified

evaluate.Verbose

Evaluates a function and prints its results if above threshold

detachPackage

Detaches packages by name

Arguments$getDoubles

Coerces to a double vector and validates

moveInSearchPath

Moves a environment in the search path to another position

eget

Gets a variable by name

Arguments$getIntegers

Coerces to a integer vector and validates

Arguments$getWritablePathname

Gets a writable pathname

setLabels.TextStatusBar

Sets new values of given labels

wrap.array

Reshape an array or a matrix by permuting and/or joining dimensions

filePath

Construct the path to a file from components and expands Windows Shortcuts along the pathname from root to leaf

isOpen.character

Checks if there is an open connection to a file

GString$getBuiltinHostname

Gets the hostname of the system running R

draw.density

Draws a density curve

equals.Options

Checks if this object is equal to another Options object

update.FileProgressBar

Updates file progress bar

Arguments$getReadablePathnames

Gets a readable pathname

Arguments$getEnvironment

Gets an existing environment

listDirectory

Gets the file names in the directory

GString$getBuiltinUsername

Gets the username of the user running R

arrayIndex

Converts vector indices to array indices

Arguments$getInstanceOf

Gets an instance of the object that is of a particular class

reset.VComments

Resets a VComments compiler

getLeaves.Options

Gets all (non-list) options in a flat list

isDone.ProgressBar

Checks if progress bar is completed

writeRaw.NullVerbose

All output methods

capture.Verbose

Captures output of a function

withLocale

Evaluate an R expression with locale set temporarily

installPackages

Install R packages by name or URL

ruler.Verbose

Writes a ruler

GString$getBuiltinPid

Gets the process id of the current R session

insert

Insert values to a vector at certain positions

setThreshold.Verbose

Sets verbose threshold

whichVector.logical

Identifies TRUE elements in a logical vector

System$findGhostscript

Searches for a Ghostview executable on the current system

isEof.connection

Checks if the current file position for a connection is at the 'End of File'

Assert$isVector

Static method asserting thatan object is a vector

removeDirectory

Removes a directory

getMessage.TimeoutException

Gets the message of the exception

popTemporaryFile

Drops a temporary suffix from the temporary pathname

isUrl

Checks if one or several pathnames is URLs

readWindowsShellLink

Reads a Microsoft Windows Shortcut (.lnk file)

saveAnywhere.Settings

Saves settings to file

onSessionExit

Registers a function to be called when the R session finishes

captureOutput

Evaluate an R expression and captures the output

createLink

Creates a link to a file or a directory

tempvar

Gets a unique non-existing temporary variable name

findSourceTraceback

Finds all 'srcfile' objects generated by source() in all call frames

dataFrame

Allocates a data frame with given column classes

popMessage.TextStatusBar

Adds a message above the status bar

withTimeout

Evaluate an R expression and interrupts it if it takes too long

loadObject

Method to load object from a file or a connection

Arguments$getReadablePathname

Gets a readable pathname

more.Verbose

Creates a cloned instance with a lower threshold

setOption

Sets a option in R

str.Options

Prints the structure of the options

System$findGraphicsDevice

Searches for a working PNG device

queryRCmdCheck

Gets the on R CMD check if the current R session was launched by it

newline.Verbose

Writes one or several empty lines

copyFile

Copies a file atomically

touchFile

Updates the timestamp of a file

hpaste

Concatenating vectors into human-readable strings

warnings.Verbose

Outputs any warnings recorded

readWindowsShortcut

Reads a Microsoft Windows Shortcut (.lnk file)

patchCode

Patches installed and loaded packages and more

pushTemporaryFile

Appends a temporary suffix to the pathname

mkdirs

Creates a directory including any necessary but nonexistent parent directories

file.info2

Extract File Information (acknowledging symbolic file links also on Windows)

resetWarnings

Resets recorded warnings

readBinFragments

Reads binary data from disjoint sections of a connection or a file

readRdHelp

Reads one or more Rd help files in a certain format

toCamelCase

Converts a string of words into a merged camel-cased word

shell.exec2

Open a file or URL using Windows File Associations

pushState.Verbose

Pushes the current indentation state of the Verbose object

Java$asShort

Converts a numeric to a Java short

getBarString.ProgressBar

Gets the progress bar string to be displayed

newline.TextStatusBar

Writes a newline

print.Verbose

Prints objects if above threshold

summary.Verbose

Generates a summary of an object if above threshold

Settings

Class for applicational settings

renameFile

Renames a file (or a directory) atomically/safely

findFiles

Finds one or several files in multiple directories

useRepos

Sets package repositories

saveObject

Saves an object to a file or a connection

isReplicated

Identifies all entries with replicated values

off.Verbose

Turn off the output

unwrap.array

Unwrap an array, matrix or a vector to an array of more dimensions

resample

Sample values from a set of elements

compressFile

Compressing and decompressing files

addFinalizerToLast

Modifies .Last() to call 'finalizeSession()

Assert$isScalar

Static method asserting thatan object is a single value

splitByPattern

Splits a single character string by pattern

setDefaultLevel.Verbose

Sets the current default verbose level

Arguments$getCharacters

Coerces to a character vector and validates

nbrOfOptions.Options

Gets the number of options set

doCall

Executes a function call with option to ignore unused arguments

as.list.Options

Gets a list representation of the options

use

Attaches or loads packages

withOptions

Evaluate an R expression with options set temporarily

seqToIntervals

Gets all contigous intervals of a vector of indices

toUrl

Converts a pathname into a URL

reset.SmartComments

Resets a SmartComments compiler

setValue.ProgressBar

Sets current value

GString$getBuiltinDatetime

Gets the current date and time

sourceTo

Parses and evaluates code from a file or a connection

promptAndSave.Settings

Prompt user to save modified settings

popBackupFile

Drops a backup suffix from the backup pathname

convertComment.VComments

Converts a verbose comment to R code

Arguments$getRegularExpression

Gets a valid regular expression pattern

validate.VComments

Validates the compiled lines

loadToEnv

Method to load objects to a new environment

displayCode

Displays the contents of a text file with line numbers and more

pushBackupFile

Appends a backup suffix to the pathname

Arguments$getLogicals

Coerces to a logical vector and validates

increase.ProgressBar

Increases (steps) progress bar

withSeed

Evaluate an R expression with a temporarily set random set

as.character.Verbose

Returns a character string version of this object

Java

Static class for Java related methods

createWindowsShortcut

Creates a Microsoft Windows Shortcut (.lnk file)

isSingle

Identifies all entries that exists exactly ones

Sources files recursively to either local or global environment

seqToHumanReadable

Gets a short human readable string representation of an vector of indices

as.character.binmode

Converts a binary/octal/hexadecimal number into a string

as.list.MultiVerbose

Gets a list of Verbose objects

finalizeSession

Function to call for finalizing the R session

System$openBrowser

Opens an HTML document using the OS default HTML browser

equals.Verbose

Checks if this object is equal to another

writeDataFrame.data.frame

Writes a data.frame to tabular text file

setTicks.ProgressBar

Sets values for which ticks should be visible

cleanup.FileProgressBar

Removes the progress file for a file progress bar

updateLabels.TextStatusBar

Sets the new values of given labels and updates the status bar

copyDirectory

Copies a directory

isPackageLoaded

Checks if a package is loaded or not

hasUrlProtocol

Checks if one or several pathnames has a URL protocol

fileAccess

Checks the permission of a file or a directory

isOn.Verbose

Checks if the output is on

getParent

Gets the string of the parent specified by this pathname

GString$getBuiltinOs

Gets the operating system of the running machine

printf.Verbose

Formats and prints object if above threshold

isZero

Checks if a value is (close to) zero or not

withSink

Evaluate an R expression while temporarily diverting output

str.Verbose

Prints the structure of an object if above threshold

readTableIndex

Reads a single column from file in table format

reset.ProgressBar

Reset progress bar

loadAnywhere.Settings

Loads settings from file

getThreshold.Verbose

Gets current verbose threshold

mapToIntervals.numeric

Maps values to intervals

getTimestampFormat.Verbose

Gets the default timestamp format

isAbsolutePath

Checks if this pathname is absolute

header.Verbose

Writes a header

Java$readUTF

Reads a Java (UTF-8) formatted string from a connection

setStepLength.ProgressBar

Sets default step length

intervalsToSeq.matrix

Generates a vector of indices from a matrix of intervals

inAnyInterval.numeric

Checks if a set of values are inside one or more intervals

isOn.NullVerbose

Checks if the output is on

isPackageInstalled

Checks if a package is installed or not

stext

Writes text in the margin along the sides of a plot

reassignInPackage

Re-assigns a new value to an existing object in a loaded package

mergeIntervals.numeric

Merges intervals

isModified.Settings

Checks if settings has been modified compared to whats on file

names.Options

Gets the full pathname of all (non-list) options

mpager

A "pager" function that outputs to standard error

mout

Miscellaneous functions for outputting via message()

intToBin

Converts an integer to a binary/octal/hexadecimal number

subplots

Creates a grid of subplots

writeBinFragments

Writes binary data to disjoint sections of a connection or a file

Java$writeShort

Writes a short (16 bits) to a connection in Java format

timestampOn.Verbose

Turns automatic timestamping on and off

setLabel.TextStatusBar

Sets the value of a label

onGarbageCollect

Registers a function to be called when the R garbage collector is (detected to be) running

Java$writeUTF

Writes a string to a connection in Java format (UTF-8)

Java$readByte

Reads a Java formatted byte (8 bits) from a connection

parse.SmartComments

Parses one single smart comment

Java$readInt

Reads a Java formatted int (32 bits) from a connection

setTimestampFormat.Verbose

Sets the default timestamp format

writeRaw.MultiVerbose

Writes to each of the Verbose objects

setProgress.ProgressBar

Sets current progress

withRepos

Evaluate an R expression with repositories set temporarily

withCapture

Evaluates an expression and captures the code and/or the output

Java$writeInt

Writes a integer (32 bits) to a connection in Java format

systemR

Launches another R process from within R

writeRaw.Verbose

Writes objects if above threshold

update.ProgressBar

Updates progress bar

validate.SmartComments

Validates the compiled lines

setMaxValue.ProgressBar

Sets maximum value

Java$writeByte

Writes a byte (8 bits) to a connection in Java format