# Various Programming Utilities

## Documentation for package ‘R.utils’ version 2.1.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P Q R S T U V W

R.utils-package | Package R.utils

## -- A --

addFinalizerToLast | Modifies .Last() to call 'finalizeSession()
addFinalizerToLast.default | Modifies .Last() to call 'finalizeSession()
Arguments | Static class to validate and process arguments
arrayIndex | Converts vector indices to array indices
arrayIndex.default | Converts vector indices to array indices
as.character.binmode | Converts a binary/octal/hexadecimal number into a string
Assert | The Assert class
attachLocally | Assigns an objects elements locally
attachLocally.data.frame | Assigns an objects elements locally
attachLocally.environment | Assigns an objects elements locally
attachLocally.list | Assigns an objects elements locally

## -- B --

bunzip2 | Compressing and decompressing files
bunzip2.default | Compressing and decompressing files
bzip2 | Compressing and decompressing files
bzip2.default | Compressing and decompressing files

## -- C --

callHooks | Call hook functions by hook name
callHooks.default | Call hook functions by hook name
callHooks.function | Call hook functions
callHooks.list | Call hook functions
capitalize | Capitalizes/decapitalizes each character string in a vector
capitalize.default | Capitalizes/decapitalizes each character string in a vector
captureOutput | Evaluate an R expression and captures the output
ccat | Miscellaneous functions for outputting via message()
cmdArg | Simple access to parsed command-line arguments
cmdArgs | Simple access to parsed command-line arguments
cmsg | Miscellaneous functions for outputting via message()
colClasses | Creates a vector of column classes used for tabular reading
colClasses.default | Creates a vector of column classes used for tabular reading
compressFile | Compressing and decompressing files
compressFile.default | Compressing and decompressing files
compressPDF | Compresses a PDF (into a new PDF)
compressPDF.default | Compresses a PDF (into a new PDF)
copyDirectory | Copies a directory
copyDirectory.default | Copies a directory
countLines | Counts the number of lines in a text file
countLines.default | Counts the number of lines in a text file
cout | Miscellaneous functions for outputting via message()
cprint | Miscellaneous functions for outputting via message()
cprintf | Miscellaneous functions for outputting via message()
createFileAtomically | Creates a file atomically
createFileAtomically.default | Creates a file atomically
createLink | Creates a link to a file or a directory
createLink.default | Creates a link to a file or a directory
createWindowsShortcut | Creates a Microsoft Windows Shortcut (.lnk file)
createWindowsShortcut.default | Creates a Microsoft Windows Shortcut (.lnk file)
cshow | Miscellaneous functions for outputting via message()
cstr | Miscellaneous functions for outputting via message()

## -- D --

dataFrame | Allocates a data frame with given column classes
dataFrame.default | Allocates a data frame with given column classes
decapitalize | Capitalizes/decapitalizes each character string in a vector
decapitalize.default | Capitalizes/decapitalizes each character string in a vector
decompressFile | Compressing and decompressing files
decompressFile.default | Compressing and decompressing files
detachPackage | Detaches packages by name
detachPackage.default | Detaches packages by name
dimNA< - | Sets the dimension of an object with the option to infer one dimension autmatically
dimNA< -.default | Sets the dimension of an object with the option to infer one dimension autmatically
dimNA<- | Sets the dimension of an object with the option to infer one dimension autmatically
dimNA<-.default | Sets the dimension of an object with the option to infer one dimension autmatically
displayCode | Displays the contents of a text file with line numbers and more
displayCode.default | Displays the contents of a text file with line numbers and more
doCall | Executes a function call with option to ignore unused arguments
doCall.default | Executes a function call with option to ignore unused arguments
downloadFile | Downloads a file
downloadFile.character | Downloads a file

## -- E --

egsub | Global substitute of expression using regular expressions
env | Creates a new environment, evaluates an expression therein, and returns the environment
evalCapture | Evaluates an expression and captures the code and/or the output
evalWithTimeout | Evaluate an R expression and interrupts it if it takes too long
extract.array | Extract a subset of an array, matrix or a vector with unknown dimensions
extract.default | Extract a subset of an array, matrix or a vector with unknown dimensions
extract.matrix | Extract a subset of an array, matrix or a vector with unknown dimensions

## -- F --

fileAccess | Checks the permission of a file or a directory
fileAccess.default | Checks the permission of a file or a directory
filePath | Construct the path to a file from components and expands Windows Shortcuts along the pathname from root to leaf
filePath.default | Construct the path to a file from components and expands Windows Shortcuts along the pathname from root to leaf
FileProgressBar | A progress bar that sets the size of a file accordingly
finalizeSession | Function to call for finalizing the R session
finalizeSession.default | Function to call for finalizing the R session
findSourceTraceback | Finds all 'srcfile' objects generated by source() in all call frames
findSourceTraceback.default | Finds all 'srcfile' objects generated by source() in all call frames

## -- G --

gcat | Parses, evaluates and outputs a GString
gcat.default | Parses, evaluates and outputs a GString
gcat.GString | Parses, evaluates and outputs a GString
getAbsolutePath | Gets the absolute pathname string
getAbsolutePath.default | Gets the absolute pathname string
getParent | Gets the string of the parent specified by this pathname
getParent.default | Gets the string of the parent specified by this pathname
getRelativePath | Gets the relative pathname relative to a directory
getRelativePath.default | Gets the relative pathname relative to a directory
GString | Character string with advanced substitutions
gstring | Parses and evaluates a GString into a regular string
gstring.default | Parses and evaluates a GString into a regular string
gstring.GString | Parses and evaluates a GString into a regular string
gunzip | Compressing and decompressing files
gunzip.default | Compressing and decompressing files
gzip | Compressing and decompressing files
gzip.default | Compressing and decompressing files

## -- H --

hasUrlProtocol | Checks if one or several pathnames has a URL protocol
hasUrlProtocol.default | Checks if one or several pathnames has a URL protocol
hpaste | Concatenating vectors into human-readable strings
hpaste.default | Concatenating vectors into human-readable strings

## -- I --

inAnyInterval.numeric | Checks if a set of values are inside one or more intervals
insert | Insert values to a vector at certain positions
insert.default | Insert values to a vector at certain positions
installPackages | Install R packages by name or URL
installPackages.default | Install R packages by name or URL
intervalsToSeq.matrix | Generates a vector of indices from a matrix of intervals
intToBin | Converts an integer to a binary/octal/hexadecimal number
intToHex | Converts an integer to a binary/octal/hexadecimal number
intToOct | Converts an integer to a binary/octal/hexadecimal number
isAbsolutePath | Checks if this pathname is absolute
isAbsolutePath.default | Checks if this pathname is absolute
isBzipped | Compressing and decompressing files
isBzipped.default | Compressing and decompressing files
isCompressedFile | Compressing and decompressing files
isCompressedFile.default | Compressing and decompressing files
isDirectory | Checks if the file specification is a directory
isDirectory.default | Checks if the file specification is a directory
isEof.connection | Checks if the current file position for a connection is at the 'End of File'
isFile | Checks if the file specification is a file
isFile.default | Checks if the file specification is a file
isGzipped | Compressing and decompressing files
isGzipped.default | Compressing and decompressing files
isOpen.character | Checks if there is an open connection to a file
isPackageInstalled | Checks if a package is installed or not
isPackageInstalled.default | Checks if a package is installed or not
isPackageLoaded | Checks if a package is loaded or not
isPackageLoaded.default | Checks if a package is loaded or not
isReplicated | Identifies all entries with replicated values
isSingle | Identifies all entries that exists exactly ones
isUrl | Checks if one or several pathnames is URLs
isUrl.default | Checks if one or several pathnames is URLs
isZero | Checks if a value is (close to) zero or not
isZero.default | Checks if a value is (close to) zero or not

## -- J --

Java | Static class for Java related methods

## -- L --

lastModified | Gets the time when the file was last modified
lastModified.default | Gets the time when the file was last modified
LComments | The LComments class
listDirectory | Gets the file names in the directory
listDirectory.default | Gets the file names in the directory
loadObject | Method to load object from a file or a connection
loadObject.default | Method to load object from a file or a connection

## -- M --

mapToIntervals.numeric | Maps values to intervals
mcat | Miscellaneous functions for outputting via message()
mergeIntervals.numeric | Merges intervals
mkdirs | Creates a directory including any necessary but nonexistent parent directories
mkdirs.default | Creates a directory including any necessary but nonexistent parent directories
mout | Miscellaneous functions for outputting via message()
mpager | A \"pager\" function that outputs to standard error
mprint | Miscellaneous functions for outputting via message()
mprintf | Miscellaneous functions for outputting via message()
mshow | Miscellaneous functions for outputting via message()
mstr | Miscellaneous functions for outputting via message()

## -- N --

NullVerbose | A Verbose class ignoring everything

## -- O --

onGarbageCollect | Registers a function to be called when the R garbage collector is (detected to be) running
onGarbageCollect.default | Registers a function to be called when the R garbage collector is (detected to be) running
onSessionExit | Registers a function to be called when the R session finishes
onSessionExit.default | Registers a function to be called when the R session finishes
Options | The Options class

## -- P --

parseRepos | Sets package repositories
patchCode | Patches installed and loaded packages and more
patchCode.default | Patches installed and loaded packages and more
popBackupFile | Drops a backup suffix from the backup pathname
popBackupFile.default | Drops a backup suffix from the backup pathname
popTemporaryFile | Drops a temporary suffix from the temporary pathname
popTemporaryFile.default | Drops a temporary suffix from the temporary pathname
printf | C-style formatted output
printf.default | C-style formatted output
ProgressBar | Provides text based counting progress bar
pushBackupFile | Appends a backup suffix to the pathname
pushBackupFile.default | Appends a backup suffix to the pathname
pushTemporaryFile | Appends a temporary suffix to the pathname
pushTemporaryFile.default | Appends a temporary suffix to the pathname

## -- Q --

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

## -- R --

R.utils | Package R.utils
readBinFragments | Reads binary data from disjoint sections of a connection or a file
readBinFragments.default | Reads binary data from disjoint sections of a connection or a file
readRdHelp | Reads one or more Rd help files in a certain format
readRdHelp.default | Reads one or more Rd help files in a certain format
readTable | Reads a file in table format
readTable.default | Reads a file in table format
readTableIndex | Reads a single column from file in table format
readTableIndex.default | Reads a single column from file in table format
readWindowsShortcut | Reads a Microsoft Windows Shortcut (.lnk file)
readWindowsShortcut.default | Reads a Microsoft Windows Shortcut (.lnk file)
removeDirectory | Removes a directory
removeDirectory.default | Removes a directory
replicates | Identifies all entries with replicated values
resample | Sample values from a set of elements
resample.default | Sample values from a set of elements
resetWarnings | Resets recorded warnings
resetWarnings.default | Resets recorded warnings

## -- S --

saveObject | Saves an object to a file or a connection
saveObject.default | Saves an object to a file or a connection
seqToHumanReadable | Gets a short human readable string representation of an vector of indices
seqToHumanReadable.default | Gets a short human readable string representation of an vector of indices
seqToIntervals | Gets all contigous intervals of a vector of indices
seqToIntervals.default | Gets all contigous intervals of a vector of indices
setOption | Sets a option in R
setOption.default | Sets a option in R
Settings | Class for applicational settings
shell.exec2 | Open a file or URL using Windows File Associations
singles | Identifies all entries that exists exactly ones
SmartComments | Abstract class SmartComments
sourceDirectory | Sources files recursively to either local or global environment
sourceDirectory.default | Sources files recursively to either local or global environment
sourceTo | Parses and evaluates code from a file or a connection
sourceTo.default | Parses and evaluates code from a file or a connection
splitByPattern | Splits a single character string by pattern
splitByPattern.default | Splits a single character string by pattern
stext | Writes text in the margin along the sides of a plot
stext.default | Writes text in the margin along the sides of a plot
subplots | Creates a grid of subplots
subplots.default | Creates a grid of subplots
System | Static class to query information about the system
systemR | Launches another R process from within R
systemR.default | Launches another R process from within R

## -- T --

TextStatusBar | A status bar at the R prompt that can be updated
TimeoutException | TimeoutException represents timeout errors
touchFile | Updates the timestamp of a file
touchFile.default | Updates the timestamp of a file
toUrl | Converts a pathname into a URL
toUrl.default | Converts a pathname into a URL

## -- U --

unwrap.array | Unwrap an array, matrix or a vector to an array of more dimensions
unwrap.data.frame | Unwrap an array, matrix or a vector to an array of more dimensions
unwrap.default | Unwrap an array, matrix or a vector to an array of more dimensions
unwrap.matrix | Unwrap an array, matrix or a vector to an array of more dimensions
useRepos | Sets package repositories

## -- V --

VComments | The VComments class
Verbose | Class to writing verbose messages to a connection or file

## -- W --

withCapture | Evaluates an expression and captures the code and/or the output
withLocale | Evaluate an R expression with locale set temporarily
withOptions | Evaluate an R expression with options set temporarily
withRepos | Evaluate an R expression with repositories set temporarily
withSeed | Evaluate an R expression with a temporarily set random set
withSink | Evaluate an R expression while temporarily diverting output
withTimeout | Evaluate an R expression and interrupts it if it takes too long
wrap.array | Reshape an array or a matrix by permuting and/or joining dimensions
wrap.data.frame | Reshape an array or a matrix by permuting and/or joining dimensions
wrap.matrix | Reshape an array or a matrix by permuting and/or joining dimensions
writeBinFragments | Writes binary data to disjoint sections of a connection or a file
writeBinFragments.default | Writes binary data to disjoint sections of a connection or a file
writeDataFrame | Writes a data.frame to tabular text file
writeDataFrame.data.frame | Writes a data.frame to tabular text file