Package: R.utils
================

Version: 1.2.4 [2009-10-30]
o ROBUSTIFICATION: Lowered the risk for saveObject() to leave an
  imcomplete file due to say power failures etc.  This is done by
  first writing to a temporary file, which is then renamed.  If the
  temporary file already exists, an exception is thrown.
o ROBUSTIFICATION: Now Arguments$getWritablePathname(path) validates 
  that there is enough file permissions so that a file can be created
  in the 'path' directory.
o CLEAN UP: On Windows Vista, createLink() produced a stderr message
  "You do not have sufficient privilege to perform this operation", when
  trying to use Windows 'mklink' command.  Those message are now silenced.


Version: 1.2.3 [2009-10-20]
o Added findSourceTraceback(), which finds the pathnames of all
  files currently being source():ed.


Version: 1.2.2 [2009-10-16]
o Some cleanup of Rd files to meet the stricter requirements.


Version: 1.2.1 [2009-10-03]
o Added createLink().
o Added createWindowsShortcut(). Currently it only works on Windows
  and version of Windows that runs VB scripts.


Version: 1.2.0 [2009-09-09]
o Fixed broken/missing Rd links.


Version: 1.1.9 [2009-06-29]
o Added argument 'useNames=FALSE' to getCharacters() of Arguments.
  For forgotten reasons, before (the default now) 'names' attributes
  were always dropped.  Now they can be kept, if wanted.
o Added dimNA<-().


Version: 1.1.8 [2009-06-07]
o BUG FIX: getParent(..., depth=0) gave an error, instead of returning
  the input path.


Version: 1.1.7 [2009-05-30]
o BUG FIX: Argument 'dThreshold' of less() for Verbose had to be named
  in order to be mapped.


Version: 1.1.6 [2009-05-19]
o UPDATE: Now getEnvironment(), getRegularExpression(), and 
  getReadablePathname() give clearer error messages if more the input
  contains more than one element.
o Now Arguments$getWritablePathname() better explains why a file cannot
  be opened for creation/modification due to wrong file permissions.


Version: 1.1.5 [2009-05-16]
o Changed argument 'asMode' for Arguments$getNumerics() to default to
  NULL instead of "numeric".  This will case the method to return integer
  if the input is integer, and double if the input is double.  The
  previous default was alway returning doubles, cf. notes on common 
  misconception of how as.numeric() works.  In the case when the input
  is neither integer or double, the default is to coerce to doubles.


Version: 1.1.4 [2009-04-04]
o Now getReadablePathname(..., mustExist=TRUE) of Arguments reports also
  the working directory if the a relative pathname is missing.
o BUG FIX: getReadablePathname(..., mustExist=TRUE) of Arguments gave an
  internal error if the pathname was in the current directory and did 
  not exist.


Version: 1.1.3 [2009-01-12]
o Added isPackageInstalled().
o FIXUP: There were some Rd warnings with the new R v2.9.0.


Version: 1.1.2 [2008-12-27]
o Now getReadablePathname(..., mustExist=TRUE) and 
  getWritablePathname(..., mkdirs=FALSE) of Arguments report which
  of the parent directories exists when the requested pathname is not 
  found.  This will help troubleshooting missing pathnames.
o Added removeDirectory() for a convenient and safe way to remove
  directories.
o Added argument 'useNames' to insert(), which is now aware of names
  of the input object.
o Added subplots() originating from (obsolete) R.graphics.


Version: 1.1.1 [2008-12-03]
o Now getReadablePathname() and getWritablePathname() of Arguments, 
  and sourceTo() use the more trusted fileAccess() instead of 
  file.access() of 'base'.  This will hopefully solve some problems
  where these methods incorrectly gives an error reporting lack of 
  file permissions; this could happen when some OSs mounted to other
  external file systems.
o Added fileAccess() which is intended to give tries harder than
  file.access() to infer file permissions.
o STABILITY: Added balance and sanity checks for exit() of Verbose.
o Now gzip() and gunzip() removes the partially written output file if
  the process is interrupted.
o BUG FIX: readWindowsShortcut() would not work with some Windows
  shortcut files linking to a Windows network file system and generated
  on Windows Vista.  Their "flags" in the file headers had more than 
  the 8 known bits, which was reported as a file format error.  Although
  we don't know what these unknown bits are for, we now accept them
  quitely accepted so at least the known part of the file format is
  returned.
o BUG FIX: filePath("\\\\shared/foo") would return "\\shared/foo".


Version: 1.1.0 [2008-10-24]
o Now sourceDirectory() also searches for source files with extensions
  *.r, *.q, *.s, and *.S, cf. R manual 'Writing R Extensions'.


Version: 1.0.9 [2008-10-17]
o BUG FIX: commandArgs() would 'Error in !attr(args, "isEnvVars") : 
  invalid argument type' if both arguments excludeReserved=TRUE and
  excludeEnvVars=TRUE were used.


Version: 1.0.8 [2008-10-16]
o Now devDone(which=1) does nothing.  Before it gave an error.
o BUG FIX: Argument 'type' of devNew() did not take function:s.


Version: 1.0.7 [2008-09-20]
o Added mapToIntervals(), inAnyInterval(), and mergeIntervals().


Version: 1.0.6 [2008-09-08]
o Now devNew() filters out arguments 'file' and 'filename' if the
  device is interactive.


Version: 1.0.5 [2008-08-04]
o Now commandArgs(...) pass '...' to base::commandArgs() making it
  fully backward compatible.  It is also updated to recognize all
  R command line options as of R v2.7.1 and R v2.8.0 devel.


Version: 1.0.4 [2008-08-01]
o Now sourceDirectory() is guaranteed to source directories and files 
  in lexicographic order.
o Added countLines() for counting number of lines in a text file.
o Added several functions for extending the current functions dealing
  with devices.  All added functions can address a device by a label
  in addition to the standard device index.  The devGetLabel() and
  devSetLabel() gets and sets the label of a give device.  devList()
  lists the indices of existing device named by their labels, cf.
  dev.list().  The functions devSet() and devOff() work like 
  dev.set() and dev.off() but accept labels as well.  Furthermore, 
  devSet(idx) will open a device with index 'idx' if it does not 
  exists, and devSet(label) a device with that label if not already
  opened.  The devIsOpen() checks if a device is open or not. The 
  devDone() function calls devOff() except for screen devices.


Version: 1.0.3 [2008-07-10]
o Added readBinFragments() and writeBinFragments() to read and write
  binary data scattered across a connection or a file.  These methods
  moved from the R.huge package.
o Added intervalsToSeq(), which is bijective to seqToIntervals().
o Added whichVector(), which is almost twice as fast which() for
  logical vectors, especially when there are no missing values.
o IMPROVEMENT: Major speed up of seqToIntervals().  
o Added gzip().
o Renamed inst/HISTORY to inst/NEWS according to new R standards.
o CLEAN UP: as.character() for 'hexmode' is only added if missing.
o BETA: Added (for now internal) toAsciiRegExprPattern().


Version: 1.0.2 [2008-03-31]
o BUG FIX: If 'x' in insert(x, ...) had zero length, an 
  "Error in from:to : NA/NaN argument" was thrown.


Version: 1.0.1 [2008-03-06]
o BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least) 
  some locale, e.g. 'C' (where 'A-z' works). The only way to specify 
  the ASCII alphabet is to list all characters explicitly, which we now
  do in all methods of the package.  See the r-devel thread 
  "invalid regular expression '[a-Z]'" on 2008-03-05 for details.


Version: 1.0.0 [2008-02-26]
o Added touchFile() for updating the timestamp of a file.
o Added colClasses() for creating "colClasses" vectors.
o Added isPackageLoaded(). 
o The default filename for eps() had extension *.ps not *.eps.
o Cleaned out empty sections from the Rd help pages.
o Now the '...' arguments to Arguments$getVerbose() are passed 
  to the constructor of Verbose.  This allows constructs such
  as Arguments$getVerbose(-10, timestamp=TRUE).
o BUG FIX: When argument 'values' of insert() was a non-list
  its values were placed in a single-element list even when 
  'ats' contained more than one element.  Should have been 
  as.list() in those cases.


Version: 0.9.8 [2007-11-26]
o Added copyFile() which safely copies a file by copying to a
  temporary file, which is then renamed.
o Added isEof() for connections to test for "End of File".
o Added reassignInPackage().
o Added dataFrame(), which allocated a data frame of given size
  and column classes.
o BUG FIX: writeRaw() of MultiVerbose returned a list of logicals.  
  Now it returns TRUE (invisibly).


Version: 0.9.7 [2007-09-17]
o BUG FIX/WORKAROUND: moveInSearchPath() would make the package 
  environment loose  the 'path' attribute, which is for instance is
  needed by packageDescription().  This would in turn cause 
  sessionInfo() to throw an error.  Now moveInSearchPath() makes sure
  to set all attributes on a moved package environment to what it
  used to be.


Version: 0.9.6 [2007-08-29]
o Made documentation for saveObject() and loadObject() public.
o Now the startup message when loading the package is generated with
  packageStartupMessage() so that it can be suppressed.
o Added flush() to TextStatusBar.  Added flush() to example(TextStatusBar)
  so it displays correctly on Rgui on Windows.
o Added bunzip2(), cf. gunzip().
o Added argument 'remove' to gunzip().
o BUG FIX: There was a typo in readWindowsShortcut() causing field
  'iconFilename' to potentially be invalid.  Thanks Tony Plate for
  reporting this. 


Version: 0.9.5 [2007-06-09]
o Updated code to pass the more strict R CMD check R v2.6.0.
o BUG FIX: Used omit.na() instead of na.omit() in static method 
  parseDebian() of System.


Version: 0.9.4 [2007-05-10]
o BUG FIX: readTable() tried to access base::read.table() but that was
  moved to 'utils' as of R v2.5.0.


Version: 0.9.3 [2007-05-09]
o BUG FIX: Using the R v2.4.x build of R.utils in R v2.5.0 gives
  "Error in parse.default(text = src) : 4 arguments passed to 
  'parse' which requires 6".  This is because the internal call
  in base::parse() use different sets of arguments in R v2.4.1 
  and R v2.5.0. The fix was to dynamically assign patch.default()
  when the package is loaded.


Version: 0.9.2 [2007-04-26]
o Added trial version of a MultiVerbose class.  With this class it
  is possible to write verbose output via multiple Verbose objects
  through one MultiVerbose object, e.g. writing to standard output
  and to log file at the same time.


Version: 0.9.1 [2007-04-12]
o BUG FIX: findGhostscript() would give error "paste(path0, collapse
  = ", ") : object "path0" not found" on Windows if Ghostscript was 
  not found.  This error was caught by CRAN.  These problems have
  not been detected locally where Ghostscript is installed.


Version: 0.9.0 [2007-04-11]
o BUG FIX: findGhostscript() of System would give error on 
  "invalid subscript type" if non of the paths to be searched exist.
  This error was caught by CRAN.


Version: 0.8.9 [2007-04-07]
o Removed never needed require(R.io) in openBrowser() for System.


Version: 0.8.8 [2007-04-03]
o Added saveObject() and loadObject().
o Removed the warning in getRelativePath() about "Cannot infer 
  relative pathname, because the two pathnames are not refering
  to the same root/device".  The warning was more confusing than
  helpful.
o BUG FIX: getAbsolutePath("C:/foo/", expandTilde=TRUE) would return
  "C://foo" and not "C:/foo".  Now the method also replace all
  multiple occurances of slashes with a single one.  This bug
  cause getRelativePath("C:/foo", "C:/") to return the wrong thing.
o BUG FIX: toCamelCase(toCamelCase(s)) would not be equal to
  toCamelCase(s), but instead result in all lower case letters.
o BUG FIX: Default value of argument 'format' of timestamp() 
  was invalid.


Version: 0.8.7 [2007-03-24]
o Added moveInSearchPath() to reshuffle the search path. Useful
  to change the order of packages after they have loaded.
o Added toCamelCase() to convert strings.
o Added loadToEnv() for loading saved data to a new environment.
o The warning message on "cannot refer relative pathname" for
  getRelativePath() didn't paste the path resulting in a funny
  looking warning.


Version: 0.8.6 [2007-02-27]
o An R.utils (v0.8.4) modified .Last() function saved in .RData from
  previous R sessions will be updated with the new modifactions
  according to R.utils v0.8.5.


Version: 0.8.5 [2007-02-26]
o Added argument 'depth' to getParent().
o BUG FIX:  Added tryCatch() and explicit check for finalizeSession().
  Otherwise if, under special circumstance, one might get the error
  'Error in .Last() : could not find function "finalizeSession"' when 
  trying to quit R with quit().  Thanks Elizabeth Purdum at UC Berkeley 
  for reporting this.
o When running R v2.5.0, Sys.getenv() is used instead of deprecated
  Sys.putenv().


Version: 0.8.4 [2007-01-10]
o Now System$findGhostscript() searches all 'Program Files' directories
  too, if on Windows.


Version: 0.8.3 [2006-11-10]
o Added arrayIndex() to get the multi-dimensional index of an array
  from a one-dimensional index.


Version: 0.8.2 [2006-10-05]
o Added popMessage() to TextStatusBar. See example().
o Added argument 'modifiedOnly' to sourceTo() so that a file is only 
  sourced if it has been modified since the last call.  Note that this
  argument is passed on by sourceDirectory() too.


Version: 0.8.1 [2006-09-16]
o BUG FIX: sourceDirectory(..., onError="error") would quietly ignore
  errors in source().
o Added methods more() and less() to the Verbose class.


Version: 0.8.0 [2006-08-21]
o Added isOpen() to check if there is another connection opened to 
  a specific file.
o pushState() of Verbose generated an unnecessary warning due to 
  a typo.


Version: 0.7.9 [2006-07-17]
o The capture() method in Verbose modified a text connection while it was
  still open; from R v2.4.0 this is not allowed.  Thanks Brian Ripley for
  pointing this out.


Version: 0.7.8 [2006-05-22]
o Added the TextStatusBar class.


Version: 0.7.7 [2006-03-30]
o The method list in the class-overview help page was missing
  for several classes.
o Added as.double() to Verbose.
o saveAnywhere() of Settings now returns (invisibly) the pathname 
  where the settings were saved.
	

Version: 0.7.6 [2006-02-15]
o Since the png2() and jpeg2() devices are in this package, the eps() 
  device from R.graphics has been moved here for consistency.
	

Version: 0.7.5 [2006-02-09]
o as.character.hexmode() is available in R v2.3.0 and forward.  Thus,
  the method is only added by this package for pre-R v2.3.0.
	

Version: 0.7.4 [2005-12-23]
o Updated getHostname() and getUsername() in System to first try to
  find the details using Sys.info().  After that system environment 
  variable and so on are checked.
o Added argument 'expandTilde=FALSE' to getAbsolutePath() so 
  that tildes (~) are expanded to there corresponding path.
o Now relative paths handle tildes too.
o Added optional automatic timestamping for the Verbose class.
  This is useful for Verbose objects writing to log files.
o BUG FIX: Added protection against infinite loops in isFile(),
  where relative path is the same as the absolute path.


Version: 0.7.3 [2005-11-24]
o Added extract() for arrays, amtrices and vectors.


Version: 0.7.2 [2005-11-22]
o BUG FIX: filePath(..., expandLinks="any") would return the relative 
  link instead of the network pathname, even if there were no local 
  pathname.
o BUG FIX: Now using scan() instead of readLines() to parse header.  
  This way the header can now also be quoted. 
o BUG FIX: Missing object 'ndim' in wrap(); should be 'ndims'. 
o BUG FIX: Sequences of length one was given as intervals by
	seqToHumanReadable(), e.g. 10-10. 
o Static Arguments class: Added getReadablePathnames(). Now getCharacter()
  accepts vectors of length zero or one only.


Version: 0.7.1 [2005-11-12]
o Added functions wrap() and unwrap() to reshape arrays (and matrices)
  by joining and splitting dimensions, respectively, and optionally 
  by permuting dimensions too.  This is for instance useful when storing
  multidimensional arrays in tabular formats.


Version: 0.7.0 [2005-11-10]
o Added trial version of readTable().  It extends the read.table()
  in two major ways.  First it allows you to specify colClasses as
  a column name to column class map.  Second, it allows you you to
  read any subset of rows, which substantially improves speed and
  decrease memory usage.  Use readTableIndex() to create a look-up
  index for rows of interest.
o Added seqToIntervals(), which finds all contigous (integer) regions
  in a set of integers, cf. seqToHumanReadable().
o BUG FIX: isDirectory() on a file would result in an infinite recursive
  loop to itself.
o Added inifite recursive call detection to listDirectory().
o Now sourceDirectory() returns the source files invisibly.
o Gathered files recursively in sourceDirectory(), but it was not needed
  since sourceDirectory() itself is recursive.


Version: 0.6.3 [2005-10-26]
o Renamed argument 'overwrite' in getWritablePathname() in Arguments to
  'mustNotExist'.  Renamed all 'mustExists' to 'mustExist' in all methods
  of class Arguments.


Version: 0.6.2 [2005-10-20]
o Update loadAnywhere() for the Settings clas so that it works on 
  objects too for which the default basename is the static basename.
o BUG FIX: getLeaves() would give an error for empty Options objects.
o BUG FIX: filePath(".") would return "".
o BUG FIX: filePath("//shared/foo") would return "/shared/foo".


Version: 0.6.1 [2005-10-17]
o BUG FIX: readWindowsShortcut() failed on some Network-only links.


Version: 0.6.0 [2005-09-24]
o Now filePath() removes repeated '/' and '\\', except for network 
  files such as \\server\foo\bar.
o BUG FIX: Argument 'pager' of displayCode() did not support functions.
o Updated Options class to make it easier for subclasses to retrieve
  options more easy.  This was needed for the future ROptions class
  to map to options().
o BUG FIX: System$openBrowser() was broken, because startsWith() and
  endsWith() were missing.
o Added trial version of jpeg2() and png2().


Version: 0.5.9 [2005-09-18]
o Added static function findGraphicsDevice() to System.  The methods
  search for a working device among a list of potential ones.  This
  is for instance useful if it is known in advance that the PNG
  device is available (then the bitmap() device is an option).


Version: 0.5.8 [2005-09-06]
o Added argument asGString=TRUE to the Verbose constructor.
o Added remove() to FileProgressBar.
o Replace argument 'gString' of getCharacters() to 'asGString', cf.
  Verbose class.
o Now Arguments$getReadablePathname() follows Windows shortcut files.
o BUG FIX: displayCode() was interpreting the code as GString:s.
o Now making use of relative pathnames internally in copyDirectory().
  Sometimes relative pathnames will work when the absolute ones does
  not (because of missing file access rights).
o BUG FIX: copyDirectory() would not return copied files if recursive==TRUE.
o BUG FIX: Smart comments preceeded by TABs would not be recognized.
o GString's parse() could return warning because it was incorrectly
  assumed that regexpr() did not return more than one value.


Version: 0.5.7 [2005-08-12]
o Function filePath() returns NULL, if no arguments or only NULL 
  arguments are passed to it.


Version: 0.5.6 [2005-08-02]
o BUG FIX: splitByPattern() tried to access non-existing class Argument.
o Arguments' getReadablePathname() no longer returns the absolute pathname
  by default. This is because on some systems the relative pathname can
  be queried wheras the absolute one may not be access due to missing
  file permissions.
o isFile() and isDirectory() is now comparing to current working directory
  if no file information is available (due to missing file permissions);
  assumes that the current working directory always exists.
o getParent() now returns NULL instead of "".
o Added argument 'caseSensitive' to getRelativePath().
o isAbsolutePath(NULL) returns FALSE.
o mkdirs() tries to create directory with relative path if absolute
  path fails. This sometimes works when the file permission are missing.
o Added argument 'code' to displayCode(). The function now also used
  file.show() to display the code.
o Added isUrl() and hasUrlProtocol().
o Added copyDirectory().
o Added getEnvironment() and getRegularExpression() to Arguments.


Version: 0.5.5 [2005-07-21]
o BUG FIX: Example illustrating Windows Shortcut methods tried to
  access 'HISTORY.lnk' and not 'HISTORY.LNK', which would fail on Unix.
o BUG FIX: getCharacters() would not coerce Object:s correctly.
o Now sourceDirectory() does 'chdir=FALSE' instead of 'chdir=FALSE'.
o Now mkdirs() has an internal check for infinit-recursive calls.


Version: 0.5.4 [2005-07-19]
o BUG FIX: If there are no files to source in a directory, and verbose
  is active, basefile() on NULL was called generating an error.
o BUG FIX: sourceTo(..., chdir=TRUE) would generate an error. This
  would for instance make sourceDirectory() useless.


Version: 0.5.3 [2005-07-18]
o Added resetWarnings() and splitByPattern().
o Added summary() to class Verbose and a corresponding VComments tag.
o Arguments$getCharacters() returned attribute 'names' too. Removed. 
o sourceDirectory() is no longer catching warnings in tryCatch(),
  because otherwise it will interrupt the call as if the warnings 
  were errors.


Version: 0.5.2 [2005-06-27]
o Added getRelativePath().
o Added LComments which is a VComments class with different defaults.
o Made SmartComments classes and methods non-static.
o Escaping double quotes in VComments messages.


Version: 0.5.1 [2005-06-23]
o Package passes R CMD check for R v2.1.0.
o Added trial version of SmartComments and subclass VComments where
  the latter are R comments with a special format generating verbose
  output if source is first pre-processed by compile() method. 
  If not preprocessed, they are just regular comments, adding no
  overhead in processing speed.  I can imagine to add, say, AComments
  that Asserts conditions at given test points in code; when code
  works, just source code without pre-processing them!
o Now it is possible to set the default verbose level used by
  all Verbose methods if not explicitly given.
o Now all Verbose messages are GString:ed. This makes VComments slim.


Version: 0.5.0 [2005-06-19]
o Package passes R CMD check for R v2.1.0.
o Now commandArgs() recognizes environment variables.
o Added attachLocally().
o When package is loaded, .Last() is modified so that 'onSessionExit' 
  hooks are called when R finishes.
o Added onSessionExit(), finalizeSession() and addFinalizerToLast().
o Added callHooks().
o Added the NullVerbose() class.
o Moved (de-)capitalize() and seqToHumanReadable() from R.basic to here.
o Added new GString class.
o Added the Assert class.
o Moved the System class from R.lang to this package. System was also
  cleaned out from several never used methods and fields.
o Added filePath() together with file methods isFile(), isDirectory(),
  isAbsolutePath(), mkdirs(), lastModified(), and toUrl().
o Moved sourceTo() from R.io to this package.
o Moved doCall() from R.basic to this package.
o Created the Options class.
o Added several methods to the Verbose class. Also added support for
  indentation by enter() and exit() of Verbose.
o Moved the Java and Verbose class from R.matlab to this package. 
  This requires that this package is on CRAN before R.matlab is updated.
o Moved the ProgressBar and FileProgressBar from the R.ui package,
  which then becomes more or less empty.
o Created.