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

Version: 2.1.0 [2015-05-27]
o Added compressPDF() to compress PDFs.
o If, and only if, 'path' is an existing directory, then
  copyFile(pathname, path) copies file 'pathname' to the 'path'
  directory (previously destination always had to be a file).
  Analogously, renameFile(pathname, path) moves file 'pathname'
  (not a directory though) to destination directory 'path'.
o CLEANUP: createLink(..., skip=TRUE) would give a false warning
  if a proper link already existed and the target was elsewhere
  than the current directory.
o INCONSISTENCY: captureOutput(..., collapse="\n") did not drop
  newline of the last line as captureOutput(..., collapse="\r")
  and any other collapse != "\n" strings.  Added package tests.
o BUG FIX: captureOutput(..., file="foo.txt") gave an error.


Version: 2.0.2 [2015-04-27]
o ROBUSTNESS: Now nchar(..., type="chars") is used internally for
  all file and directory names.
o BUG FIX: Arguments$getReadablePathname(NA, mustExist=FALSE) no
  longer gives an error with recent R devel (>= 2015-04-23) related
  to an update on how nchar() handles missing values. This bug
  affected only Windows.


Version: 2.0.1 [2015-04-24]
o CLEANUP: R.utils no longer generates a warning if the R session
  is saved when R exits.  Thanks to Jose Alquicira Hernandez for
  reporting on this.
o BUG FIX: toCamelCase() with missing values would give an error
  in R devel (>= 2015-04-23) due to an update how nchar() handles
  missing values.


Version: 2.0.0 [2015-02-28]
o ROBUSTNESS: Package test coverage is 66%.
o ROBUSTNESS: Now %<-% evaluates the expression in a local()
  environment, and it assign to environments, e.g. env$a %<-% 1.
o R.utils::use() without arguments attaches 'R.utils'.
o Added compressFile(), decompressFile() and isCompressedFile() methods,
  which gzip()/gunzip() and the new bzip2()/bunzip2() now use.
  Thanks to Peter Hickey for pushing for this.
o Now eget() uses inherits=FALSE (was TRUE) and mode="default"
  (was "any"), where "default" corresponds to the mode of argument
  'default', unless it's NULL when mode="any" is used.
o Now commandArgs(asValues=TRUE, adhoc=TRUE) interprets 'x:=1:10'
  such that 'x' become the integer vector 1:10.  Likewise, you can
  do 'x:=seq(1,3, by=0.1)' and 'x:=pi'.  To get the string "pi",
  use quotation marks, i.e. 'x:="pi"', or just 'x=pi'.
o Added cmsg(), cout(), ccat(), cprintf(), cprint(), cstr(), cshow()
  for outputting to "console", which is neither R stdout nor stderr
  and can therefor not be intercepted via capture.output(), sink()
  or similar.  These functions are useful for outputting messages
  that requires user's attention and are often followed by a prompt
  via readline(), which also cannot be captured.
o Added mpager() which is a "pager" function compatible with
  file.show() that will display file contents on standard error.
o Just like for listDirectory(), argument 'recursive' of findFiles()
  can in addition to be FALSE (depth=0) and TRUE (depth=+Inf), be any
  non-negative numeric number specifying how deeply the recursive
  search should be done.
o On Windows, Arguments$getReadablePathname() now gives an informative
  warning if a pathname of length 256 or longer is used/generated,
  which are not supported on Windows.
o DOCUMENTATION: Fixed mistake in help("captureOutput").
  Thanks to Mikko Korpela (Issue #4) for reporting on this.
o ROBUSTNESS: Forgot to declare "default" warnings() as an S3 method.
o BUG FIX: use(..., quietly=FALSE) no longer captures/buffers the
  output, which prevented it from displaying full prompt messages
  that required a user response.  use(..., quietly=TRUE), which is
  the default, no longer tries to ask user of Windows and OS X if
  they wish to install from source if the binary is older.
o BUG FIX: Now the returned value of all withNnn() functions preserves
  the "visibility" of the eval():uated expression.  Added package tests.
o BUG FIX: withCapture({}) no longer generates a warning.
o BUG FIX: Now isUrl(NA) returns FALSE (instead of NA).
o BUG FIX: seqToIntervals(integer(0)) gave error "object 'res' not found".
o BUG FIX: attachLocally() on an environment would remove the
  attached fields/variables from that environment.


Version: 1.34.0 [2014-10-07]
o Added URL and BugReports fields to DESCRIPTION.
o Submitted to CRAN.


Version: 1.33.10 [2014-10-03]
o Added shell.exec2(), which does a better job than shell.exec() in
  opening pathnames with forward slashes and files on mapped drives,
  which may or may not open depending software, e.g. Google Chrome
  fails to open the latter.  Add options(browser=function(...)
  R.utils::shell.exec2(...)) to your ~/.Rprofile file to make
  browseURL() use this function instead of shell.exec().  This
  function is only useful on Windows.
o BUG FIX: Now Arguments$getReadablePathname(file, path) ignores
  'path' if 'file' specifies an absolute pathname.


Version: 1.33.9 [2014-10-03]
o Now countLines() automatically supports gzipped files as well.
  Thanks to Sarah Nelson at Dept of Biostatistics at University
  of Washington for the suggestion.
o Now downloadFile("https://...") will use 'curl', and if not available
  'wget', to download the file over the HTTPS protocol.  Previously
  only 'wget' was used.  The 'curl' software is available on more
  operating systems, include OS X, whereas 'wget' sometimes needs
  a separate installation.


Version: 1.33.8 [2014-10-02]
o Added argument 'unmap' to filePath() for "following" paths that are
  on mapped Windows drives.
o CLEANUP: use() would try temporarily set package repository options
  even when not needed.  This could trigger unnecessary warnings for
  users who haven't set a default CRAN mirror and using use() to
  load/attach an already installed package.


Version: 1.33.7 [2014-09-18]
o New default for writeDataFrame() - argument 'col.names=!append'.
  Also, if append=TRUE, header comments are only written if specified.
  Added package system test for writeDataFrame().


Version: 1.33.6 [2014-09-16]
o BUG FIX: getAbsolutePath("/tmp", expandTilde=TRUE) returned "//tmp".
  This would in turn have implications on getRelativePath(), e.g.
  getRelativePath("/tmp/a", relativeTo="/tmp") returned "../../tmp/a".


Version: 1.33.5 [2014-09-15]
o Added withSeed() and withSink().
o ROBUSTNESS: Now withOptions() also resets all the options available
  upon entry even if no explicit options were specified.  This covers
  the case when 'expr' changes the options and/or adds new options, e.g.
  withOptions({ options(width=10, foo="new"); str(letter) }).


Version: 1.33.4 [2014-09-05]
o ROBUSTNESS: Arguments$getWritablePathname() could sometimes generate
  warning "file.remove(pathnameT) : cannot remove file 'file...',
  reason 'Permission denied'.  Now it tries to remove that files
  several times before giving up.


Version: 1.33.3 [2014-09-04]
o ROBUSTNESS: Now copyDirectory(), just as copyFile() already did,
  silently drops arguments 'copy.mode' and 'copy.date' for older
  R versions where base::file.copy() does not support them.


Version: 1.33.2 [2014-09-01]
o BUG FIX: mkdirs() could return "object 'res' not found" error.


Version: 1.33.1 [2014-08-25]
o BUG FIX: countLines() would not count the last line if it did
  not contain a newline.  It would also give an error if the newline
  characters were only CR.  This despite it was documented that both
  cases were supported.  Added package system tests for them.


Version: 1.33.0 [2014-08-24]
o Added mprint(), mcat(), mstr(), mshow() and mprintf() that work like
  the corresponding print(), cat(), etc., but output using message(),
  which in turn sends to standard error (instead of standard output).
  See also mout().
o Added withLocale().
o Now the test for target discrepancies by createLink(..., skip=TRUE)
  is more forgiving on Windows (by assuming a case-insensitive file
  system) before generating a warning.
o Now useRepos(..., fallback=TRUE), and hence use(), will fallback to
  known/predefined CRAN repositories in case '@CRAN@' is not set.
  If done, it will give an informative warning message.
o BUG FIX: commandArgs() would drop command-line arguments with periods,
  hyphens, or underscores in their names, e.g. --src_file=x.


Version: 1.32.6 [2014-08-12]
o BUG FIX: withCapture({ if (T) 1 else 2 }) would give a parse error on
  "unexpected 'else'", because the internal deparsing puts the 'else'
  statement on a new line whenever an if-else statement is enclosed
  in an { ... } expression.  This problem is also described in R help
  thread "deparse() and the 'else' statement" by Yihui Xie on 2009-11-09
  [http://tolstoy.newcastle.edu.au/R/e8/help/09/11/4204.html].  The
  workaround is to detect standalone 'else' statements and merge them
  with the previous line.  Added package system test for this case.


Version: 1.32.5 [2014-05-15]
o BUG FIX: egsub() would return an invalid expression if the input had
  definitions of functions without arguments, e.g.
  egsub("x", "x", substitute(y <- function() 0)) which would throw
  "Error: badly formed function expression" if deparsed/printed.
  Added package test for this.


Version: 1.32.4 [2014-05-14]
o Now egsub() also works with functions, in case it substitutes on
  the body of the function.
o DOCUMENTATION: Added clarification to help("withTimeout") on the
  limitations of the function and when it is/is not possible to
  interrupt a function via timeouts.
o Made the package test on absolute and relative paths less conservative,
  because it gave an error on Windows systems that have set R_USER to a
  Cygwin-flavored directory, which causes normalizePath("~") to return a
  non-existing directory.  Thanks Uwe Ligges (CRAN) for reporting on this.


Version: 1.32.3 [2014-05-08]
o filePath("./././././") now returns "." (was "").  Added package
  system tests for filePath().


Version: 1.32.2 [2014-05-07]
o Added support for substitution of expressions in withCapture()
  based on regular expressions utilizing new egsub().
o Added egsub(), which is gsub() for expressions with some bells
  and whistles.


Version: 1.32.1 [2014-05-04]
o Now downloadFile() "adjusts" the output filename by decoding URL
  encoded characters, e.g. 'Hello%20world.txt' becomes 'Hello world.txt'.
  Also, unsafe filename characters (':', '*', '\') are encoded, e.g.
  'How_to:_RSP.txt' becomes 'How_to%3A_RSP.txt'.
o Added argument 'adjust' to Arguments$getReadablePathname().  When
  adjust="url" it decodes and encodes the filename the same way as
  downloadFile() now adjusts it (see above).


Version: 1.32.0 [2014-05-01]
o Added captureOutput() which is much faster than capture.output()
  for large outputs.  withCapture() utilizes this now.  Added package
  system tests for both functions.
o use() now installs missing packages from all set repositories (as before)
  and uses the mainstream (CRAN and BioC) ones as fall backs.
o Added withRepos() for installing/updating packages using a set of
  temporarily set repositories.  It is possible to specify repositories
  by names, which are then selected from a set of known repositories,
  e.g. withRepos(install.packages("edgeR"), repos="[[BioC]]").
o Added withOptions() for evaluating an expression with a set of
  options temporarily set.
o Renamed evalCapture() to withCapture() and evalWithTimeout() and
  withTimeout().  The old name is kept for backward compatibility,
  but will eventually be deprecated.


Version: 1.31.1 [2014-04-29]
o ROBUSTNESS: Now use("<repos>::<pkg>") will detect when a repository
  is unknown and give an informative error message on how to update
  option 'repos'.


Version: 1.31.0 [2014-04-26]
o Added assignment operator %<-% for delayed assignments.
o Added option "evalCapture/newline".


Version: 1.30.7 [2014-04-26]
o Added argument 'xtrim' to draw() for density object.
o CLEANUP: createLink(..., skip=TRUE) no longer warns if the link file
  was skipped.  Now it only warns if the skipped link file links to a
  different file than the intended target file.
o CLEANUP: Dropping '::' in calls where possible.


Version: 1.30.6 [2014-04-24]
o Added argument 'newline' to evalCapture().


Version: 1.30.5 [2014-04-22]
o Added argument 'substitute' to evalCapture() for substituting
  symbols "on the fly" in the expression before it is evaluated.


Version: 1.30.4 [2014-04-18]
o Added argument 'modifiedOnly' to sourceDirectory(), which was
  previously passed via '...' to sourceTo(), and it now defaults
  to TRUE.


Version: 1.30.3 [2014-04-15]
o BUG FIX: use() would not install package dependencies.


Version: 1.30.2 [2014-04-08]
o Added argument 'max.deparse.length' to evalCapture().


Version: 1.30.1 [2014-04-06]
o Now evalCapture() utilizes deparse() to get the source code and
  acknowledges options 'deparse.cutoff' to control the code wrapping.
  Previously capture.output(print()) was used.
o WORKAROUND: moveInSearchPath() redirects any messages to stderr that
  base::attach() sent to stdout.  UPDATE: This attach() issue has been
  fixed in R 3.1.0 patched.


Version: 1.30.0 [2014-04-06]
o Vectorized detachPackage(), getAbsolutePath(), getRelativePath(),
  isAbsolutePath(), isDirectory(), isFile(), isOpen(),
  isPackageInstalled(), touchFile() and toUrl(). Added package system
  tests for several of them.  For backward compatibility,
  getAbsolutePath(), getRelativePath(), isAbsolutePath(), isFile() and
  isDirectory() treats an empty vector of path/pathnames equal to ".".
  However, in a future version, empty results will returned by these too.
o BUG FIX: toCamelCase(character(0L)) gave an error.


Version: 1.29.11 [2014-04-02]
o BUG FIX: str() and summary() for Verbose did not acknowledge
  argument 'level'.


Version: 1.29.10 [2014-02-28]
o DOCUMENTATION: Added a help section on privileges required on Windows
  in order for createLink() to work.


Version: 1.29.9 [2014-02-24]
o ROBUSTNESS: Added a package redundancy test for a bug occurring in
  R.oo (< 1.18.0) causing R to core dump (with "Error: SET_VECTOR_ELT()
  can only be applied to a 'list', not a 'integer'") or gives an error
  (with "Error: not a weak reference") under certain conditions when a
  registered finalizer tried to reload R.oo if it was unloaded.  This
  occurred only on R prior to R 3.0.2 patched (2014-02-21 r65057).  Also,
  the 'methods' package needs to be attached, so it is still not clear
  what is the true cause of the bug.  In R.oo (>= 1.18.0) this bug is
  avoided.


Version: 1.29.8 [2014-01-27]
o BUG FIX: Although eget(K=2, cmdArgs=TRUE) would use command-line
  argument 'K=1' as the default (instead of K=2), calling
  eget("K", 2, cmdArgs=TRUE) would not.
o BUG FIX: commandArgs(excludeReserved=TRUE) failed to drop reserved
  arguments of type --<key>=<value>, e.g. --encoding=ASCII.


Version: 1.29.7 [2014-01-27]
o Added trial version of the CmdArgsFunction class.


Version: 1.29.6 [2014-01-27]
o Added cmdArgsCall() for easy calling of functions from the command
  line, e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.


Version: 1.29.5 [2014-01-27]
o doCall() gained argument 'envir', which also means that the new
  behavior is to evaluate the call within the calling frame.  Also,
  doCall() now accepts call a function object in addition to a name
  of a function.


Version: 1.29.4 [2014-01-26]
o Added argument 'unique' to cmdArgs().
o Now commandArgs(asValues=TRUE) returns no-named arguments as a
  list element with the argument as the value and with a "" name.
  For instance, in the past one would get list(R=NA, a="1", noname=NA)
  whereas now one gets list("R", a="1", "noname").
o BUG FIX: Now attachLocally() no longer tries to attach elements with
  an empty name, e.g. list(a=1, 2).  Previously it gave an error.
  Added a package system test for attachLocally().


Version: 1.29.3 [2014-01-19]
o CONSISTENCY: Now createLink(..., method="windows-shortcut") returns
  the path/pathname to the link (and not the target) just like it does
  for the other types of file links.  By link we here mean the
  path/pathname without the *.lnk extension.
o ROBUSTNESS: Added package system tests for createLink().


Version: 1.29.2 [2014-01-12]
o Now Arguments$getCharacters() preserves attributes.  Also, made
  argument 'useNames' defaults to TRUE.
o Added [() for GenericSummary.


Version: 1.29.1 [2014-01-10]
o Added argument 'what' to Sys.readlink2(), where what="corrected"
  makes sure to return the proper target path (not just the one
  relative to where the link lives).


Version: 1.29.0 [2014-01-07]
o The following file I/O methods follows symbolic links (also on Windows)
  and returns information based on the target file/directory (rather than
  the link itself): fileAccess(), file.info2(), isDirectory(), isFile()
  and lastModified().
o Added file.info2() for retrieving file information such that symbolic
  file links are also acknowledged on Windows.
o Added Sys.readlink2() for reading symbolic file links also on Windows.
o removeDirectory() can now be used to remove symbolic directory links
  (also on Windows where neither file.remove() nor unlink() work).
  The target directory will never be removed.
o BUG FIX: renameFile() would give an error on directories.
o Added package system tests for copyFile() and renameFile().
o ROBUSTNESS: createLink() will no longer try to create Windows file
  links on non-Windows platforms.
o ROBUSTNESS: Updated a shell() calls that assume the Windows command
  interpreter to explicitly specify shell=Sys.getenv("COMSPEC").


Version: 1.28.6 [2014-01-06]
o Added argument 'skip' (in addition to existing 'overwrite') to copyFile()
  to allow for better control on how to handle existing destination files.
  For backward compatibilities, it defaults to FALSE, but may be changed
  to skip=!overwrite in a future version.  Furthermore, copyFile() now
  passes (known) arguments '...' to base::file.copy() making it possible
  to copy with or without file permissions etc.  Thanks Taku Tokuyasu (UCSF)
  for reporting on this.


Version: 1.28.5 [2013-12-15]
o Now argument 'asGString' for Arguments$getCharacters() defaults to
  getOption("Arguments$getCharacters/args/asGString", TRUE).  This makes
  it possible to disable this feature, even when it is not possible to
  directly pass that argument.  This will also make it possible to
  set the default to FALSE in the future (instead of TRUE as today).
o Added argument 'inherits' to evaluate() for GString.  Default
  is TRUE for backward compatibility.


Version: 1.28.4 [2013-11-20]
o Minor updates to NAMESPACE file.


Version: 1.28.3 [2013-11-15]
o Added method c() for GenericSummary.


Version: 1.28.2 [2013-11-15]
o CLEANUP: Arguments$getNumerics(NA, range=c(0,1)) no longer gives
  warnings on "no non-missing arguments to min()" etc.


Version: 1.28.1 [2013-10-30]
o BUG FIX: System$getMappedDrivesOnWindows() failed to return the
  proper path for 'net use' mounted drives, iff the path contained
  spaces.


Version: 1.28.0 [2013-10-20]
o CLEANUP: Removed a few non-used internal objects.
o Forgot to declare enterf() for Verbose as an S3 method.


Version: 1.27.6 [2013-10-13]
o CLEANUP: Some methods had to attach 'R.utils' in the past in order
  to work properly.  These are no longer attaching 'R.utils':
  copyDirectory(), createLink(), createWindowsShortcut(),  downloadFile(),
  installPackages(), removeDirectory(), and sourceDirectory().
o Bumped up package dependencies.


Version: 1.27.5 [2013-10-07]
o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
o CLEANUP: Dropped obsolete autoload():s.
o ROBUSTNESS: The overriding of getOption() to become a generic
  function does now call base::getOption() in the default, instead
  of copy the latter.
o Bumped up package dependencies.


Version: 1.27.4 [2013-09-28]
o Now argument 'recursive' of listDirectory() can also specify the
  maximum recursive depth, e.g listDirectory(..., recursive=5L).
o Now the 'R.utils' Package object is also available when the
  package is only loaded (but not attached).


Version: 1.27.3 [2013-09-20]
o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().


Version: 1.27.2 [2013-09-15]
o TYPO: An error message of dimNA<-() was referring to 'files'
  rather than to 'elements'.


Version: 1.27.1 [2013-09-10]
o BUG FIX: commandArgs(asValues=TRUE) failed to set the value of
  the very last argument to TRUE if it was a flag, e.g.
  'R --args --bar'.  Thanks to Stijn van Dongen at EMBL-EBI in
  Cambridge/Hinxton, UK for reporting on this.


Version: 1.27.0 [2013-08-30]
o Added use() for easy attaching/loading and automatic installation
  of packages.
o Now isPackageInstalled() suppresses warnings.


Version: 1.26.4 [2013-08-27]
o CLEANUP: Arguments$getReadablePathnames(files, paths=NULL) no longer
  warns about "rep(paths, length.out = nbrOfFiles) : 'x' is NULL so
  the result will be NULL" if length(files) > 0.
o CLEANUP: Package no longer utilizes ':::'.
o DOCUMENTATION: Help for installPackages() was missing.  Thanks
  Gabor Grothendieck for reporting on this.


Version: 1.26.3 [2013-08-20]
o Forgot to declare default inherits() as an S3 method.


Version: 1.26.2 [2013-07-30]
o ROBUSTNESS/BUG FIX: System$findGhostscript() could still
  give errors.  Completely rewrote how Ghostscripts is searched.
  On Windows, environment variable 'GSC' is now also searched.
  Thanks to Brian Ripley for the feedback.


Version: 1.26.1 [2013-07-29]
o BUG FIX: System$findGhostscript() would give "Error in pathname
  [sapply(pathname, FUN = isFile)]: invalid subscript type 'list'"
  if no device was found.


Version: 1.26.0 [2013-07-27]
o Added tempvar() for creating non-existing temporary variables.
o Added enterf() to Verbose, which is an sprintf-like enter().
o Now System$findGhostscript() returns system variable 'R_GSCMD' if
  set and it refers to an existing executable (and unless force=TRUE).
  It then checks with Sys.which().  On Windows, it finally searches
  for 'gswin64c.exe' and 'gswin32c.exe' on known locations.  Added
  arguments 'firstOnly' and 'force'.
o Now getAbsolutePath() shortens paths if possible, e.g. "C:/foo/.."
  becomes "C:/".
o Added argument 'skip' to gzip() and gunzip().
o BUG FIX: gunzip() would ignore argument 'overwrite'.
o BUG FIX: filePath("C:/foo/..") returned "C:", which should be "C:/".


Version: 1.25.3 [2013-07-27]
o BUG FIX: findSourceTraceback() would give an error "Unknown class of
  'srcfile': character" for source(..., keep.source=FALSE) in recent
  R devel and R v3.0.1 patched.  Thanks Duncan Murdoch for the report.


Version: 1.25.2 [2013-07-03]
o Now installPackages() may also install from https URLs.
o Now more methods can be used without attaching ("loading") the
  package: copyFile(), copyDirectory(), removeDirectory(), createLink(),
  createWindowsShortcut(), downloadFile(), sourceDirectory(), and
  installPackages(), e.g. R.utils::downloadFile().
o Now touchFile() utilizes base::Sys.setFileTime(), iff available.


Version: 1.25.1 [2013-07-01]
o Bumped up package dependencies.


Version: 1.25.0 [2013-06-27]
o UPDATE: Now gzip()/gunzip() returns the output file (was number
  of output bytes processed which are now returned as an attribute).
o Added argument 'temporary' to gzip()/gunzip().
o Added isGzipped() for testing whether a file is gzipped or not.


Version: 1.24.4 [2013-06-17]
o Now argument 'dims' of extract() can also be dimension names.


Version: 1.24.3 [2013-05-25]
o Minor speedups by replacing rm() calls with NULL assignments.
o SPEEDUP: readTable() no longer calls gc().


Version: 1.24.2 [2013-05-20]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
o CRAN POLICY: Now all Rd example lines are at most 100 characters long.


Version: 1.24.1 [2013-05-13]
o The workaround needed by isDirectory() due to a bug in
  file.info() is now applied only for R (< 3.0.2), since the
  bug was been fixed in R 3.0.1 patched (PR#15302).


Version: 1.24.0 [2013-04-18]
o Several methods now output messages and verbose output
  to standard error (instead of standard output), including
  addFinalizerToLast(), filePath(), patchCode(), readWindowsShellLink(),
  readWindowsShortcut(), and loadAnywhere() for Settings.


Version: 1.23.4 [2013-04-15]
o BUG FIX: capitalize()/decapitalize() would return "NANA" for
  missing values.  Reported by Liviu Andronic.


Version: 1.23.3 [2013-03-29]
o BUG FIX: downloadFile('https://...') did not work if 'username'
  or 'password' was NULL.


Version: 1.23.2 [2013-03-22]
o BUG FIX: Previous update caused commandArgs(..., adhoc=TRUE)
  to coerce 'T' and 'F' to logicals TRUE and FALSE.  They are
  now preserved as character string.


Version: 1.23.1 [2013-03-21]
o Now commandArgs(..., adhoc=TRUE) utilizes utils::type.convert().


Version: 1.23.0 [2013-03-20]
o Added ecget() which is like eget() with the default value
  corresponding to the command-line argument.
o Added eget() for retrieving a single variable, with a
  fallback to a default value, e.g. n <- eget(n=42).
o Added support for cmdArg(n=42) as an alias to cmdArg("n", 42).


Version: 1.22.0 [2013-03-14]
o Added cmdArg() for retrieving a single command line argument
  with a default value and type, e.g. n <- cmdArg("n", 42).


Version: 1.21.2 [2013-03-11]
o Bumped up package dependencies.


Version: 1.21.1 [2013-03-08]
o Added an Authors@R field to the DESCRIPTION.


Version: 1.21.0 [2013-03-07]
o Major improvement of commandArgs().  For instance, now it never
  consider arguments after '--args' to be reserved or environment
  variable arguments; they are always user arguments.  It is also
  doing a better job on interpreting -*<key>=<value> arguments;
  previously it could happen that it would split the <value>.
  Added systems test for commandArgs() and cmdArgs().


Version: 1.20.2 [2013-03-07]
o Now argument 'eps' for isZero() may also be a character string
  specifying either "double.eps" or "single.eps".


Version: 1.20.1 [2013-03-04]
o DOCUMENTATION: Updated the help usage section for all static methods.


Version: 1.20.0 [2013-02-24]
o Added cmdArgs() which is short for R.utils::commandArgs(asValues=TRUE,
  adhoc=TRUE, unique=TRUE, excludeReserved=TRUE, ...)[-1L].
o Now it is possible to specify default arguments in commandArgs().
  In addition, if asValues=TRUE, then the values of the parsed
  command-line arguments will be coerced to the data type of the
  default ones if they share names.  If adhoc=TRUE, arguments will
  be coerced to numerics unless the result is NA.
o For conveniency, getAbsolutePath() and getRelativePath() returns
  the same pathname if it is a URL.
o Added gstring() and gcat().
o Now it is possible to escape the sed-like search replace format
  for GString:s via quoting, e.g. ${'R.rsp/HttpDaemon/RspVersion'} .
o BUG FIX: getParent() and filePath() as well as System$mapDriveOnWindows()
  and System$unmapDriveOnWindows() did not handle paths with a lower case
  Windows drive letter.  Oddly, it is only now that we have received
  an single report (on a Windows 7 system) that such getwd() may return
  such drive letters, e.g. 'c:/path/' instead of 'C:/path/'.
o BUG FIX: evaluate(..., where="parent") for GString would result
  in an endless loop.
o BUG FIX: displayCode(code) incorrectly processed 'code' as GString:s.


Version: 1.19.5 [2013-01-11]
o BUG FIX: Specifying argument 'version' to isPackageLoaded() would give
  "Error: 'manglePackageName' is defunct." in recent versions of R.
  Thanks to Brian Ripley (R core) for reporting on this.


Version: 1.19.4 [2013-01-07]
o Now '.Last.lib' is exported.
o Bumped up package dependencies.


Version: 1.19.3 [2012-12-19]
o Utilizing new startupMessage() of R.oo.


Version: 1.19.2 [2012-12-18]
o R CMD check for R devel no longer gives a NOTE on attach().


Version: 1.19.1 [2012-12-02]
o CLEANUP: R CMD check no longer warns on global assignments.
o BUG FIX: Arguments$getIndices(x, max=0, disallow="NaN") where 'x'
  contains only NA_integer_, would give "Exception: Argument 'x' is
  of length 1 although the range ([0,0]) implies that is should be
  empty." although it should return 'x' as is.


Version: 1.19.0 [2012-11-29]
o CLEANUP: Dropped lapply() for MultiVerbose.
o Added as.list() to MultiVerbose.


Version: 1.18.4 [2012-11-21]
o Now declaring all S3 methods in the namespace.


Version: 1.18.3 [2012-11-06]
o BUG FIX: queryRCmdCheck() did not detect "tests" evidences when
  'R CMD check' was testing multiple architectures.


Version: 1.18.2 [2012-11-04]
o CLEANUP: Replaced all whichVector() with which(), because the
  latter is now the fastest again.
o CLEANUP: Dropped pre-R 2.3.0 patch of as.character.hexmode().
o CLEANUP: Dropped pre-R 2.5.0 patch of Sys.setenv().
o BUG FIX: The 'columnClasses' header field created by writeDataFrame()
  would contain "integer" for "factor":s.  Now using class(x)[1] instead
  of storage.mode(x) to infer column classes.
o BUG FIX: Despite documented header fields 'createdBy' and 'createdOn'
  to be ignored if NULL, they did set the corresponding' element in
  'header' argument to NULL if they were NULL.


Version: 1.18.1 [2012-10-31]
o Now gzip()/gunzip()/bunzip2() creates the directory of destination
  pathname 'destfile', iff missing.


Version: 1.18.0 [2012-10-29]
o Added trial version of readWindowsShellLink(), which eventually
  will replace readWindowsShortcut().
o GENERALIZATION: Now filePath() does a better job reading Windows
  Shell Links/Windows Shortcut (*.lnk) files.
o ROBUSTNESS: Now createWindowsShortcut() uses an improved validation
  strategy of the created *.lnk file.


Version: 1.17.4 [2012-10-26]
o BUG FIX: example(createWindowsShortcut) could throw an error on
  some systems.  The exact reason for this is unknown, so for now
  it's instead generating a warning rather that an error.


Version: 1.17.3 [2012-10-26]
o RECOMMENDATION: Since R v2.11.0, you should use base::which() instead
  of whichVector(), which now help("whichVector") also explains.  Also,
  whichVector() was removed from the help index of the package.
o CRAN POLICY: Made the examples run faster for R CMD check.


Version: 1.17.2 [2012-10-21]
o ROBUSTNESS: Added argument 'maxTries' to Arguments$getWritablePathname()
  to have the method try to create missing directories multiple times
  before giving up.  This also means that it will take a longer for
  this method to fail creating a directory.
o Now Arguments$getWritablePathname() gives a more informative error
  if failed, analogously to Arguments$getReadablePathname().


Version: 1.17.1 [2012-10-19]
o mkdirs(path) could generate a warning if the path was created
  by another process as a race condition.  Now it always checks to
  see if the directory already exists just before trying to create
  the directory.


Version: 1.17.0 [2012-10-16]
o Moved Arguments$getFilename() from R.filesets to R.utils.
  Added Rd help.
o ROBUSTNESS: Bumped up package dependencies.


Version: 1.16.6 [2012-10-09]
o BUG FIX: evalWithTimeout() would not reset the time limits after
  returning.  Thanks to Gregory Ryslik at Yale University for
  reporting on this.


Version: 1.16.5 [2012-09-26]
o Added argument 'skip' to createLink().
o ROBUSTNESS: Now createLink(..., overwrite=TRUE) will try to undo
  the overwrite, iff it failed to create the new link.
o BUG FIX: createLink(..., overwrite=TRUE) would give an error saying
  "file already exists" (iff that is true) when it tries to create
  a "unix-symlink" link.  Thanks Taku Tokuyasu at UCSF for the report.


Version: 1.16.4 [2012-09-24]
o BUG FIX: Arguments$getReadablePath(..., mustExist=FALSE) did not work.


Version: 1.16.3 [2012-09-21]
o Now insert() silently expands 'values' to be of the same length
  as 'ats', iff length(values) == 1.
o toCamelCase(..., preserveSameCase=TRUE) makes all-upper-case
  words into same-case words, e.g. toCamelCase("HTML View",
  preserveSameCase=TRUE) outputs "htmlView" (not "hTMLView").
  Added system tests for toCamelCase().


Version: 1.16.2 [2012-09-12]
o ROBUSTNESS/CRAN POLICY: moveInSearchPath() no longer calls
  .Internal(detach(...)) but instead base::detach() in such a
  way that neither detach hooks nor .Last.lib() are called.


Version: 1.16.1 [2012-09-07]
o Now createLink() also supports targets with '~' in the path.
o ROBUSTNESS: createLink(target="C:/") would try to create a link with
  name "C:", which is not valid resulting is the somewhat confusing
  error on "cannot symlink 'S:' to 'S:', reason 'Access is denied'".
  Now it instead throws "Cannot infer a valid link name from argument
  'target': C:/".
o ROBUSTNESS/BUG FIX: On Windows, it could happen that createLink()
  would generate a zero-size link file that did not link to the target
  as a result of a failed file.symlink().  This is now tested for such
  that if an invalid link file was created, it is removed again.


Version: 1.16.0 [2012-07-11]
o CLEANUP: Dropped the graphics device related functions that
  were moved to R.devices.
o System$findGraphicsDevice() no longer tries to create a PNG
  device using png2(), because that has now moved to R.devices.
o Updated package dependencies.


Version: 1.15.1 [2012-06-16]
o Now package only imports/no longer depends on the 'utils' package.
  This means that all packages that depends on 'R.utils' for loading
  'utils' for them need to explicitly load it themselves.


Version: 1.15.0 [2012-05-22]
o Added systemR() for launching an external R process.
o Package no longer loads (via a DESCRIPTION Depends) the
  R.devices package, because that would cause a circular
  package dependency.  Instead, we're keeping the graphical
  device functions here until all reverse dependent packages
  have been set to explicitly use R.devices.


Version: 1.14.0 [2012-05-01]
o Copied all functions related to graphics devices to new package
  R.devices (v2.1.1), which is now on CRAN.  For backward
  compatibility, the R.utils package will for now depend and
  hence load the R.devices package.


Version: 1.13.1 [2012-04-16]
o Added findFiles(), which orginates from the affxparser package.


Version: 1.13.0 [2012-04-07]
o Added toBMP() and toTIFF().


Version: 1.12.2 [2012-04-05]
o Now it is possible to have devEval() rename incompletely generated
  image files, by using argument onIncomplete="rename".  This will simplify
  troubleshooting.  The default is still to remove incomplete files.
o ROBUSTNESS: Updated package dependencies.


Version: 1.12.1 [2012-03-20]
o BUG FIX: .onAttach() would try to call getMessage(ex) on an 'error'
  if there was a problem adding a finalizer, resulting in "no applicable
  method for 'getMessage' applied to an object of class "c('simpleError',
  'error', 'condition')".  Now using 'ex$message' instead.


Version: 1.12.0 [2012-03-08]
o CRAN POLICY: Renamed remove() for FileProgressBar to cleanup(),
  because otherwise it would be inevitable to create an internal
  copy of base::remove() which contains an .Internal() call.
  This move may break existing code that calls remove() on an
  FileProgressBar object.
o CRAN POLICY: Removed all internal copies of 'base' and 'utils'
  functions that have .Internal() calls.
o CLEANUP: Removed relibrary() function, because it has not worked
  properly since R introduced namespaces, which is several years.


Version: 1.11.2 [2012-02-29]
o CRAN POLICY: Now capture() for Verbose uses withVisible() instead
  of an .Internal(eval.with.vis()) call.


Version: 1.11.1 [2012-02-28]
o ROBUSTNESS: The creation of image files by devEval() is now
  close to being "atomic".  That is, if the code for plotting the
  figure is interrupted (e.g. by a user interrupt or an error),
  then any created image file is removed.  This avoids leaving
  incomplete/blank image files behind.


Version: 1.11.0 [2012-02-26]
o GENERALIZATION: Now devOptions() accepts passing a device function
  in addition a string, e.g. devOptions(png) and devOptions("png").
o Added argument 'scale' to devNew().
o BUG FIX: Before devNew(..., aspectRatio=1) would ignore
  devOptions(...)$width if neither argument 'width' nor 'height'
  was given.


Version: 1.10.0 [2012-02-23]
o Added swapXY() and draw() for 'density' objects.  Used to be
  in the aroma.core package.
o ROBUSTNESS: Package now explicitly depends on 'utils' and
  'R.methodsS3'. Before it relied on 'R.oo' to load those.


Version: 1.9.11 [2012-01-17]
o ROBUSTNESS: Now System$findGraphicsDevice() not only assert that
  an image file is generated, but also that its filesize is non-zero.
  This avoids returning a device that generates empty image files.
  Also updated the time out to 10 secs (was 30 secs).


Version: 1.9.10 [2012-01-12]
o CLEANUP: reassignInPackage() calls function that are considered
  "unsafe" by the new CRAN policies, i.e. unlockBinding() and
  assignInNamespace().  However, we still wish to keep this method
  available to advanced users.  In order to avoid getting NOTEs
  from R CMD check, we have "hidden" those unsafe function calls.


Version: 1.9.9 [2012-01-11]
o BUG FIX: writeRaw() for Verbose would throw error "Trying to coerce
  more than one character string to a GString, which is not supported."
  iff passing a vector of strings.


Version: 1.9.8 [2011-12-30]
o DOCUMENTATION: The help now explains that evalWithTimeout(readline())
  does not throw a timeout exception until after readline() returns.


Version: 1.9.7 [2011-12-16]
o BUG FIX: evalWithTimeout() would not detect timeouts in R sessions
  that use a non-English locale.
o BUG FIX: Now evalWithTimeout(..., onTimeout="silent") works.  Thanks
  Nicholas Beeton (Univ. of Tasmania, Australia) for reporting on this.


Version: 1.9.6 [2011-11-23]
o BUG FIX: evalCapture() with argument 'envir' defaulting to parent.frame()
  would not be evaluated in the parent frame as it should.  It appears
  that the internal capture.output() prevents this from happening, unless
  argument 'envir' is explictly evaluated within evalCapture().


Version: 1.9.5 [2011-11-19]
o ROBUSTNESS: Now parse() and as.character() handles "empty" GString:s.
o ROBUSTNESS: Now GString() asserts that it only holds one string.


Version: 1.9.4 [2011-11-15]
o SPEEDUP: Now Arguments$getCharacters(s, asGString=TRUE) is much
  faster for elements of 's' that are non-GStrings.  For long
  character vectors the speedup is 100-200x times.
o SPEEDUP: Now as.character() and parse() for GString return
  faster if the string is a plain string without markup etc.
  This made as.character() about 10-15 times faster.


Version: 1.9.3 [2011-11-07]
o Added 'quarts' to the list of (possible) devices for devOptions().
o BUG FIX: devOptions() assumed that all devices exist on
  all platforms, causing it to give an error on some.


Version: 1.9.2 [2011-11-06]
o Added evalCapture() for evaluating an expression and
  capturing its deparsed code and/or output.


Version: 1.9.1 [2011-11-05]
o Added toEPS(), toPDF(), toPNG() and toSVG().
o Added devOptions().
o Added default 'width' and 'height' values to eps().
o Turned png2() and jpeg2() into plain functions without a generic.
  This is consistent with how eps() is defined.
o GENERALIZATION: Now the default 'width' is inferred from
  devOptions() if needed.
o DOCUMENTATION: Added an example to help(devEval).


Version: 1.9.0 [2011-11-03]
o Added queryRCmdCheck(), which retrieves the status of 'R CMD check',
  iff it is running.


Version: 1.8.8 [2011-11-01]
o Added argument 'dims' to extract() for arrays.  Also, argument 'drop'
  was moved to the end.


Version: 1.8.7 [2011-11-01]
o CLEANUP: Fixed a R CMD check NOTE that would show up in R v2.15.0 devel.


Version: 1.8.6 [2011-10-31]
o Added argument 'field' to devEval().


Version: 1.8.5 [2011-10-16]
o CORRECTION: Arguments$getNumerics(c(Inf), disallow="Inf") would report
  that it contains "NA" instead of "Inf" values.


Version: 1.8.4 [2011-10-08]
o Now the default for argument 'methods' of createLink() can be set
  via option "createLink/args/methods".


Version: 1.8.3 [2011-09-30]
o Added installPackages() for installing R packages by names or URLs.
  This method was previously in the hbLite.R script of braju.com.


Version: 1.8.2 [2011-09-24]
o devNew() no longer gives a warning about argument 'aspectRatio' is
  specified when both or neither of 'width' and 'height' are given,
  and 'aspectRatio' is 1.
o Internal readDWord() and readQWord() of readWindowsShortcut() would
  try read 4- and 8-byte integers as non-signed, which is not supported
  by base::readBin() and hence instead read as signed integers.
  Starting with R v2.13.1 this would generate a lot of warnings.


Version: 1.8.1 [2011-09-19]
o Now System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
  System$getMappedDrivesOnWindows() also handles Windows UNC paths
  (i.e. network resource).  This was triggered by a discussion with
  Keith Jewell at Campden BRI Group, UK.
o WORKAROUND: isDirectory("C:/") would not return TRUE due to a
  bug in file.info("C:/") causing it to return NAs.
o Now attachLocally() returns a character vector also of length
  zero.  Before NULL was returned.


Version: 1.8.0 [2011-09-14]
o Added writeDataFrame().
o ROBUSTNESS: Added sanity checks to example(capitalize).
o DOCUMENTATION: Improved example(commandArgs).
o BUG FIX: commandArgs() would not handle '-<key> <value>' and
  '--<key> <value>' properly in all cases.


Version: 1.7.8 [2011-07-24]
o Undoing v1.7.7 to again exports '.conflicts.OK' in order to avoid
  several warnings when loading package.


Version: 1.7.7 [2011-07-23]
o '.conflicts.OK' is no longer exported, because it would cause
  other "downstream" packages to generate a WARNING in R CMD check.


Version: 1.7.6 [2011-04-30]
o Added isReplicated() and replicates() for identifying entries
  in a vector that are non-unique.  Corresponding isSingle() and
  singles() identifies entries that exists only once.


Version: 1.7.5 [2011-04-12]
o Now devEval("jpg", ...) is recognized as devEval("jpeg", ...).


Version: 1.7.4 [2011-04-03]
o Now hpaste(..., sep=" ", maxHead=Inf) corresponds to
  paste(..., sep=" ", collapse=", ").  Added to example.


Version: 1.7.3 [2011-04-02]
o Added hpaste() for human-readable pasting, e.g. "1, 2, 3, ..., 10".
o Now argument 'force' of devEval() defaults to
  getOption("devEval/args/force", TRUE).


Version: 1.7.2 [2011-03-18]
o Now argument 'path' of devEval() defaults to
  getOption("devEval/args/path", "figures/").
o Now devEval() does a better job of "cleaning up" 'name' and 'tags'.


Version: 1.7.1 [2011-03-18]
o devNew() gained option 'devNew/args/par', which can be used to specify
  the default graphical parameters for devNew().  Any additional
  parameters passed via argument 'par' will override such default ones,
  if both specifies the same parameter.
o The automatic archiving of devEval() is not considered unless
  the R.archive package is loaded, regardless of option settings.
o DOCUMENTATION: The title of help(devDone) was incorrect.


Version: 1.7.0 [2011-03-10]
o Now argument 'aspectRatio' of devNew() defaults to 1 (not NULL).
o Added setOption(), the "set version" of getOption().
o Added env() for creating an environment and evaluating an
  expression inside of it in one go.
o Added argument 'path' to sourceTo().
o REPRODUCIBLE RESEARCH: Now devEval() archives any generated
  image files if R.archive option 'devEval' is TRUE.
o BUG FIX: sourceTo() would not work for URLs.


Version: 1.6.6 [2011-03-08]
o Now Arguments$getWritablePath(NULL) returns NULL without asserting
  write permission, which is analogue to how it is done with
  Arguments$getReadablePath(NULL).
o Added argument 'timestamp' to printf() for Verbose so that the
  timestamp can be turned off/on explicitly as for cat().


Version: 1.6.5 [2011-03-03]
o Added trial version of createFileAtomically() for creating files
  atomically, by writing to a temporary file which is then renamed.
o Added trial versions of push-, popBackupFile() for backing up
  and restoring a file.
o Added trial versions of push-, popTemporaryFile() for working
  toward a temporary file.
o Added trial version of renameFile(), which to additional
  validation afterward.


Version: 1.6.4 [2011-02-28]
o (Incomplete revision submitted to CRAN by mistake)


Version: 1.6.3 [2011-02-20]
o Added argument 'par' to devNew() for applying graphical parameters
  at the same time as the device is opened, which is especially
  useful when using devEval().
o Changed argument 'force' of devEval() to default to TRUE.


Version: 1.6.2 [2011-02-14]
o Added trial version of devEval() for simple creation of images.
o Added argument 'aspectRatio' to devNew(), which updates/sets
  the 'height' or the 'width', if the one of the other is not given.


Version: 1.6.1 [2011-02-01]
o ROBUSTNESS: Now using argument 'fixed' (not 'fix') in regexpr() calls.


Version: 1.6.0 [2010-12-07]
o Added evalWithTimeout().


Version: 1.5.8 [2010-11-21]
o ROBUSTNESS: Now loadObject() asserts that the file exists.  If file
  doesn't exist, an informative error message is thrown.
o ROBUSTNESS: Now System$mapDriveOnWindows() does not give an error if
  trying to map the same drive letter to the same path multiple times.
o TYPO: Static methods getVector() and getRegularExpression() of
  Arguments would report the incorrect argument name.
o BUG FIX: System$mapDriveOnWindows() and System$unmapDriveOnWindows()
  did not work if the path contained a space.  Now the path is quoted.
o BUG FIX: Now removeDirectory() also works for paths starting with
  a tilde (~).  The reason was/is that base::unlink() used internally
  does not support that.  We now use base::path.expand() first.


Version: 1.5.7 [2010-11-07]
o ROBUSTNESS: Now read/writeBinFragments() assert that argument 'idxs'
  contains only non-negative indices.
o Added support to readBinFragments() to start reading from either the
  current file position (default; as previously) or from the start of
  the connection.  For backward compatibility, we keep the default to
  be relative to the current position, but this may change in the future.


Version: 1.5.6 [2010-11-03]
o Added resample(), which contrary to sample() also works
  when drawing from a single element.


Version: 1.5.5 [2010-10-26]
o Now argument 'which' to devSet() can be any object.  If not a
  single numeric or a single character string, then a checksum
  character string is generated using digest::digest(which).


Version: 1.5.4 [2010-10-13]
o Now the 'link' argument of createLink() is inferred from the
  'target' argument if it is "." (or NULL).


Version: 1.5.3 [2010-09-29]
o Added an example to help(findSourceTraceback).
o BUG FIX: Each entry identified by findSourceTraceback()
  would be duplicated.


Version: 1.5.2 [2010-09-15]
o fileAccess() no longer returns a named value if file.access() is used.
o ROBUSTNESS: Added a more robust test for fileAccess(path, mode=2)
  when 'path' is a directory.  Thanks Chao Chen at University of
  Chicago for reporting issues with this.
o BUG FIX: Now fileAccess(..., mode=1) only utilizes file.info()$exe
  if it is a file and on Windows, otherwise it relies on file.access().
o DOCUMENTATION: Added an example to help(fileAccess).
o MISC: Added support for readRdHelp(..., format="text") in R < 2.10.0.


Version: 1.5.1 [2010-08-28]
o Added readRdHelp() for locating and reading installed
  Rd help pages in various formats.
o Now downloadFile() supports authentication, if 'wget' is
  available on the system.


Version: 1.5.0 [2010-08-04]
o Added stext(), which previously was in the aroma.core package.


Version: 1.4.4 [2010-07-05]
o Now arrayIndex() returns an @integer @matrix.
o DOCUMENTATION: Now the help of arrayIndex() links to the
  new arrayInd() in the base package.


Version: 1.4.3 [2010-06-23]
o BUG FIX: getAbsolutePath("//server/dir/") would incorrectly drop
  the initial double-slashes ('//') and return "/server/dir/".
  Thanks Richard Cotton at Health and Safety Laboratory (HSL), UK,
  for reporting this.


Version: 1.4.2 [2010-06-09]
o Added printf(), as a convenient wrapper for cat(sprintf(...)).


Version: 1.4.1 [2010-05-26]
o Added downloadFile() for safer and more convenient downloads.


Version: 1.4.0 [2010-03-24]
o Now R.utils requires R v2.5.0 (circa 2007) or newer.  This
  is because there was a change in base::parse() from R v2.4.1
  and R v2.5.0.  See news for R.utils v0.9.3.
o Added a NAMESPACE.


Version: 1.3.4 [2010-03-02]
o Added alpha version of an onGarbageCollect() method.
o BUG FIX: findSourceTraceback() stopped working; probably due to some
  recent updates in base::source().


Version: 1.3.3 [2010-01-25]
o ROBUSTNESS: Added validation of argument 'range' in Arguments methods.


Version: 1.3.2 [2010-01-09]
o sourceTo(..., modifiedOnly=FALSE) followed by a sourceTo(...,
  modifiedOnly=TRUE) will now work as expected.  Before you had to
  do at least one modifiedOnly=TRUE call before for it to work.
o sourceTo() no longer gives a warning if there is a missing EOL.


Version: 1.3.1 [2010-01-08]
o Added System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and
  System$getMappedDrivesOnWindows() for associating drive letters
  with paths on Windows.


Version: 1.3.0 [2010-01-02]
o Added argument 'max' to Arguments$getIndices().
o Added Arguments$getInstanceOf(...).
o Now Arguments$getWritablePath() and Arguments$getWritablePathname()
  throws an error is an NA file/directory is specified.
o Now Arguments$getReadablePath() and Arguments$getReadablePathname()
  throws an error is an NA file/directory is specified, unless
  'mustExist' is FALSE.
o Moved private GenericSummary from aroma.core to R.utils.
o ROBUSTNESS: Now getParent(), getAbsolutePath() and getRelativePath()
  returns a (character) NA if the input is NA.
o ROBUSTNESS: Any NA arguments in '...' to filePath(...) would be parsed
  as "NA" resulting in paths such as "NA/foo/NA" (just as file.path()
  does it).  Now a (character) NA is returned.
o BUG FIX: The example(GString) code escaped a backslash incorrectly.
o BUG FIX: Arguments$getCharacters(s) would return a *logical* instead
  of a *character* vector if 's' contained all NAs.
o BUG FIX: Now isFile(NA) and isDirectory(NA) return FALSE.
  Before it gave an unexpected error.


Version: 1.2.6 [2009-12-19]
o Added argument envir=new.env() to loadToEnv().


Version: 1.2.5 [2009-11-20]
o If 'x' is a logical vector, Arguments$getIndices(x) will now return
  the same as if x <- which(x).


Version: 1.2.4 [2009-10-30]
o ROBUSTIFICATION: Lowered the risk for saveObject() to leave an
  incomplete 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.
