Package: aroma.apd
==================

Version: 0.6.0 [2015-02-24]
o ROBUSTNESS: Added package tests (from examples).
o ROBUSTNESS: Importing suggested functions using ::.
o ROBUSTNESS: Declaring all S3 methods.
o Bumped package dependencies.


Version: 0.5.0 [2014-02-25]
o Bumped up package requirements.


Version: 0.4.1 [2014-01-05]
o Now celToApd() throws a more informative error message if it fails
  to located an APD map file.
o Now the 'aroma.apd' Package object is also available when the
  package is only loaded (but not attached).
o CLEANUP: Removed unnecessary import statements from NAMESPACE.
o ROBUSTNESS: Now writeApd() is atomic, which is achieved by first
  writing to a temporary file which is then renamed upon completion.
o ROBUSTNESS: Some of the examples assumed that the suggested
  'affxparser' was installed and attached.
o BUG FIX: celToApd() assumed that affxparser was already attached.
o Bumped up package version requirements.


Version: 0.4.0 [2013-09-21]
o CLEANUP: Removed fallback attachments of 'R.utils' and 'R.huge' as
  these are no longer needed with R.oo (>= 1.15.1).
o CLEANUP: Package no longer utilizes import(), only importFrom():s.
o CLEANUP: Now only using 'Authors@R' in DESCRIPTION, which is possible
  since R (>= 2.14.0).
o CLEANUP: Dropped obsolete R (< 2.0.0) code that was never used.
o BUG FIX: cdfToApdMap() did not validate and assign argument 'verbose'.
o BUG FIX: Forgot to import trim() from 'R.oo'.


Version: 0.3.0 [2013-08-02]
o CLEANUP: Package no longer attaches/loads R.utils and R.huge (only
  imports them).   However, they will be attached dynamically, when
  certain methods are called.
o Utilizing new startupMessage() of R.oo.
o BUG FIX: Several functions incorrectly assumed that the affxparser
  package had been attached ("loaded").  Although this is almost always
  the case, because this package is only used by aroma.affymetrix which
  loads affxparser, this was an incorrect assumption.


Version: 0.2.5 [2013-05-25]
o Minor speedup by replacing rm() calls with NULL assignments.


Version: 0.2.4 [2013-05-22]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.


Version: 0.2.3 [2012-06-30]
o Updated package dependencies.


Version: 0.2.2 [2012-04-04]
o Now package only imports R.methodsS3.


Version: 0.2.1 [2012-04-01]
o CLEANUP: Now package no longer gives an 'R CMD check' NOTE that
  .onAttach() tries to load the 'affxparser' package.


Version: 0.2.0 [2011-07-23]
o Now the package depends on R.huge v0.3.0, which now also
  has a namespace.


Version: 0.1.9 [2011-02-20]
o Now this package will try to install affxparser, if missing
  and in interactive mode.


Version: 0.1.8 [2011-01-31]
o Using packageStartupMessage() instead of cat().


Version: 0.1.7 [2009-10-16]
o Fixed a few broken Rd links to the affxparser package.


Version: 0.1.6 [2009-06-11]
o Made it explicit in the title and the description that this
  package should now be considered deprecated.


Version: 0.1.5 [2009-05-16]
o Updated {read|update|write}Apd() to coerce argument 'writeMap' to
  integer indices.  readApd() also coerce argument 'indices' to the
  same.  Before it used to coerce to doubles, if using R.utils v1.1.4
  or before.  These updates should make no difference to anyone.
  The main purpose is just to use Arguments$getIndices() instead of
  Arguments$getNumerics() where ever possible.
o Fixed a syntax error in one Rdoc comment.
o Renamed the file HISTORY (this one) to NEWS.


Version: 0.1.4 [2007-05-24]
o Added a namespace to the package.


Version: 0.1.3 [2006-06-19]
o Forgot to use autoload("setMethodS3", package="R.oo") etc.
  Packaged would not install on Linux.


Version: 0.1.2 [2006-03-18]
o Added updateApdUnits().
o Now all probe indices are not longer zero-based but one-based.
  However, there is still an option to change this to zero-based
  indices again by using argument 'indexOffset=0'.  This option
  might be remove in the future, because zero-based indices are
  really confusing in R.


Version: 0.1.1 [2006-03-14]
o There is now a quite large set of methods to process APD files.
o All of the methods to re-arrange CDF structures and to create
  cell-index maps have been moved to the affxparser package.


Version: 0.1.0 [2006-02-23]
o Created.

