Package: R.huge
===============

Version: 0.9.0 [2014-02-22]
o ROBUSTNESS: Now declaring all S3 methods in NAMESPACE.


Version: 0.8.0 [2014-02-25]
o ROBUSTNESS: Now the package runs the garbage collector if unloaded
  in order to make sure finalize() is called on any deleted
  AbstractFileArray objects.
o Bumped package dependencies.


Version: 0.7.0 [2014-01-05]
o CLEANUP: Package no longer attaches R.oo - only imports it.
o Bumped package dependencies.


Version: 0.6.1 [2014-01-05]
o Now the 'R.huge' Package object is also available when the
  package is only loaded (but not attached).
o CLEANUP: Bumped package requirements and no-longer needed
  import statements from NAMESPACE.


Version: 0.6.0 [2013-09-21]
o CLEANUP: Package no longer utilizes import(), only importFrom():s.
o CLEANUP: Removed fallback attachments of 'R.utils' as these are no
  longer needed with R.oo (>= 1.15.1).
o CLEANUP: Cleaned out unnecessary appendVarArgs().
o ROBUSTNESS: Added another package system test.
o ROBUSTNESS: Now declaring all S3 methods in NAMESPACE.
o ROBUSTNESS/WORKAROUND: For now, package attaches the 'R.oo' package.
  This is needed due to what appears to be a bug in how R.oo
  finalizes Object:s assuming R.oo is/can be attached.  Until that
  is resolved, we make sure R.oo is attached.


Version: 0.5.1 [2013-08-02]
o Utilizing new startupMessage() of R.oo.


Version: 0.5.0 [2013-08-02]
o CLEANUP: Package no longer attaches/loads R.utils (only imports it).
  However, it will attach ("load") R.utils dynamically, when certain
  methods are called.


Version: 0.4.4 [2013-05-25]
o Minor speedup by replacing rm() calls with NULL assignments.


Version: 0.4.3 [2013-05-22]
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.


Version: 0.4.2 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
  R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
  for you; missing documentation, a bug or just me?' on Oct 16, 2012.


Version: 0.4.1 [2012-06-29]
o Updated package requirements.


Version: 0.4.0 [2012-04-12]
o Updated package requirements.
o CLEANUP: Package no longer call .Internal() functions.  This will
  cause a slowdown, because we now have to deal with overhead in
  functions such as seek(), readBin() and writeBin().
o CLEANUP: Package no longer creates new generic functions for
  as.vector() and as.matrix() such that R CMD check no longer complaints.


Version: 0.3.0 [2011-07-23]
o Added a namespace to the package, which will be more or less
  a requirement in the next major release of R.
o BUG FIX: Recently R devel automatically adds a namespace to
  a package, if missing.  This caused some of the PSCBS examples
  to throw an exception related to incorrect dispatching of cat().


Version: 0.2.2 [2011-02-01]
o ROBUSTNESS: Now using argument 'nchars' (not 'nchar') when calling
  readChar().


Version: 0.2.1 [2010-11-08]
o Now "["() for FileMatrix explicitly specifies origin="current" in the
  call to readBinFragment(), which is an argument added in R.utils 1.5.7.
o CLEANUP: Removed some defunct Rd aliases.


Version: 0.2.0 [2009-10-16]
o Some cleanup of Rd files to meet the stricter requirements.


Version: 0.1.9 [2009-09-22]
o DOCUMENTATION: Now the package description lists alternative packages.
o BUG FIX: From R v2.10.0, writeValues() of AbstractFileArray would give
  "Error: 4 arguments passed to .Internal(writeBin) which requires 5".
  Updated so it works with all versions of R.


Version: 0.1.8 [2009-06-11]
o Made it explicit in the title and the description that this
  package should now be considered deprecated.


Version: 0.1.7 [2009-05-20]
o ROBUSTNESS: Now open() of AbstractFileArray first tries to open the
  file for reading and updating (as before).  If that fails, then it
  tries to open the file for reading only.  It might be that the file
  is only used for reading, so if the permission allows for that but
  not updating, then open it.
o EXCEPTION HANDLING: Methods that creates/modifies files will give
  a clear error message if the file permissions does not allow it.


Version: 0.1.6 [2008-07-03]
o Moved internal readBinFragments() and writeBinFragments() to R.utils.
o No bug fixes was made in this version.
o Renamed the HISTORY file to NEWS.


Version: 0.1.5 [2006-08-29]
o Now the startup message when loading the package is generated with
  packageStartupMessage() so that it can be suppressed.
o BUG FIX: Argument 'dimOrder' of the AbstractFileArray constructor was
  not recognized causing weird results if it was intended to be in a
  non-increasing order, e.g. FileMatrix(..., byrow=TRUE).
o BUG FIX: Reading/writing data from and to a FileMatrix via
  "["()/"[<-"() was broken. Thanks Jens Oehlschlägel for troubleshooting
  and reporting this.
o Added private readBinFragments() and writeBinFragments().
o Added tests/ scripts.


Version: 0.1.4 [2006-05-21]
o Committed to CRAN.
o Package passed R CMD check on R v2.5.0 and R v2.6.0 devel.


Version: 0.1.3 [2006-05-09]
o Package passed R CMD check on R v2.5.0.
o Added more Rdoc comments.


Version: 0.1.2 [2006-03-14]
o Added getComments() and setComments() to AbstractFileArray.
o Added a default buffer of free bytes after the header comments.
  This will make it easier to update the comments.  Had to change
  the file format.


Version: 0.1.1 [2006-01-28]
o Added FileVector and abstract superclass AbstractFileArray.
  The FileVector class is now used by the APS methods in
  the affxparser.extras package.


Version: 0.1.0 [2006-01-22]
o Created.  The main purpose is to provide quick and easy access
  to large number of microarray data sets.  All code is currently
  written in plain R, but will most likely be re-implemented bit
  by bit in native code to speed up the access further.  When this
  will happen I do not know.
