
Package: aroma.Base
===================

Version: 0.4.8 [2009-09-17]
o Fixed some Rd errors.


Version: 0.4.7 [2009-06-05]
o BUG FIX: attachParameters() of BaseFileParameters did not work at all.
o BUG FIX: getAllDataFiles() for BaseFile referenced object 'base' 
  instead of 'this'.  Caught by the R code tools.
o BUG FIX: Replaced several occurances of on.exit(..., append=TRUE)
  with on.exit(..., add=TRUE).
o BUG FIX: setColumns() for BaseFileSpots references Argument instead
  of Arguments.
o BUG FIX: setDataFields() of BaseFileSpots references 'assays' which
  was never assigned.


Version: 0.4.6 [2007-05-09]
o Package pass R CMD check on R v2.5.0.


Version: 0.4.5 [2007-02-13]
o BUG FIX: When temporarily overriding base::capabilities(), we
  now have to unlock the binding first.
o BUG FIX: Removed the namespace again; too many problems were 
  introduced.

Version: 0.4.4 [2006-08-06]
o Added a namespace.
o Added the MGED8 poster to the documentation.
o Updated help pages slightly.

Version: 0.4.3 [2006-03-28]
o Removed deprecated BasePlugin class. Use BasePluginDispatcher instead.
o Updated broken Rd links.
o Updated references.

Version: 0.4.2 [2006-02-04]
o BUG FIX: memory.size() and memory.limit() do only exist on Windows.  
  Because of this, aroma.Base was giving an error about missing object
  when run on other platforms.

Version: 0.4.1 [2006-01-21]
o Added more details on system and locale to the plugin.log file. 
  Good for troubleshooting. 

Version: 0.4.0 [2005-12-21]
o Renamed argument 'name[s]' in getSection[s]() of BaseFile to 'type[s]' 
  to be more consistent with the 'type' argument of the BaseFileSection
  constructor.
o Added appendSection() to the BaseFile class.
o replaceSection(old, new, append=TRUE) in BaseFile would not work if
  'old' did not exist.  Forgot to set name of new sections to its type.
  Same problem was also found in writeBaseFileSection(). Thanks to
  Julien Gagneur at EMBL/HTFG, Heide
lberg for reporting this.
o Added setAnnotationColumns() to BaseFileAssays.
o BUG FIX: When reading data cached to file, data cells containing spaces
  would generate an error in the internal read.table(). Forgot to specify
  sep="\t" when reading cached data.

Version: 0.3.7 [2005-10-27]
o Package requires R.utils v0.6.3 or newer. Trust me!
o Rebuild package to verify it conforms to the renaming of argument
  'overwrite' to 'mustNotExist' and 'mustExists' to 'mustExist' in
  the static methods of the Arguments class.
o The about Rd page would not compile in LaTeX.

Version: 0.3.6 [2005-09-07]
o Now withCallingHandlers() is used by BasePluginDispatcher to log
  warnings and errors immediately whenever they occur.  This will make 
  it easier to track where warnings were generated.
o BUG FIX: Now the log is not preprocessing source code output via
  GStrings in BasePluginDispatcher.
o Now the 'plugin.progress' is removed if the plugin is successful.
o Now all copyDirectory() in BasePluginDispatcher is automatically
  overwriting preexisting files.
o Now options() are also logged upon startup.
o Now warnings are printed as soon as they occur.
o The BASE plugin dispatcher recognized Windows shortcuts (*.lnk). 

Version: 0.3.4 [2005-08-01]
o Updated all displayCode() calls to be compatible with updated R.utils.

Version: 0.3.3 [2005-07-24]
o Now readBaseFileSection() looks for the 'count' header when reading
  data tables. If it exists, it can read all rows at once without having
  to search for an empty line (indicating end of table). The speed up is
  approximately 8 times!
o writeBaseFileSection() adds the header 'count' to 'spots' sections.

Version: 0.3.2 [2005-07-21]
o Renamed class BasePlugin to BasePluginDispatcher. The startup script
  was renamed (from runBasePlugin) to basePluginDispatcher.
o Added support to patch code and packages by source all *.R files in
  directory <plugin-path>/../patch/ before calling the plugin dispatcher.
o If an executable script 'postPluginScript' exists in the plugin 
  directory, it is called after the plugin dispatcher finished. 
  This makes it possible to post-process plugin output utilizing any
  language, say via a perl och a bash script.
o BUG FIX: isSerial() in BaseFile used non-existing 'base' instead of 'this'.

Version: 0.3.1 [2005-07-08]
o BUG FIX: writeBaseFile() and getData() of BaseFileSection was generating
  data file names on the fly from the 'assays' header before re-reading
  data tables, which won't work if 'assays' is modified. Now the data file
  names are taken from header 'dataFiles'.
o BaseFilePlugin$main() now asserts that the received data is in a
  serial format.
o Added setName() and setParents() to class BaseFileAssays.
o Added hasColumns(), setColumns() and addColumn() to class BaseFileSection.
o Added isSerial() and replaceSection() to class BaseFile.

Version: 0.3.0 [2005-06-26]
o As soon as the plugin 'parameters' section is read, i) additional source
  files in the directory specified by optional parameter 'sourcePath' are
  loaded, and then ii) the onParameters() is called making it possible
  to validate and preprocess plugin parameters.

Version: 0.2.1 [2005-06-23]
o Updated to support VComments too.

Version: 0.2.0 [2005-06-19]
o First version that is tested in a live BASE environment.

Version: 0.1.0 [2005-05-24]
o Created. Package contains functions readBaseFile() and writeBaseFile().

