1.5-3  2009-11-30
       - Fixed bug in merging in Haar Seg
       - Fixed bug in wavelets (putting together lists of results)

1.5-2  2009-10-28
       - png figures have a max. size so huge chromosomes do not
         result in black figures
       - pch is changed to 0.5 and 0.1 depending on number of points
	 
1.5-1  2009-07-13
       - Major clean-ups of code, eliminating debuggin code, etc.
       - No longer any usage of "<- environment" to pass global
         variables.
       - Make usage of papply clearer and more explicit.
       - More testing, including very large files with Wavi.
       - Web app error code moved in here.
       - Changes from 1.3-12 up are large enough to warrant
         increase in minor number!

1.3-14 2009-06-08
       - Changes in plots to make them faster; genomewide off by default,
       JS off by default, etc. And minimize usage of "environment" 
       and minimal function calls.

1.3-13 2009-05-26
       - Added HaarSeg.
       - snapCGH as of v. 1.12 has a NAMESPACE and fit.model is not exported
         (even if documented). But now BioHMM does not work because of a
	 bug in snapCGH (see BioC email list, 2009-05-12).

1.3-12 2009-05-13
       - Allow usage with DNAcopy 1.18.0 and 1.19.0
       - Fixed original bug in snapCGH for ansari in mergeLevels

1.3-11 2009-01-29
       - Better information on help about mapping to -1/0/1
       - Colors is a user passed parameter
       - Production of figures with html and javascript: optional
       - Production of superimposed figures: optional

1.3-10
       - Adapted error checking functions to usage with server.
       - Allow usage with DNAcopy 1.17.1 (which now uses a NAMESPACE)
       - No WARNINGS under R-devel for \code in help files.
       - Missing values caught early on
       - Fix in SegmentPlotWrite when mergeSegs = FALSE
       - Crashes in some figures when chromosomes had a single observation.

1.3-9	2008-10-27
	- Changed call to changepoints of DNAcopy to allow usage with
	v. 1.17.0 and 1.16.0 of DNAcopy. (First noticed by Sean Davis,
	email 2008-10-07; later by Jian Li, email 2008-10-25).

1.3-8	2008-10-03
	- I finally included Henrik's suggestion for having GLAD
	as suggested.

1.3-7	2008-04-30
	- Changed call to changepoints (DNAcopy) to adapt to DNAcopy
	v. 1.13-3. 
	- Minor documentation fixes
	- Minor change to mpiInit (less annoying behavior).

1.3-6	2008-01-24
	- Bugs on sending to PaLS fixed.
	- Bug on radius of png regions for maps in figures

1.3-5	2007-11-28
	- mpiInit now takes another argument so that, by default R is NOT
	killed if mpiInit fails.

1.3-4	2007-09-25
	- Fixed a few help files (encoding and method usage) for new R
	versions.
	- Added citation.

1.3-3	2007-07-10
	- Fix bugs to allow handling a single chromosome with arbitrary 
	number

1.3-2	2007-06-27
	- Minor bug in some of the quit functions.

1.3-1	2007-05-14
	- Rmpi as "Suggests", not "Depends" since not needed for purely
	sequential operation, and leads to problems when installing as
	root (cannot lamboot as root)
	- Minor cleaning of other stuff

1.3	2007-04-25
	- Automatic recategorization of CGHseg states to three levels.
	- Parameterization of the S parameter for optimal penalization 
	  in CGHseg.
	- A little bit of CGHseg testing (compared to paper)

1.2-2	2007-04-24
	- Bug in CGHseg when k = 1

1.2	2007-04-05
	- Possibility of using either parallelization granularity
	with an "auto" option  based on  benchmarks (see our
	paper).

1.1	2007-03-29
	- Parallelization of BioHMM, HMM, DNAcopy, ACE over
	arrays * chromosomes for segmentation
	
1.0-1	2007-03
	- Much more extenssive testing and bug fixes

0.99	2007-01-15
	- Major changes in some existing code:
	  - parallelize PSW over arrays
	  - parallelize plotting code (chromosomes)
	- Added BioHMM, CGHseg (Piccard's), GLAD, HMM

0.9-5	2006-12-19
	- Some changes in interfaces
	- Further testing incorporated

0.9-3	2006-12-11
	- Bug fixes and improvements from extensive testing with the
	ADaCGH web-based application.
	
0.9	2006-12-02
	- Major changes to move a lot of dispersed code inside functions,
	such as plotting, etc.
	
0.8-3.	2006-10-03
	- Minor changes to accommodate merge levels and cghMCR.
	
0.8-2.	2006-03-08
	- Fixed bug in ACE that, with large numbers of genes,
	led to problems in output for figures.
