Changes in version 2.47.2 (2025-04-08):
	- Updated NEWS: Removed dependency on GLAD:
	  GLAD was failing in 2025-02 on all platforms on BioC 3.21;
	  it is now an Enhances.

Changes in version 2.47.1 (2025-02-19):
	- Removed dependency on GLAD. GLAD fails in all platforms on BioC 3.21.

Changes in version 2.43.1 (2024-02-06):
	- Removed dependency from snapCGH (and functionality related to snapCGH).
      	  The snapCGH package was deprecated in Bioconductor 3.18 and removed in 3.19.

Changes in version 2.39.1 (2023-04-14):
	- Fixed "DLL requires the use of native symbols" with R-4.3.0.

Changes in version 2.35.1 (2022-04-19):
	- Added required code from ffbase (as ffbase no longer in CRAN)
	  (ffbase authors added to authors' list). ffbase no longer
	  a dependency.

Changes in version 2.28/29.1 (2020-08-21):
	- Use mc.cores = 2 to avoid errors with checks as in CRAN
	- More strict routine registration

Changes in version 2.21.1 (2018-07-16)
	- Removed all mentions to old installer

Changes in version 2.19.2 (2018-04-19)
	- More on warning on Windows in linking from Rd files.

Changes in version 2.19.1 (2018-04-17)
	- Prevent warning on Windows in linking from Rd files.

Changes in version 2.11.2 (2016-04-29)
	- GLAD is now in Depends, not Imports, as it gives warnigns and
          notes.

Changes in version 2.11.1 (2016-03-29)
	- Vignette changes to avoid Windoze build issues?
        - Changes in NAMESPACE

Changes in version 2.9.3 (2015-05-30)
	- Fixed Note about require(Cairo).
	- Fixed failure with changes in ffbase and not exporting min.ff
	and max.ff

Changes in version 2.9.2 (2015-05-07)
	- Remove wrong {} in CITATION.

Changes in version 2.9.1 (2015-04-30)
	- Added the CITATION file (which was never uploaded to the svn repos)
	- Added in one reference in pSegement.Rd

Changes in version 2.5.2 (2014-10-03)
	- Corrected help for "inputToADaCGH"

Changes in version 2.5.1 (2014-10-03)
	- Fixed bug reading files when R object was called "inputData"

Changes in version 2.5.0
	- Bumped BioC version.

Changes in version 2.4.0
	- Bumped BioC version.

Changes in version 2.3.10 (2013-12-27)
	- Minor changes to main vignette with a new section "Why ADaCGH2
	instead of a manual solution".

Changes in version 2.3.10 (2013-12-27)
        - Change in NAMESPACE to adapt to changes in ffbase or bit (we
	  were getting warnings of "replacing previous import by
	  ffbase::[.ff when loading ADaCGH2"")

Changes in version 2.3.9 (2013-11-28)
	- Minor changes to "benchmarks.pdf": consistent usage of lty and
	  pch for figures of reading and analysis.

Changes in version 2.3.8 (2013-11-26)
	- Minor changes to "benchmarks.pdf".

Changes in version 2.3.7 (2013-11-26)
	- Minor changes to "benchmarks.pdf".

Changes in version 2.3.6 (2013-11-24)
	- Help for inputToADaCGH has a more verbose section on the need to
	  use the right mc.cores.
	- Made default for mc.cores to inputToADaCGH be half the number of
	  cores.
	- More changes to benchmarks.pdf, including the link to all the data.


Changes in version 2.3.5 (2013-11-11)
       - Changes in vignette: unified all benchmarking in benchmark.pdf.
       - Clarified help for pSegment on loadBalance and say explicitly not
         the default for HaarSeg.
       - Note versions 2.3.3 and 2.3.4 were never placed in BioC repos.


Changes in version 2.3.4 (2013-11-09)
       - Reorganized file location for additional files (benchmarks,
         long-vignette).
       - Addedd loadBalance as an argument to the pSegment and pChromPlot
         functions, so that the user can choose to use load balancing-like
         with both forking and MPI. See additional benchmarking vignette
         for tables with results. Added code to the long vignette to
	 exercise this.

Changes in version 2.3.3 (2013-11)
	- Playing with clusterApplyLB.

Changes in version 2.3.2 (2013-10-22)
       - Import aCGH and snapCGH again. Corresponding changes in Author,
         init.c, R code, and C code: basically, all the code taken from
	 those packages is not here.

Changes in version 2.3.1 (2013-10-20)
       - Added aCGH and snapCGH code: new R and C files, with minor
         modifications and updates (registration of routines, no partial
	 matching of arguments, etc)
       - NAMESPACE and Description reflect no longer dependency on snapCGH
         or aCGH.
       - This version works, passes tests, is checked to give the same
         results as previous ones, etc. But never made it into BioC repos,
	 as on 2013-10-23 I realized aCGH and snapCGH were again in BioC
	 devel.

Changes in version 2.3.0 (2013-10-20)
       - Version bump for new BioC devel.

Changes in version 2.1.7 (2013-10-09)
       - Added mc.cores option to inputToADaCGH
       - changed "cores" to "mc.cores" in cutFile, for consistency.


Changes in version 2.1.6 (2013-09-23)
       - Started testing against R beta 3.0.2. Fixed Imports and Depends.
       - chromData: using "short", not "ushort", to catch more user errors.
       - pSegmentGLAD: using a custom daglad that minimizes unneeded
         calls, specially sorting, that can be very expensive.
       - Added "certain_noNA" as an option of segmentation methods.
       - Started testing against R-devel (to become R-3.1.0).


Changes in version 2.1.5 (2013-09-16)
       - Fixed typos.
       - Minimized usage of ":::", removed unused functions for Ansari,
       and some assignemts that no longer made sense (all packages now
       have namespaces).
       - Minimize "Depends" and use "Suggests" and "Imports" in
       DESCRIPTION with "importFrom" in NAMESPACE.
       - No longer using our own mergeLevels, since identical to the ones
       in aCGH package.
       - GLAD uses now the recommended fastest option (smoothfunc=haarseg).


Changes in version 2.1.4 (2013-07-01)
       - Fixed missing entry in bib of vignette.

Changes in version 2.1.3 (2013-06-20)
       - Default merging of pSegmentDNAcopy changed to "MAD", to reflect
       our usage.
       - Added more benchmarking results and recommendations to the
       vignette, and fixed some typos.

Changes in version 2.1.2 (2013-06-17)
       - More changes in cutFile to try and get it to run under Mac.
       - Fixed names in long examples that were leading to mistakenly
       reporting results as different.
       - Added new benchmarking results.

Changes in version 2.1.1 (2013-06-16)
       - Many small changes and adaptations in vignette and help to get it
       to work unded Win and Mac.
       - Changes in cutFile to try and get it to run under Mac.

Changes in version 2.1.0 (2013-05-30)
       - This is a major rewrite of a most of the code, has new
       functions, major changes in existing functions, new vignettes, etc.
       - We no longer use snowfall.
       - Major changes in parallelization, using forking.
       - Reading of data: many more options, parallelized reading.

Changes in version 1.3.3  (2011-10-19)
       - Added more "Sys.sleep" to see if we can get it not to crash in
       Windoze.

Changes in version 1.3.2  (2011-10-18)
       - Added unloading of rlecuyer, to prevent problems with cleanEx
       during R CMD check.

Changes in version 1.2.1  (2011-06-06)
       - Changed "if" in stop.na.inf, as per Dundan Murdoch's suggestion.

Changes in version 1.2.0  (2011-04-14)
       - Version in BioC 2.8

Changes in version 1.1.1  (2011-03-27)
       - Trying to pass check in Windows 64-bit: all examples now
       execute within their temp dirs, which get deleted. And more
       Sys.sleep.
       - Further work in code to remove some unneeded temporary
       ff objects inside functions.

Changes in version 1.1.0  (2010-10-28)
       - Clean up changes inside functions, deleting tmp. objects.
       (all in BioC devel version)


Changes in version 1.0.0  (2010-10-16)
       - First version in BioC release (2.7).


Changes in version 0.99.3 (2010-10-16)
	- Clean up in examples.

Changes in version 0.99.2 (2010-10-15)
	- Added clean ups to vignette to build OK under Windows (stoping
	cluster and deleting ff objects and tmp directory).

Changes in version 0.99.1 (2010-10-13)
	- multicore moved to "Enhances" to allow easier R CMD check in
	Windows.

Changes in version 0.99.0 (2010-10-06)
	- First version in BioC; same as 2.1.3 as per old numbering system.

	- These are entries for former numbering system:
	        2.1.3	2010-10-06
		- Rmpi in "Enhances", not "Suggests", to allow for R CMD
		check in Mac and Windows.

	    	 2.1.2	2010-10-04
		- rsprng no longer in depends; L'Ecuyer as default random
		number generator.
		- Using R's registration mechanism for C routines.
		- Decreased size of example to speed up R CMD check.
		- SOCK is default cluster, and Rmpi not loaded by us.

		2.1.1	2010-09-30
		- Output to CGHregions and input from limma and
		snapCGH. Changes in functions, help, vignnette.
		- Can also use rlecuyer.
		- Works with R-2.11 (adapted to differences in "inherits").

		2.1.0	2010-09-23
		- First fully working version for BioC. Versioning changed!
