NEWS

---

ADaCGH2 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.

ADaCGH2 2.39.1 (2023-04-14)

• Fixed "DLL requires the use of native symbols" with R-4.3.0.

ADaCGH2 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.

ADaCGH2 2.28 (2020-08-21)

• Use mc.cores = 2 to avoid errors with checks as in CRAN
• More strict routine registration

ADaCGH2 2.21.1 (2018-07-16)

• Removed all mentions to old installer

ADaCGH2 2.19.2 (2018-04-19)

• More on warning on Windows in linking from Rd files.

ADaCGH2 2.19.1 (2018-04-17)

• Prevent warning on Windows in linking from Rd files.

ADaCGH2 2.11.2 (2016-04-29)

• GLAD is now in Depends, not Imports, as it gives warnigns and notes.

ADaCGH2 2.11.1 (2016-03-29)

• Vignette changes to avoid Windoze build issues?
• Changes in NAMESPACE

ADaCGH2 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

ADaCGH2 2.9.2 (2015-05-07)

• Remove wrong {} in CITATION.

ADaCGH2 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

ADaCGH2 2.5.2 (2014-10-03)

• Corrected help for "inputToADaCGH"

ADaCGH2 2.5.1 (2014-10-03)

• Fixed bug reading files when R object was called "inputData"

ADaCGH2 2.5.0

• Bumped BioC version.

ADaCGH2 2.4.0

• Bumped BioC version.

ADaCGH2 2.3.10 (2013-12-27)

• Minor changes to main vignette with a new section "Why ADaCGH2 instead of a manual solution".
• 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"")

ADaCGH2 2.3.9 (2013-11-28)

• Minor changes to "benchmarks.pdf": consistent usage of lty and pch for figures of reading and analysis.

ADaCGH2 2.3.8 (2013-11-26)

• Minor changes to "benchmarks.pdf".

ADaCGH2 2.3.7 (2013-11-26)

• Minor changes to "benchmarks.pdf".

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 2.3.3

• Playing with clusterApplyLB.

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 2.3.0 (2013-10-20)

• Version bump for new BioC devel.

ADaCGH2 2.1.7 (2013-10-09)

• Added mc.cores option to inputToADaCGH
• changed "cores" to "mc.cores" in cutFile, for consistency.

ADaCGH2 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).

ADaCGH2 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).

ADaCGH2 2.1.4 (2013-07-01)

• Fixed missing entry in bib of vignette.

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 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.

ADaCGH2 1.3.3 (2011-10-19)

• Added more "Sys.sleep" to see if we can get it not to crash in Windoze.

ADaCGH2 1.3.2 (2011-10-18)

• Added unloading of rlecuyer, to prevent problems with cleanEx during R CMD check.

ADaCGH2 1.2.1 (2011-06-06)

• Changed "if" in stop.na.inf, as per Dundan Murdoch's suggestion.

ADaCGH2 1.2.0 (2011-04-14)

• Version in BioC 2.8

ADaCGH2 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.

ADaCGH2 1.1.0 (2010-10-28)

• Clean up changes inside functions, deleting tmp. objects. (all in BioC devel version)

ADaCGH2 1.0.0 (2010-10-16)

• First version in BioC release (2.7).

ADaCGH2 0.99.3 (2010-10-16)

• Clean up in examples.

ADaCGH2 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).

ADaCGH2 0.99.1 (2010-10-13)

• multicore moved to "Enhances" to allow easier R CMD check in Windows.

ADaCGH2 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!