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!