Change history of package kebabs:
====================================

Version 1.43.1:
- updated DESCRIPTION file to new format (Authors@R)

Version 1.43.0:
- new branch for Bioconductor 3.22 devel

Version 1.42.0:
- release as part of Bioconductor 3.21

Version 1.41.0:
- new branch for Bioconductor 3.21 devel

Version 1.40.0:
- release as part of Bioconductor 3.20

Version 1.39.0:
- new branch for Bioconductor 3.20 devel

Version 1.38.0:
- release as part of Bioconductor 3.19

Version 1.37.2:
- changed e-mail address of maintainer
- updated README.md and formatting of package vignette
- updated references in documentation
- fixed registration of API calls to C/C++ routines

Version 1.37.1:
- minor changes to C++ source code to avoid warnings related to printf-style
  format strings

Version 1.37.0:
- new branch for Bioconductor 3.19 devel

Version 1.36.0:
- release as part of Bioconductor 3.18

Version 1.35.0:
- new branch for Bioconductor 3.18 devel

Version 1.34.0:
- release as part of Bioconductor 3.17

Version 1.33.2:
- fix in src/Kebabs.h in order to avoid memory problems on 32-bit architectures

Version 1.33.1:
- fixes in several help pages to avoid warnings

Version 1.33.0:
- new branch for Bioconductor 3.17 devel

Version 1.32.0:
- release as part of Bioconductor 3.16

Version 1.31.2:
- changed dependency to 'Matrix' package (now requires at least version 1.5-0)

Version 1.31.1:
- minor changes in coercions in accordance with latest version of 'Matrix' package

Version 1.31.0:
- new branch for Bioconductor 3.16 devel

Version 1.30.0:
- release as part of Bioconductor 3.15

Version 1.29.1:
- fixed C++ code to work with newer version of Rcpp (enforced STRICT_R_HEADERS)
- updated URLs and DOIs (now requires R version >= 3.3.0)

Version 1.29.0:
- new branch for Bioconductor 3.15 devel

Version 1.28.0:
- release as part of Bioconductor 3.14

Version 1.27.2:
- fix in evaluatePrediction() (avoid length>1 logical condition)

Version 1.27.1:
- fix to avoid warnings arising from compiled code
- fix in kebabsDemo() to avoid build warnings; executing this function now does
  not have any side effects anymore (previously, data objects were loaded into the
  global workspace)

Version 1.27.0:
- new branch for Bioconductor 3.14 devel

Version 1.26.0:
- release as part of Bioconductor 3.13

Version 1.25.2:
- removed 'register' from macro in ksort.h in order to avoid warnings on Mac OS

Version 1.25.1:
- minor fix in MismatchC.cpp

Version 1.25.0:
- new branch for Bioconductor 3.13 devel

Version 1.24.0:
- release as part of Bioconductor 3.12

Version 1.23.0:
- new branch for Bioconductor 3.12 devel

Version 1.22.0:
- release as part of Bioconductor 3.11

Version 1.21.0:
- new branch for Bioconductor 3.11 devel

Version 1.20.0:
- release as part of Bioconductor 3.10

Version 1.19.1:
- removed change history from package vignette for easier maintenance

Version 1.19.0:
- new branch for Bioconductor 3.10 devel

Version 1.18.0:
- release as part of Bioconductor 3.9

Version 1.17.0:
- new branch for Bioconductor 3.9 devel

Version 1.16.0:
- release as part of Bioconductor 3.8

Version 1.15.0:
- new branch for Bioconductor 3.8 devel

Version 1.14.0:
- release as part of Bioconductor 3.7

Version 1.13.0:
- new branch for Bioconductor 3.7 devel

Version 1.12.0:
- release as part of Bioconductor 3.6

Version 1.11.0:
- new branch for Bioconductor 3.6 devel

Version 1.10.0:
- release as part of Bioconductor 3.5

Version 1.9.0:
- new branch for Bioconductor 3.5 devel

Version 1.8.0:
- release as part of Bioconductor 3.4

Version 1.7.3:
- fix of citation info file
- fix of inst/NEWS

Version 1.7.2:
- version number bump for technical reasons related to Bioconductor
  build servers

Version 1.7.1:
- version number bump for technical reasons related to Bioconductor
  build servers

Version 1.7.0:
- new branch for Bioconductor 3.4 devel

Version 1.6.0:
- release as part of Bioconductor 3.3

Version 1.5.4
- importing apcluster package for avoiding method clashes
- improved and completed change history in inst/NEWS and
  package vignette

Version 1.5.3
- correction in prediction via feature weights for very large 
  sparse explicit representation
- adaption of vignette template
- vignette engine changed from Sweave to knitr

Version 1.5.2
- correction in distance weights for mixed distance weighted
  spectrum and gappy pair kernel
- allow featureWeights as numeric vector for method
  getPredictionProfile
- correction for plot of single prediction profile 
  without legend
- change of copyright note
- namespace fixes

Version 1.5.1
- new method to compute prediction profiles from models
  trained with mixture kernels
- correction for position specific kernel with offsets
- corrections for prediction profile of motif kernel
- additional hint on help page of kbsvm

Version 1.5.0:
- devel branch created from version 1.4.0

Version 1.4.0:
- release as part of Bioconductor 3.2

Version 1.3.4:
- correction of Ubuntu problem with realloc for 0 elements in
  linearKernel generating a sparse empty kernel matrix
- correction of problem with feature weights and prediction
  profiles for position specific gappy pair kernel
- correction of problem with feature weights and prediction
  profiles for position specific motif kernel
- corrections for feature weights, prediction via feature
  weights and prediction profile for distance weighted kernels
- update of KeBABS citation

Version 1.3.3:
- new export kebabsCollectInfo for collection of package info
- update of version dependency to Biostrings, XVector, S4Vector
- correction for leading + or - in factor label
- change of bibtex style sheet in vignette to plainnat.bst

Version 1.3.2:
- correction of error in kernel lists
- user defined sequence kernel example SpectrumKernlabKernel
  moved to separate directory

Version 1.3.1
- correction of error in model selection for processing
  via dense LIBSVM
- remove problem in check for loading of SparseM

Version 1.3.0:
- devel branch created from version 1.2.0

Version 1.2.0:
- release as part of Bioconductor 3.1

Version 1.1.9
- inclusion of dense LIBSVM 3.20 for dense kernel matrix support
  to provide a reliable way for training with kernel matrices
- new accessors folds and performance for CrossValidationResult
- removed fold performance from show of CV result
- adaptions for user defined sequence kernel with new export
  isUserDefined, example in inst/examples/UserDefinedKernel
- correction of errors with position offset for position specific
  kernels
- computation of AUC via trapezoidal rule
- changes for auto mode in CV, grid search, model selection
- check for non-negative mixing coefficients in spectrum and
  gappy pair kernel
- build warnings on Windows removed
- added definition of performance parameters for binary
  and multiclass classification to vignette
- update of citation file and reference section in help pages

Version 1.1.8
- new accessors selGridRow, selGridCol and fullModel for class
  ModelSelectionResult
- change of naming of feature weights because of change in
  LiblineaR 1.94-2
- GCC warnings in Linux removed

Version 1.1.7
- change in LiblineaR - upgrade to LIBLINEAR 1.94
  in function LiblineaR the parameter labels was renamed to target
- correction in model selection for performance parameters
- error correction of vector length overflow in sparse explicit
  representation for very large number of sequences in spectrum,
  gappy pair and motif kernel
- error correction for AUC in cross validation
- minor changes in help pages
- minor changes in vignette

Version 1.1.6
- error correction for training with position specific kernel and
  computation of feature weights
- error correction in coercion of kernel to character for distance
  weighting
- error correction in spectrum, gappy pair and motif kernel
  for kernel matrix - last feature was missing in kernel value
  in rare situations
- correction of Windows build problem in linearKernel
- build warnings on Windows removed
- minor changes in help pages
- minor changes in vignette

Version 1.1.5
- new method heatmap to display heatmap of prediction profiles
- extension of function linearKernel to optionally return
  a sparse kernel matrix
- correction of computation of feature weights for
  LiblineaR with more than 3 classes
- new accessor SVindex for class KBModel
- correction in subsetting of sparse explicit representation for
  head / tail
- error correction in subsetting of prediction profile
- error correction in mismatch kernel
- check uniqueness of motifs in motif kernel
- minor changes in help pages
- change name of vignette Rnw to lowercase
- minor changes in vignette

Version 1.1.4:
- added two help pages

Version 1.1.3
- fix to adapt for changed Biostrings/S4Vectors API

Version 1.1.2
- minor C code changes for mismatch kernel
- correction of MCC
- new class ROCData and new function computeROCandAUC for
  binary classification added
- new plot function for ROCData to plot ROC for binary classes
- AUC as additional performance parameter in cross validation
  and as performance objective in grid search

Version 1.1.1
- correction for cross validation with factor label
- correction for storing prob model in kebabs model for kernlab
- removal of clang warnings for unused functions

Version 1.1.0:
- devel branch created from version 1.0.0

Version 1.0.0:
- first official release as part of Bioconductor 3.0
