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

The following list highlights the change history of the package.
It only mentions versions in which actual changes have been made
(leaving out automatic version number increments that have been made
within the Bioconductor release cycle without any actual change
of code or documentation).

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

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 1.33.2:
- 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 1.31.2:
- 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 1.29.1:
- 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 1.27.2:
- 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 1.25.2:
- 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 1.19.1:
- removed change history from package vignette for easier maintenance

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 1.5.4
- 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 1.3.4:
- 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 1.1.9
- 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 1.0.0:
- first official release as part of Bioconductor 3.0
