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bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:36:00
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.34.0
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+Version: 1.35.0
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 Date: 2023-04-21
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:36:00
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.33.2
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+Version: 1.34.0
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 Date: 2023-04-21
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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fix to avoid memory problems on 32-bit architectures; version number bumped to 1.33.2

UBod authored on 21/04/2023 10:53:53
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.33.1
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-Date: 2022-11-16
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+Version: 1.33.2
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+Date: 2023-04-21
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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fixes in several help pages to avoid warnings; version number bumped to 1.33.1

UBod authored on 16/11/2022 16:06:00
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.33.0
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-Date: 2022-09-20
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+Version: 1.33.1
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+Date: 2022-11-16
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:10:39
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.32.0
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+Version: 1.33.0
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 Date: 2022-09-20
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:10:39
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.31.2
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+Version: 1.32.0
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 Date: 2022-09-20
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Fixed dependency to Matrix package

UBod authored on 20/09/2022 10:23:33
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.31.1
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-Date: 2022-08-23
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+Version: 1.31.2
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+Date: 2022-09-20
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -50,7 +50,7 @@ Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
50 50
         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
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         symmetricPair.R svm.R utils.R zzz.R
52 52
 Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab
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-Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
53
+Imports: methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector (>= 0.7.3),
54 54
         S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices,
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         utils, apcluster
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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minor changes in coercions in accordance with latest version of 'Matrix' package

UBod authored on 23/08/2022 08:25:11
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.31.0
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-Date: 2022-01-14
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+Version: 1.31.1
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+Date: 2022-08-23
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:22:32
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.30.0
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+Version: 1.31.0
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 Date: 2022-01-14
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:22:32
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.29.1
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+Version: 1.30.0
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 Date: 2022-01-14
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Fixed compatibility with STRICT_R_HEADERS; now builds with Rcpp 1.0.8

UBod authored on 14/01/2022 13:57:31
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.29.0
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-Date: 2020-06-18
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+Version: 1.29.1
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+Date: 2022-01-14
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -49,7 +49,7 @@ Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
49 49
         trainsvm-methods.R predictsvm-methods.R predict-methods.R
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         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
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         symmetricPair.R svm.R utils.R zzz.R
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-Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
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+Depends: R (>= 3.3.0), Biostrings (>= 2.35.5), kernlab
53 53
 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
54 54
         S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices,
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         utils, apcluster
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bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:17:16
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.28.0
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+Version: 1.29.0
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 Date: 2020-06-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:17:15
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.27.2
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+Version: 1.28.0
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 Date: 2020-06-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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fix in evaluatePrediction(); version number bumped to 1.27.1

UBodenhofer authored on 18/06/2021 12:50:36
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.27.1
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-Date: 2020-06-16
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+Version: 1.27.2
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+Date: 2020-06-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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minor fix in C++ code; fix in kebabsDemo(); version number bumped to 1.27.1

UBodenhofer authored on 16/06/2021 20:25:06
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.27.0
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-Date: 2020-05-16
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+Version: 1.27.1
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+Date: 2020-06-16
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:09:10
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.26.0
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+Version: 1.27.0
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 Date: 2020-05-16
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:09:10
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.25.2
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+Version: 1.26.0
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 Date: 2020-05-16
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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fixed Mac OS warning; version number bumped to 1.25.2

UBodenhofer authored on 16/05/2021 19:49:23
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.25.1
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-Date: 2020-05-05
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+Version: 1.25.2
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+Date: 2020-05-16
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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fix in MismatchC.cpp; version number bumped to 1.25.1

UBodenhofer authored on 05/05/2021 19:48:12
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.25.0
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-Date: 2020-05-01
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+Version: 1.25.1
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+Date: 2020-05-05
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:00:26
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.24.0
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+Version: 1.25.0
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 Date: 2020-05-01
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:00:26
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.23.1
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+Version: 1.24.0
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 Date: 2020-05-01
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Replace use of DataTable with DataFrame

Hervé Pagès authored on 02/05/2020 06:04:24
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.23.0
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-Date: 2019-10-18
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+Version: 1.23.1
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+Date: 2020-05-01
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -51,7 +51,7 @@ Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
51 51
         symmetricPair.R svm.R utils.R zzz.R
52 52
 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
53 53
 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
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-        S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
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+        S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices,
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         utils, apcluster
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, Biobase, BiocGenerics, knitr
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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:44:54
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.22.0
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+Version: 1.23.0
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 Date: 2019-10-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:44:54
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.21.0
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+Version: 1.22.0
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 Date: 2019-10-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:38:32
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.20.0
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+Version: 1.21.0
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 Date: 2019-10-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:09:06
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.19.1
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+Version: 1.20.0
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 Date: 2019-10-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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removed change history from vignette; version number bumped to 1.19.1

UBodenhofer authored on 18/10/2019 13:39:21
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.19.0
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-Date: 2018-03-15
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+Version: 1.19.1
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+Date: 2019-10-18
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -57,5 +57,4 @@ LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, Biobase, BiocGenerics, knitr
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 VignetteBuilder: knitr
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2016-04-21 07:58:19 UTC; bodenhof
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 NeedsCompilation: yes
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bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:53
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.18.0
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+Version: 1.19.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:50
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.17.0
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+Version: 1.18.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:33
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.16.0
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+Version: 1.17.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:56
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.15.2
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+Version: 1.16.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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additional updates from BiocInstaller to BiocManager

LiNk-NY authored on 06/09/2018 15:51:50
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@@ -1,7 +1,7 @@
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.15.1
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+Version: 1.15.2
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:51:10
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@@ -1,7 +1,7 @@
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.15.0
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+Version: 1.15.1
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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updated DESCRIPTION (add GitHub URL)

Ulrich Bodenhofer authored on 15/05/2018 12:23:51
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@@ -36,6 +36,7 @@ Description: The package provides functionality for kernel-based analysis of
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         relevance of sequence sections for the learning result and the
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         underlying biological functions.
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 URL: http://www.bioinf.jku.at/software/kebabs/
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+     https://github.com/UBod/kebabs
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 ##Roxygen: list(wrap=TRUE)
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 License: GPL (>= 2.1)
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 Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
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bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:40
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.14.0
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+Version: 1.15.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:35
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.13.1
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+Version: 1.14.0
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 Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Remove C function getXStringSetClass()

C function getXStringSetClass() was a wrapper around C function
get_XStringSet_xsbaseclassname() defined in the Biostrings package,
which is itself a wrapper around C function get_List_elementType()
defined in the S4Vectors package. However, get_XStringSet_xsbaseclassname()
is about to be removed from Biostrings so any call to it should be replaced
with a call to get_List_elementType(). But since getXStringSetClass() is
not used, I removed it instead of fixing it (the fix would have been to
make it a wrapper around get_List_elementType() instead of around
get_XStringSet_xsbaseclassname()).

Hervé Pagès authored on 16/03/2018 02:31:17
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.13.0
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-Date: 2016-08-31
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+Version: 1.13.1
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+Date: 2018-03-15
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:53:51
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bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:40:44
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-Version: 1.11.0
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+Version: 1.12.0
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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 Package: kebabs
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-Version: 1.10.0
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+Version: 1.11.0
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 Date: 2016-08-31
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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 Package: kebabs
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-Version: 1.9.1
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+Version: 1.10.0
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

follow renaming of union classes in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@126387 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 01/02/2017 12:59:21
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 Package: kebabs
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+Version: 1.9.1
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bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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 Package: kebabs
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-Version: 1.8.0
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+Version: 1.9.0
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 Date: 2016-08-31
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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 Package: kebabs
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.7.3
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+Version: 1.8.0
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 Date: 2016-08-31
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

fixes of citation and news file; version number bumped to 1.7.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@120614 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 31/08/2016 08:23:38
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 Package: kebabs
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.7.2
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-Date: 2016-04-28
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+Version: 1.7.3
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+Date: 2016-08-31
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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 Package: kebabs
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-Version: 1.7.1
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+Version: 1.7.2
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 Date: 2016-04-28
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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 Package: kebabs
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-Version: 1.7.0
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+Version: 1.7.1
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 Date: 2016-04-28
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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-Version: 1.6.0
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+Version: 1.7.0
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 Date: 2016-04-28
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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 Package: kebabs
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.5.4
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+Version: 1.6.0
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 Date: 2016-04-28
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

further minor improvements; version number bumped to 1.5.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@116911 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 29/04/2016 05:26:22
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 Package: kebabs
2 2
 Type: Package
3 3
 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.5.3
5
-Date: 2016-04-26
4
+Version: 1.5.4
5
+Date: 2016-04-28
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: The package provides functionality for kernel-based analysis of
... ...
@@ -51,9 +51,9 @@ Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
51 51
 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
52 52
 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
53 53
         S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
54
-        utils
54
+        utils, apcluster
55 55
 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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-Suggests: SparseM, apcluster, Biobase, BiocGenerics, knitr
56
+Suggests: SparseM, Biobase, BiocGenerics, knitr
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 VignetteBuilder: knitr
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
59 59
 Packaged: 2016-04-21 07:58:19 UTC; bodenhof
Browse code

Various minor fixes and improvements; version number bumped to 1.5.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@116780 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 26/04/2016 07:03:34
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 Package: kebabs
2 2
 Type: Package
3 3
 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.5.2
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-Date: 2016-04-12
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+Version: 1.5.3
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+Date: 2016-04-26
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 Author: Johannes Palme
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 Description: The package provides functionality for kernel-based analysis of
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@@ -39,21 +39,22 @@ URL: http://www.bioinf.jku.at/software/kebabs/
39 39
 ##Roxygen: list(wrap=TRUE)
40 40
 License: GPL (>= 2.1)
41 41
 Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
42
-         kebabs.R kebabsData.R runtimeMessage.R parameters.R
43
-         sequenceKernel.R annotationSpecificKernel.R
44
-         positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
45
-         motif.R explicitRepresentation.R coerce-methods.R
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-         featureWeights.R heatmap-methods.R kbsvm-methods.R
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-         performCrossValidation-methods.R gridSearch.R modelSelection.R
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-         trainsvm-methods.R predictsvm-methods.R predict-methods.R
49
-         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
50
-         symmetricPair.R svm.R utils.R zzz.R
42
+        kebabs.R kebabsData.R runtimeMessage.R parameters.R
43
+        sequenceKernel.R annotationSpecificKernel.R
44
+        positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
45
+        motif.R explicitRepresentation.R coerce-methods.R
46
+        featureWeights.R heatmap-methods.R kbsvm-methods.R
47
+        performCrossValidation-methods.R gridSearch.R modelSelection.R
48
+        trainsvm-methods.R predictsvm-methods.R predict-methods.R
49
+        predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
50
+        symmetricPair.R svm.R utils.R zzz.R
51 51
 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
52 52
 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
53
-         S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
54
-	 utils
53
+        S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
54
+        utils
55 55
 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
56
-Suggests: SparseM, apcluster, Biobase, BiocGenerics
56
+Suggests: SparseM, apcluster, Biobase, BiocGenerics, knitr
57
+VignetteBuilder: knitr
57 58
 biocViews: SupportVectorMachine, Classification, Clustering, Regression
58
-Packaged: 2016-04-11 22:31:29 UTC; jo
59
+Packaged: 2016-04-21 07:58:19 UTC; bodenhof
59 60
 NeedsCompilation: yes
Browse code

several minor adaptations; version number bumped to 1.5.2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@116213 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 13/04/2016 06:35:58
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1 1
 Package: kebabs
2 2
 Type: Package
3 3
 Title: Kernel-Based Analysis Of Biological Sequences
4
-Version: 1.5.1
5
-Date: 2015-10-28
4
+Version: 1.5.2
5
+Date: 2016-04-12
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: The package provides functionality for kernel-based analysis of
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@@ -39,20 +39,21 @@ URL: http://www.bioinf.jku.at/software/kebabs/
39 39
 ##Roxygen: list(wrap=TRUE)
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 License: GPL (>= 2.1)
41 41
 Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
42
-        kebabs.R kebabsData.R runtimeMessage.R parameters.R
43
-        sequenceKernel.R annotationSpecificKernel.R
44
-        positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
45
-        motif.R explicitRepresentation.R coerce-methods.R
46
-        featureWeights.R heatmap-methods.R kbsvm-methods.R
47
-        performCrossValidation-methods.R gridSearch.R modelSelection.R
48
-        trainsvm-methods.R predictsvm-methods.R predict-methods.R
49
-        predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
50
-        symmetricPair.R svm.R utils.R zzz.R
42
+         kebabs.R kebabsData.R runtimeMessage.R parameters.R
43
+         sequenceKernel.R annotationSpecificKernel.R
44
+         positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
45
+         motif.R explicitRepresentation.R coerce-methods.R
46
+         featureWeights.R heatmap-methods.R kbsvm-methods.R
47
+         performCrossValidation-methods.R gridSearch.R modelSelection.R
48
+         trainsvm-methods.R predictsvm-methods.R predict-methods.R
49
+         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
50
+         symmetricPair.R svm.R utils.R zzz.R
51 51
 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
52 52
 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
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-        S4Vectors (>= 0.5.11), e1071, LiblineaR
53
+         S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
54
+	 utils
54 55
 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
55 56
 Suggests: SparseM, apcluster, Biobase, BiocGenerics
56 57
 biocViews: SupportVectorMachine, Classification, Clustering, Regression
57
-Packaged: 2015-04-17 03:38:36 UTC; biocbuild
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+Packaged: 2016-04-11 22:31:29 UTC; jo
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 NeedsCompilation: yes
Browse code

new function and error corrections

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@110019 bc3139a8-67e5-0310-9ffc-ced21a209358

Johannes Palme authored on 28/10/2015 06:07:23
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.5.0
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-Date: 2015-10-12
4
+Version: 1.5.1
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+Date: 2015-10-28
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: The package provides functionality for kernel-based analysis of
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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 Package: kebabs
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.4.0
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+Version: 1.5.0
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 Date: 2015-10-12
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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 Package: kebabs
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-Version: 1.3.4
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+Version: 1.4.0
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 Date: 2015-10-12
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

error corrections

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@109570 bc3139a8-67e5-0310-9ffc-ced21a209358

Johannes Palme authored on 13/10/2015 11:23:08
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.3.3
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-Date: 2015-05-21
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+Version: 1.3.4
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+Date: 2015-10-12
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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         relevance of sequence sections for the learning result and the
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         underlying biological functions.
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 URL: http://www.bioinf.jku.at/software/kebabs/
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-Roxygen: list(wrap=TRUE)
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+##Roxygen: list(wrap=TRUE)
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 License: GPL (>= 2.1)
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 Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
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         kebabs.R kebabsData.R runtimeMessage.R parameters.R
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
55 55
 Suggests: SparseM, apcluster, Biobase, BiocGenerics
56 56
 biocViews: SupportVectorMachine, Classification, Clustering, Regression
57
-Packaged: 2015-05-21 09:31:14 UTC; jo
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+Packaged: 2015-04-17 03:38:36 UTC; biocbuild
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 NeedsCompilation: yes
Browse code

Minor updates; version number bumped to 1.3.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@104033 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/05/2015 12:02:52
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.3.2
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-Date: 2015-05-08
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+Version: 1.3.3
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+Date: 2015-05-21
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 Author: Johannes Palme
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         trainsvm-methods.R predictsvm-methods.R predict-methods.R
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         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
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         symmetricPair.R svm.R utils.R zzz.R
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-Depends: R (>= 3.2.0), Biostrings (>= 2.33.14), kernlab
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-Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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-        S4Vectors (>= 0.2.4), e1071, LiblineaR
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+Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
52
+Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
53
+        S4Vectors (>= 0.5.11), e1071, LiblineaR
54 54
 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
55 55
 Suggests: SparseM, apcluster, Biobase, BiocGenerics
56 56
 biocViews: SupportVectorMachine, Classification, Clustering, Regression
57
-Packaged: 2015-05-08 15:35:21 UTC; jo
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+Packaged: 2015-05-21 09:31:14 UTC; jo
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 NeedsCompilation: yes
Browse code

Minor fixes and updates; version number bumped to 1.3.2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@103616 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 11/05/2015 06:26:25
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.3.1
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-Date: 2015-04-21
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+Version: 1.3.2
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+Date: 2015-05-08
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -54,5 +54,5 @@ Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-04-21 14:37:02 UTC; jo
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+Packaged: 2015-05-08 15:35:21 UTC; jo
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 NeedsCompilation: yes
Browse code

Minor fixes and updates; version number bumped to 1.3.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@102887 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/04/2015 15:15:12
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.3.0
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-Date: 2015-04-10
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+Version: 1.3.1
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+Date: 2015-04-21
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-04-10 13:15:58 UTC; jo
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+Packaged: 2015-04-21 14:37:02 UTC; jo
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+NeedsCompilation: yes
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Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.2.0
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+Version: 1.3.0
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 Date: 2015-04-10
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.9
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+Version: 1.2.0
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 Date: 2015-04-10
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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major update with several extensions and fixes; version number bumbed to 1.1.9

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@102273 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 10/04/2015 14:10:05
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.8
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-Date: 2015-03-02
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+Version: 1.1.9
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+Date: 2015-04-10
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -47,11 +47,11 @@ Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
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         performCrossValidation-methods.R gridSearch.R modelSelection.R
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         trainsvm-methods.R predictsvm-methods.R predict-methods.R
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         predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
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-        symmetricPair.R utils.R zzz.R
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-Depends: R (>= 3.1.0), Biostrings (>= 2.33.14), kernlab
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+        symmetricPair.R svm.R utils.R zzz.R
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+Depends: R (>= 3.2.0), Biostrings (>= 2.33.14), kernlab
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 Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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         S4Vectors (>= 0.2.4), e1071, LiblineaR
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-03-02 21:12:31 UTC; jo
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+Packaged: 2015-04-10 13:15:58 UTC; jo
Browse code

Added accessors to ModelSelectionResult class; version bump to 1.1.8

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@100078 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 02/03/2015 22:00:19
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.7
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-Date: 2015-02-08
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+Version: 1.1.8
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+Date: 2015-03-02
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -54,4 +54,4 @@ Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-02-08 22:20:12 UTC; jo
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+Packaged: 2015-03-02 21:12:31 UTC; jo
Browse code

Upgrade to 1.1.7 in order to fix issues with the latest version of LiblineaR

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@99221 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 09/02/2015 07:43:55
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.6
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-Date: 2015-01-21
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+Version: 1.1.7
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+Date: 2015-02-08
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -54,4 +54,4 @@ Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-01-21 11:10:57 UTC; jo
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+Packaged: 2015-02-08 22:20:12 UTC; jo
Browse code

Several updates -> new version 1.1.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@98550 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/01/2015 12:59:19
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 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.5
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-Date: 2014-01-12
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+Version: 1.1.6
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+Date: 2015-01-21
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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@@ -54,4 +54,4 @@ Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.5.8),
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 LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
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 Suggests: SparseM, apcluster, Biobase, BiocGenerics
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 biocViews: SupportVectorMachine, Classification, Clustering, Regression
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-Packaged: 2015-01-12 13:37:03 UTC; jo
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+Packaged: 2015-01-21 11:10:57 UTC; jo
Browse code

Updates to version 1.1.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@98267 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 12/01/2015 14:17:22
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1 1
 Package: kebabs
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 Type: Package
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 Title: Kernel-Based Analysis Of Biological Sequences
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-Version: 1.1.4
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-Date: 2014-12-03
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+Version: 1.1.5
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+Date: 2014-01-12
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 Author: Johannes Palme
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The package provides functionality for kernel-based analysis of
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         sequenceKernel.R annotationSpecificKernel.R
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         positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
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