1. msa
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 14:43:22
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.34.0
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+Version: 1.35.0
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 Date: 2023-09-20
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 14:43:22
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DESCRIPTION
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.33.2
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+Version: 1.34.0
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 Date: 2023-09-20
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Update DESCRIPTION

UBod authored on 20/09/2023 13:52:24 • GitHub committed on 20/09/2023 13:52:24
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.33.1
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-Date: 2023-07-11
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+Version: 1.33.2
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+Date: 2023-09-20
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

update of msaConsensusSequence() and msaConsensusSequence() methods to account for recent change in function Biostrings::consensusMatrix(); version number bumped to 1.33.1

UBod authored on 11/07/2023 10:35:17
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DESCRIPTION
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.33.0
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-Date: 2023-03-28
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+Version: 1.33.1
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+Date: 2023-07-11
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

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

J Wokaty authored on 25/04/2023 14:39:34
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DESCRIPTION
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.32.0
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+Version: 1.33.0
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 Date: 2023-03-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:39:34
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DESCRIPTION
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 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
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-Version: 1.31.7
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+Version: 1.32.0
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 Date: 2023-03-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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added -std=c++14 to ClustalW; version number bumped to 1.31.7

UBod authored on 28/03/2023 14:42:11
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.6
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-Date: 2023-03-23
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+Version: 1.31.7
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+Date: 2023-03-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17; version number bumped to 1.31.6

UBod authored on 23/03/2023 15:22:56
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DESCRIPTION
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 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.5
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-Date: 2023-03-22
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+Version: 1.31.6
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+Date: 2023-03-23
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17; version number bumped to 1.31.5

UBod authored on 22/03/2023 09:32:33
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DESCRIPTION
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 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.4
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-Date: 2023-02-22
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+Version: 1.31.5
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+Date: 2023-03-22
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

fix in src/Muscle/subfams.cpp to avoid conflicting definitions on some Mac systems; version number bumped to 1.31.4

UBod authored on 22/02/2023 11:11:11
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DESCRIPTION
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 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.3
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-Date: 2023-02-20
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+Version: 1.31.4
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+Date: 2023-02-22
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

Update to config.sub/config.guess in ClustalW and ClustalOmega; version number bumped to 1.31.3

UBod authored on 20/02/2023 12:40:56
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.2
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-Date: 2022-12-14
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+Version: 1.31.3
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+Date: 2023-02-20
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

msa() function changed such that it also works if the package is not attached to the workspace; version number bumped to 1.31.2

UBod authored on 14/12/2022 06:25:02
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
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-Version: 1.31.1
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-Date: 2022-12-05
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+Version: 1.31.2
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+Date: 2022-12-14
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

Update of gc; version number bumped to 1.31.1

UBod authored on 05/12/2022 11:55:56
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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 Version: 1.31.1
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-Date: 2022-12-02
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+Date: 2022-12-05
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

update of gc; version number bumped to 1.31.1

UBod authored on 02/12/2022 11:06:59
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.31.0
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-Date: 2022-09-28
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+Version: 1.31.1
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+Date: 2022-12-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:11:38
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
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-Version: 1.30.0
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+Version: 1.31.0
5 5 
 Date: 2022-09-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:11:38
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
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-Version: 1.29.3
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+Version: 1.30.0
5 5 
 Date: 2022-09-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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Fix for lowercase sequences; version number bumped to 1.29.3

UBod authored on 28/09/2022 11:24:00
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DESCRIPTION
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.29.2
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-Date: 2022-06-24
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+Version: 1.29.3
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+Date: 2022-09-28
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

fix in texshade.sty as suggested on TeXshade homepage at CTAN; version number bumped to 1.29.2

UBod authored on 24/06/2022 17:41:17
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DESCRIPTION
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.29.1
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-Date: 2022-06-02
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+Version: 1.29.2
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+Date: 2022-06-24
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

Fix to avoid compilation problems on newest Mac OS; version number bumped to 1.29.1

UBod authored on 02/06/2022 10:03:38
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.29.0
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-Date: 2022-03-21
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+Version: 1.29.1
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+Date: 2022-06-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:25:21
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.28.0
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+Version: 1.29.0
5 5 
 Date: 2022-03-21
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 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 15:25:21
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.27.2
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+Version: 1.28.0
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 Date: 2022-03-21
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

applied patch to allow msa to work with the new Windows UCRT toolchain; version number bumped to 1.27.2

UBod authored on 21/03/2022 12:58:40
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1 1 
 Package: msa
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 Title: Multiple Sequence Alignment
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-Version: 1.27.1
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-Date: 2022-02-17
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+Version: 1.27.2
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+Date: 2022-03-21
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
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various fixes; version number bumped to 1.27.1

UBodenhofer authored on 17/02/2022 12:58:20
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DESCRIPTION
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.27.0
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-Date: 2021-10-20
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+Version: 1.27.1
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+Date: 2022-02-17
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -16,10 +16,10 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to
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 URL: http://www.bioinf.jku.at/software/msa/
17 17 
 License: GPL (>= 2)
18 18 
 Copyright: See file inst/COPYRIGHT
19 
-Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)
19 
+Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0)
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 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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         S4Vectors, tools
22 
-Suggests: Biobase, knitr, seqinr, ape, phangorn
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+Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn
23 23 
 LinkingTo: Rcpp
24 24 
 SystemRequirements: GNU make
25 25 
 VignetteBuilder: knitr
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:20:34
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DESCRIPTION
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1 1 
 Package: msa
2 2 
 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.26.0
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+Version: 1.27.0
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 Date: 2021-10-20
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:20:34
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DESCRIPTION
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.25.3
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+Version: 1.26.0
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 Date: 2021-10-20
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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further fixes of warnings; version number bumped to 1.25.3

UBod authored on 20/10/2021 08:40:40
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DESCRIPTION
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.25.2
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-Date: 2021-10-18
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+Version: 1.25.3
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+Date: 2021-10-20
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
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removed build/ directory from repo to avoid installation problems; version number bumped to 1.25.2

UBod authored on 18/10/2021 07:09:47
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.25.1
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-Date: 2021-10-14
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+Version: 1.25.2
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+Date: 2021-10-18
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
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Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 12:35:07
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-<<<<<<< HEAD
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 Version: 1.25.1
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 Date: 2021-10-14
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-=======
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-Version: 1.25.0
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-Date: 2021-04-29
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->>>>>>> upstream/master
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
13 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 12:17:47
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Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 10:54:55
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DESCRIPTION
History View file @ d236535
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@@ -28,7 +28,8 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
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         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
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         msaClustalOmega.R msaConvert.R msaCheckNames.R
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-	msaConsensusSequence-methods.R msaConservationScore-methods.R
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+        msaConsensusSequence-methods.R msaConservationScore-methods.R
32 32 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
34 34 
 NeedsCompilation: yes
35 
+Packaged: 2021-10-15 08:56:43 UTC; ulrich
Browse code

update of gc; version number bumped to 1.25.1

UBod authored on 14/10/2021 10:09:56 • GitHub committed on 14/10/2021 10:09:56
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1 1 
 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.23.1
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-Date: 2021-04-29
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+Version: 1.25.1
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+Date: 2021-10-14
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8 
 Description: The 'msa' package provides a unified R/Bioconductor interface to
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:13:32
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.24.0
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+Version: 1.25.0
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 Date: 2021-04-29
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:13:32
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DESCRIPTION
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1 1 
 Package: msa
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 Title: Multiple Sequence Alignment
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-Version: 1.23.1
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+Version: 1.24.0
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 Date: 2021-04-29
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

updated texshade.sty; version number bumped to 1.23.1

UBodenhofer authored on 29/04/2021 12:32:02
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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 15:05:14
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Nitesh Turaga authored on 27/10/2020 15:05:14
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addressed UPGMA error in msaClustalW() on Windows using R 4.0.x

UBodenhofer authored on 12/08/2020 13:44:51
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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 18:48:56
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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 18:48:56
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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 17:39:24
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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 17:09:18
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removed change history from vignette; version number bumped to 1.17.2

UBodenhofer authored on 18/10/2019 13:53:51
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Various fixes related to Windows build; version number bumped to 1.17.1

UBodenhofer authored on 12/09/2019 07:42:34
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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 16:12:41
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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 15:53:55
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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 15:54:34
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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 15:41:58
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:52:42
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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 14:41:41
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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 14:35:37
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minor fix in ClustalW; version number bumped to 1.11.2

Ulrich Bodenhofer authored on 27/04/2018 06:42:31
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fix of custom substitution matrices in ClustalW; version number bumped to 1.11.1

Ulrich Bodenhofer authored on 23/04/2018 11:29:24
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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 16:54:10
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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 16:40:51
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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/msa@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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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/msa@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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Fix for clang 4 on Mac OS; version number bumped to 1.7.2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@128803 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 17/04/2017 19:52:29
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New functionality for computing consensus sequences and conservation scores; version number bumped to 1.7.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@127901 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 31/03/2017 11:35:08
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 Copyright: See file inst/COPYRIGHT
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-Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
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+Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)
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 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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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/msa@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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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/msa@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix; version number bumped to 1.5.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@119986 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 09/08/2016 14:50:55
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minor fixes (see inst/NEWS); version number bumped to 1.5.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@119484 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 20/07/2016 13:18:53
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conversions extended + corresponding changes in documentation; version number bumped to 1.5.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@118902 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 23/06/2016 13:33:29
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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/msa@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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 Package: msa
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 Title: Multiple Sequence Alignment
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-Version: 1.5.1
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+Version: 1.5.2
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 Date: 2016-05-02
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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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/msa@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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bump version after creating 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:30:44
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Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
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Last-minute fix of msaPrettyPrint(); version number bumped to 1.3.7

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@116969 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 02/05/2016 09:23:23
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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Minor corrections and extensions (see inst/NEWS); version number bumped to 1.3.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@116456 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 18/04/2016 15:12:00
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-Description: This package provides a unified R/Bioconductor interface to the
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-	     multiple sequence alignment algorithms ClustalW, ClustalOmega,
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+Description: The 'msa' package provides a unified R/Bioconductor interface to
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+             the multiple sequence alignment algorithms ClustalW, ClustalOmega,
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 	     and Muscle. All three algorithms are integrated in the package,
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 	     therefore, they do not depend on any external software tools
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 	     and are available for all major platforms. The multiple sequence
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Minor changes in the way the help text is displayed by the msa() function; version number bumped to 1.3.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@116078 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 10/04/2016 14:57:52
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 Description: This package provides a unified R/Bioconductor interface to the
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Added a new function msaCheckNames; version number bumped to 1.3.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@115880 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 06/04/2016 12:24:49
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-Version: 1.3.3
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 Description: This package provides a unified R/Bioconductor interface to the
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 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
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         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
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+        msaClustalOmega.R msaConvert.R msaCheckNames.R
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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 NeedsCompilation: yes
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added new conversion tools; version number bumped to 1.3.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@114012 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 25/02/2016 15:23:41
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 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
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 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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         S4Vectors, tools
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+Suggests: Biobase, knitr, seqinr
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 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
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         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
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further fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@111693 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/12/2015 10:29:13
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-Version: 1.3.1
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+Version: 1.3.2
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-Packaged: 2015-10-07 16:20:45 UTC; bodenhof
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Don't depend on R's presence on search path during install

- use "${R_HOME}/bin${R_ARCH_BIN}/R" & friends in Makevars files


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@111425 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 11/12/2015 22:59:15
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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/msa@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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Bumped versions of all packages prior to creating 3.2 branch.

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

Dan Tenenbaum authored on 13/10/2015 19:36:05
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