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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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 Package: msa
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 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
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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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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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Update of gc; version number bumped to 1.31.1

UBod authored on 05/12/2022 11:55:56
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 Version: 1.31.1
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-Date: 2022-12-02
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+Date: 2022-12-05
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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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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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update of gc; version number bumped to 1.31.1

UBod authored on 02/12/2022 11:06:59
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 Package: msa
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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
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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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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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 15:11:38
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-Version: 1.30.0
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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 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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 Package: msa
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-Version: 1.29.3
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+Version: 1.30.0
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 Date: 2022-09-28
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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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Fix for lowercase sequences; version number bumped to 1.29.3

UBod authored on 28/09/2022 11:24:00
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 Package: msa
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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
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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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-Version: 1.29.1
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+Version: 1.29.2
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+Date: 2022-06-24
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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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-Version: 1.29.0
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+Version: 1.29.1
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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 15:25:21
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 Package: msa
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-Version: 1.28.0
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+Version: 1.29.0
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 Date: 2022-03-21
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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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 Package: msa
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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>
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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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-Version: 1.27.1
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+Version: 1.27.2
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 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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 Package: msa
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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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 URL: http://www.bioinf.jku.at/software/msa/
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 License: GPL (>= 2)
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 Copyright: See file inst/COPYRIGHT
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-Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)
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+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
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-Suggests: Biobase, knitr, seqinr, ape, phangorn
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+Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn
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 LinkingTo: Rcpp
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 SystemRequirements: GNU make
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 VignetteBuilder: knitr
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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 16:20:34
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 Package: msa
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-Version: 1.26.0
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+Version: 1.27.0
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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>
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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 16:20:34
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 Package: msa
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-Version: 1.25.3
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+Version: 1.26.0
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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>
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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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-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>
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 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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 Package: msa
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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>
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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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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 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 12:17:47
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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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@@ -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
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
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 NeedsCompilation: yes
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+Packaged: 2021-10-15 08:56:43 UTC; ulrich
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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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 Package: msa
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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
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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 16:13:32
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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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 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 16:13:32
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-Version: 1.23.1
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updated texshade.sty; version number bumped to 1.23.1

UBodenhofer authored on 29/04/2021 12:32:02
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-Version: 1.23.0
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-Date: 2020-08-12
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+Version: 1.23.1
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+Date: 2021-04-29
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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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-Version: 1.22.0
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+Version: 1.23.0
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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 15:05:14
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-Version: 1.21.1
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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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-Version: 1.21.0
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+Version: 1.21.1
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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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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 Package: msa
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-Version: 1.20.0
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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 18:48:56
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-Version: 1.19.0
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+Version: 1.20.0
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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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-Version: 1.18.0
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+Version: 1.19.0
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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 17:09:18
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 Package: msa
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-Version: 1.17.2
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+Version: 1.18.0
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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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-Version: 1.17.1
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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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-Version: 1.17.0
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+Version: 1.17.1
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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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 Package: msa
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-Version: 1.16.0
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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 15:53:55
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-Version: 1.15.0
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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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-Version: 1.14.0
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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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-Version: 1.13.1
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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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-Date: 2017-03-31
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+Version: 1.7.2
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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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 Package: msa
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-Version: 1.7.0
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-Date: 2016-08-09
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+Version: 1.7.1
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+Date: 2017-03-31
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -16,7 +16,7 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to
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 URL: http://www.bioinf.jku.at/software/msa/
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 License: GPL (>= 2)
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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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         S4Vectors, tools
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 Suggests: Biobase, knitr, seqinr, ape, phangorn
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@@ -28,6 +28,7 @@ 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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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
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 NeedsCompilation: yes
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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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-Version: 1.5.5
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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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+Version: 1.5.5
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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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+Version: 1.5.4
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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: 1.5.2
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+Version: 1.5.3
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+Date: 2016-06-23
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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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-Suggests: Biobase, knitr, seqinr
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+Suggests: Biobase, knitr, seqinr, ape, phangorn
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 LinkingTo: Rcpp
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 SystemRequirements: GNU make
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 VignetteBuilder: knitr
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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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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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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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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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+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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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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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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 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
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 NeedsCompilation: yes
Browse code

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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-Date: 2015-12-21
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+Date: 2016-02-25
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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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 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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 NeedsCompilation: yes
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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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+Date: 2015-12-21
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
... ...
@@ -21,7 +21,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21
         S4Vectors, tools
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 Suggests: Biobase, knitr
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 LinkingTo: Rcpp
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-SystemRequirements:
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+SystemRequirements: GNU make
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 VignetteBuilder: knitr
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 LazyLoad: yes
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 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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@@ -31,4 +31,3 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
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 NeedsCompilation: yes
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-Packaged: 2015-10-07 16:20:45 UTC; bodenhof
Browse code

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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@@ -1,7 +1,7 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.3.0
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+Version: 1.3.1
5 5
 Date: 2015-10-13
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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

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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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.2.0
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+Version: 1.3.0
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 Date: 2015-10-13
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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

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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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.1.3
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+Version: 1.2.0
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 Date: 2015-10-13
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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

Last-minute fixes; version number bumped to 1.1.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@109581 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 13/10/2015 17:35:42
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.1.2
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-Date: 2015-10-10
4
+Version: 1.1.3
5
+Date: 2015-10-13
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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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 Description: This package provides a unified R/Bioconductor interface to the
Browse code

Multiple new features and fixes; version number bumped to 1.1.2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@109473 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 10/10/2015 13:46:31
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.1.1
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-Date: 2015-06-12
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+Version: 1.1.2
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+Date: 2015-10-10
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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 Description: This package provides a unified R/Bioconductor interface to the
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@@ -17,15 +17,18 @@ URL: http://www.bioinf.jku.at/software/msa/
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 License: GPL (>= 2)
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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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-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
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-	 tools
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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
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 LinkingTo: Rcpp
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 SystemRequirements:
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 VignetteBuilder: knitr
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 LazyLoad: yes
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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
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-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing
27
+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28
+        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29
+        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30
+        msaClustalOmega.R
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+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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+        Sequencing
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+NeedsCompilation: yes
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+Packaged: 2015-10-07 16:20:45 UTC; bodenhof
Browse code

fix of msa() function; version number bumped to 1.1.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@104866 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 12/06/2015 08:49:45
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.1.0
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-Date: 2015-04-16
4
+Version: 1.1.1
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+Date: 2015-06-12
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
Browse code

Bump versions in trunk after creation of 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 20:02:44
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@@ -1,7 +1,7 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.0.0
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+Version: 1.1.0
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 Date: 2015-04-16
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Bump versions prior to creating 3.1 branch.

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

Dan Tenenbaum authored on 16/04/2015 19:42:01
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@@ -1,7 +1,7 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 0.99.7
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+Version: 1.0.0
5 5
 Date: 2015-04-16
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Adapted handling of signs of gap penalties; version number bumped to 0.99.7

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102560 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 16/04/2015 08:25:08
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 0.99.6
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-Date: 2015-04-15
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+Version: 0.99.7
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+Date: 2015-04-16
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
... ...
@@ -17,18 +17,15 @@ URL: http://www.bioinf.jku.at/software/msa/
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 License: GPL (>= 2)
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 Copyright: See file inst/COPYRIGHT
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 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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-        S4Vectors, tools
20
+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
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+	 tools
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 Suggests: Biobase, knitr
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 LinkingTo: Rcpp
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 SystemRequirements:
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 VignetteBuilder: knitr
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 LazyLoad: yes
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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
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-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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-        Sequencing
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-NeedsCompilation: yes
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-Packaged: 2015-04-15 13:16:43 UTC; bodenhof
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+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R 
28
+         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29
+	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 
30
+         msaClustalOmega.R
31
+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing
Browse code

Multiple fixes; final comit before release; version number bumped to 0.99.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102514 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 15/04/2015 13:20:09
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 0.99.5
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-Date: 2015-04-12
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+Version: 0.99.6
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+Date: 2015-04-15
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
... ...
@@ -17,15 +17,18 @@ URL: http://www.bioinf.jku.at/software/msa/
17 17
 License: GPL (>= 2)
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 Copyright: See file inst/COPYRIGHT
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 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
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-	 tools
20
+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21
+        S4Vectors, tools
22 22
 Suggests: Biobase, knitr
23 23
 LinkingTo: Rcpp
24
-SystemRequirements: GNU make
24
+SystemRequirements:
25 25
 VignetteBuilder: knitr
26 26
 LazyLoad: yes
27
-Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R 
28
-         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29
-	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 
30
-         msaClustalOmega.R
31
-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing
27
+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28
+        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29
+        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30
+        msaClustalOmega.R
31
+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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+        Sequencing
33
+NeedsCompilation: yes
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+Packaged: 2015-04-15 13:16:43 UTC; bodenhof
Browse code

Further fixes for Mac platform; version number bumped to 0.99.5

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102357 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 12/04/2015 19:59:20
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1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 0.99.4
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-Date: 2015-04-11
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+Version: 0.99.5
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+Date: 2015-04-12
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
Browse code

Fixes for Mac Mavericks platform; version number bumped to 0.99.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102336 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 12/04/2015 00:13:25
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@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 0.99.3
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-Date: 2015-04-10
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+Version: 0.99.4
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+Date: 2015-04-11
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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: This package provides a unified R/Bioconductor interface to the
... ...
@@ -13,21 +13,19 @@ Description: This package provides a unified R/Bioconductor interface to the
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 	     alignment algorithms are complemented by a function for
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 	     pretty-printing multiple sequence alignments using the LaTeX
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 	     package TeXshade.
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+URL: http://www.bioinf.jku.at/software/msa/
16 17
 License: GPL (>= 2)
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 Copyright: See file inst/COPYRIGHT
18 19
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
19
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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-        S4Vectors, tools
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+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
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+	 tools
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 Suggests: Biobase, knitr
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 LinkingTo: Rcpp
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 SystemRequirements: GNU make
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 VignetteBuilder: knitr
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 LazyLoad: yes
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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
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-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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-        Sequencing
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-NeedsCompilation: yes
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-Packaged: 2015-04-10 22:07:02 UTC; bodenhof
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+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R 
28
+         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29
+	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 
30
+         msaClustalOmega.R
31
+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing
Browse code

Various fixes and improvements; version number bumped to 0.99.3

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102303 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 10/04/2015 22:38:22
Showing1 changed files
... ...
@@ -1,18 +1,18 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
4
-Version: 0.99.2
5
-Date: 2015-04-09
4
+Version: 0.99.3
5
+Date: 2015-04-10
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8
-Description: This package provides a unified R/Bioconductor interface
9
-        to the multiple sequence alignment algorithms ClustalW,
10
-        ClustalOmega, and Muscle. All three algorithms are integrated
11
-        in the package, therefore, they do not depend on any external
12
-        software tools and are available for all major platforms. The
13
-        multiple sequence alignment algorithms are complemented by a
14
-        function for pretty-printing multiple sequence alignments using
15
-        the LaTeX package TeXshade.
8
+Description: This package provides a unified R/Bioconductor interface to the
9
+	     multiple sequence alignment algorithms ClustalW, ClustalOmega,
10
+	     and Muscle. All three algorithms are integrated in the package,
11
+	     therefore, they do not depend on any external software tools
12
+	     and are available for all major platforms. The multiple sequence
13
+	     alignment algorithms are complemented by a function for
14
+	     pretty-printing multiple sequence alignments using the LaTeX
15
+	     package TeXshade.
16 16
 License: GPL (>= 2)
17 17
 Copyright: See file inst/COPYRIGHT
18 18
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
... ...
@@ -20,6 +20,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
20 20
         S4Vectors, tools
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 Suggests: Biobase, knitr
22 22
 LinkingTo: Rcpp
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+SystemRequirements: GNU make
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 VignetteBuilder: knitr
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 LazyLoad: yes
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 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
... ...
@@ -29,3 +30,4 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
29 30
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
30 31
         Sequencing
31 32
 NeedsCompilation: yes
33
+Packaged: 2015-04-10 22:07:02 UTC; bodenhof
Browse code

add package to the repository

msa


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 10/04/2015 00:12:33
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1 1
new file mode 100644
... ...
@@ -0,0 +1,31 @@
1
+Package: msa
2
+Type: Package
3
+Title: Multiple Sequence Alignment
4
+Version: 0.99.2
5
+Date: 2015-04-09
6
+Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7
+Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8
+Description: This package provides a unified R/Bioconductor interface
9
+        to the multiple sequence alignment algorithms ClustalW,
10
+        ClustalOmega, and Muscle. All three algorithms are integrated
11
+        in the package, therefore, they do not depend on any external
12
+        software tools and are available for all major platforms. The
13
+        multiple sequence alignment algorithms are complemented by a
14
+        function for pretty-printing multiple sequence alignments using
15
+        the LaTeX package TeXshade.
16
+License: GPL (>= 2)
17
+Copyright: See file inst/COPYRIGHT
18
+Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
19
+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
20
+        S4Vectors, tools
21
+Suggests: Biobase, knitr
22
+LinkingTo: Rcpp
23
+VignetteBuilder: knitr
24
+LazyLoad: yes
25
+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
26
+        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
27
+        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
28
+        msaClustalOmega.R
29
+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
30
+        Sequencing
31
+NeedsCompilation: yes