1. msa
  2. DESCRIPTION
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
Showing1 changed files
DESCRIPTION
History View file @5447559
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.31.1
5 
-Date: 2022-12-05
4 
+Version: 1.31.2
5 
+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
Showing1 changed files
DESCRIPTION
History View file @398d017
... ... 
@@ -2,7 +2,7 @@ Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 4 
 Version: 1.31.1
5 
-Date: 2022-12-02
5 
+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
Showing1 changed files
DESCRIPTION
History View file @79494b5
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.31.0
5 
-Date: 2022-09-28
4 
+Version: 1.31.1
5 
+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
Showing1 changed files
DESCRIPTION
History View file @f08931e
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.30.0
4 
+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
Showing1 changed files
DESCRIPTION
History View file @9ce42ab
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.29.3
4 
+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>
Browse code

Fix for lowercase sequences; version number bumped to 1.29.3

UBod authored on 28/09/2022 11:24:00
Showing1 changed files
DESCRIPTION
History View file @d737051
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.29.2
5 
-Date: 2022-06-24
4 
+Version: 1.29.3
5 
+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
Showing1 changed files
DESCRIPTION
History View file @d6f4b25
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.29.1
5 
-Date: 2022-06-02
4 
+Version: 1.29.2
5 
+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
Showing1 changed files
DESCRIPTION
History View file @b04803a
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.29.0
5 
-Date: 2022-03-21
4 
+Version: 1.29.1
5 
+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
Showing1 changed files
DESCRIPTION
History View file @3a035de
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.28.0
4 
+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>
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @b9511f3
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.27.2
4 
+Version: 1.28.0
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>
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
Showing1 changed files
DESCRIPTION
History View file @4be735d
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.27.1
5 
-Date: 2022-02-17
4 
+Version: 1.27.2
5 
+Date: 2022-03-21
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

various fixes; version number bumped to 1.27.1

UBodenhofer authored on 17/02/2022 12:58:20
Showing1 changed files
DESCRIPTION
History View file @c6a568a
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.27.0
5 
-Date: 2021-10-20
4 
+Version: 1.27.1
5 
+Date: 2022-02-17
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
... ... 
@@ -16,10 +16,10 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to
16 16 
 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)
20 20 
 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21 
         S4Vectors, tools
22 
-Suggests: Biobase, knitr, seqinr, ape, phangorn
22 
+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
Showing1 changed files
DESCRIPTION
History View file @85abce7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.26.0
4 
+Version: 1.27.0
5 5 
 Date: 2021-10-20
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_14 branch

Nitesh Turaga authored on 26/10/2021 16:20:34
Showing1 changed files
DESCRIPTION
History View file @2b1349d
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.25.3
4 
+Version: 1.26.0
5 5 
 Date: 2021-10-20
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

further fixes of warnings; version number bumped to 1.25.3

UBod authored on 20/10/2021 08:40:40
Showing1 changed files
DESCRIPTION
History View file @9e7acaf
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.25.2
5 
-Date: 2021-10-18
4 
+Version: 1.25.3
5 
+Date: 2021-10-20
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

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
Showing1 changed files
DESCRIPTION
History View file @a759391
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.25.1
5 
-Date: 2021-10-14
4 
+Version: 1.25.2
5 
+Date: 2021-10-18
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

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 12:35:07
Showing1 changed files
DESCRIPTION
History View file @a1a1906
... ... 
@@ -1,13 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-<<<<<<< HEAD
5 4 
 Version: 1.25.1
6 5 
 Date: 2021-10-14
7 
-=======
8 
-Version: 1.25.0
9 
-Date: 2021-04-29
10 
->>>>>>> upstream/master
11 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
12 7 
 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
Showing0 changed files
Browse code

Upgraded to GC 7.6.12 + corresponding changes in package

UBod authored on 15/10/2021 10:54:55
Showing1 changed files
DESCRIPTION
History View file @d236535
... ... 
@@ -28,7 +28,8 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28 28 
         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29 29 
         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30 30 
         msaClustalOmega.R msaConvert.R msaCheckNames.R
31 
-	msaConsensusSequence-methods.R msaConservationScore-methods.R
31 
+        msaConsensusSequence-methods.R msaConservationScore-methods.R
32 32 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
33 33 
         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
Showing1 changed files
DESCRIPTION
History View file @58801f8
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.23.1
5 
-Date: 2021-04-29
4 
+Version: 1.25.1
5 
+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
Showing1 changed files
DESCRIPTION
History View file @5f2297b
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.24.0
4 
+Version: 1.25.0
5 5 
 Date: 2021-04-29
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_13 branch

Nitesh Turaga authored on 19/05/2021 16:13:32
Showing1 changed files
DESCRIPTION
History View file @d939cac
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.23.1
4 
+Version: 1.24.0
5 5 
 Date: 2021-04-29
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 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
Showing1 changed files
DESCRIPTION
History View file @7606297
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.23.0
5 
-Date: 2020-08-12
4 
+Version: 1.23.1
5 
+Date: 2021-04-29
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_12 branch

Nitesh Turaga authored on 27/10/2020 15:05:14
Showing1 changed files
DESCRIPTION
History View file @d7b257c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.22.0
4 
+Version: 1.23.0
5 5 
 Date: 2020-08-12
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_12 branch

Nitesh Turaga authored on 27/10/2020 15:05:14
Showing1 changed files
DESCRIPTION
History View file @78bb238
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.21.1
4 
+Version: 1.22.0
5 5 
 Date: 2020-08-12
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

addressed UPGMA error in msaClustalW() on Windows using R 4.0.x

UBodenhofer authored on 12/08/2020 13:44:51
Showing1 changed files
DESCRIPTION
History View file @6331ee3
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.21.0
5 
-Date: 2019-10-17
4 
+Version: 1.21.1
5 
+Date: 2020-08-12
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_11 branch

Nitesh Turaga authored on 27/04/2020 18:48:56
Showing1 changed files
DESCRIPTION
History View file @0ff2dd0
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.20.0
4 
+Version: 1.21.0
5 5 
 Date: 2019-10-17
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_11 branch

Nitesh Turaga authored on 27/04/2020 18:48:56
Showing1 changed files
DESCRIPTION
History View file @d8361a7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.19.0
4 
+Version: 1.20.0
5 5 
 Date: 2019-10-17
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 odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:39:24
Showing1 changed files
DESCRIPTION
History View file @179c40e
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.18.0
4 
+Version: 1.19.0
5 5 
 Date: 2019-10-17
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_10 branch

Nitesh Turaga authored on 29/10/2019 17:09:18
Showing1 changed files
DESCRIPTION
History View file @bfbaad2
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.17.2
4 
+Version: 1.18.0
5 5 
 Date: 2019-10-17
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

removed change history from vignette; version number bumped to 1.17.2

UBodenhofer authored on 18/10/2019 13:53:51
Showing1 changed files
DESCRIPTION
History View file @e487eb3
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.17.1
5 
-Date: 2019-09-12
4 
+Version: 1.17.2
5 
+Date: 2019-10-17
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

Various fixes related to Windows build; version number bumped to 1.17.1

UBodenhofer authored on 12/09/2019 07:42:34
Showing1 changed files
DESCRIPTION
History View file @6d5174b
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.17.0
5 
-Date: 2018-04-27
4 
+Version: 1.17.1
5 
+Date: 2019-09-12
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 versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:12:41
Showing1 changed files
DESCRIPTION
History View file @6abe9dc
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.16.0
4 
+Version: 1.17.0
5 5 
 Date: 2018-04-27
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 versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:55
Showing1 changed files
DESCRIPTION
History View file @be1cf21
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.15.0
4 
+Version: 1.16.0
5 5 
 Date: 2018-04-27
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 versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:34
Showing1 changed files
DESCRIPTION
History View file @8e00ed7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.14.0
4 
+Version: 1.15.0
5 5 
 Date: 2018-04-27
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 versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:58
Showing1 changed files
DESCRIPTION
History View file @b311929
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.13.1
4 
+Version: 1.14.0
5 5 
 Date: 2018-04-27
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:52:42
Showing1 changed files
DESCRIPTION
History View file @d1609f4
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.13.0
4 
+Version: 1.13.1
5 5 
 Date: 2018-04-27
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 versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:41
Showing1 changed files
DESCRIPTION
History View file @0dc4e75
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.12.0
4 
+Version: 1.13.0
5 5 
 Date: 2018-04-27
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 versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:37
Showing1 changed files
DESCRIPTION
History View file @5c9af26
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.11.2
4 
+Version: 1.12.0
5 5 
 Date: 2018-04-27
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

minor fix in ClustalW; version number bumped to 1.11.2

Ulrich Bodenhofer authored on 27/04/2018 06:42:31
Showing1 changed files
DESCRIPTION
History View file @8848fc7
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.11.1
5 
-Date: 2018-04-23
4 
+Version: 1.11.2
5 
+Date: 2018-04-27
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 of custom substitution matrices in ClustalW; version number bumped to 1.11.1

Ulrich Bodenhofer authored on 23/04/2018 11:29:24
Showing1 changed files
DESCRIPTION
History View file @23e990d
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.11.0
5 
-Date: 2017-04-17
4 
+Version: 1.11.1
5 
+Date: 2018-04-23
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

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
Showing1 changed files
DESCRIPTION
History View file @b77c792
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.10.0
4 
+Version: 1.11.0
5 5 
 Date: 2017-04-17
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 versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:40:51
Showing1 changed files
DESCRIPTION
History View file @0c9cc33
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.9.0
4 
+Version: 1.10.0
5 5 
 Date: 2017-04-17
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 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
Showing1 changed files
DESCRIPTION
History View file @fa7c43d
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.8.0
4 
+Version: 1.9.0
5 5 
 Date: 2017-04-17
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 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
Showing1 changed files
DESCRIPTION
History View file @29f2b81
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.7.2
4 
+Version: 1.8.0
5 5 
 Date: 2017-04-17
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @a760f3e
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.7.1
5 
-Date: 2017-03-31
4 
+Version: 1.7.2
5 
+Date: 2017-04-17
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

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
Showing1 changed files
DESCRIPTION
History View file @5ad9386
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.7.0
5 
-Date: 2016-08-09
4 
+Version: 1.7.1
5 
+Date: 2017-03-31
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
... ... 
@@ -16,7 +16,7 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to
16 16 
 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 (>= 2.30.0)
19 
+Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)
20 20 
 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21 
         S4Vectors, tools
22 22 
 Suggests: Biobase, knitr, seqinr, ape, phangorn
... ... 
@@ -28,6 +28,7 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28 28 
         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29 29 
         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30 30 
         msaClustalOmega.R msaConvert.R msaCheckNames.R
31 
+	msaConsensusSequence-methods.R msaConservationScore-methods.R
31 32 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
32 33 
         Sequencing
33 34 
 NeedsCompilation: yes
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @6def718
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.6.0
4 
+Version: 1.7.0
5 5 
 Date: 2016-08-09
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 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
Showing1 changed files
DESCRIPTION
History View file @2b6c62b
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.5
4 
+Version: 1.6.0
5 5 
 Date: 2016-08-09
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @f2d8b3d
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.4
5 
-Date: 2016-07-20
4 
+Version: 1.5.5
5 
+Date: 2016-08-09
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

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
Showing1 changed files
DESCRIPTION
History View file @b9525fd
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.3
5 
-Date: 2016-06-23
4 
+Version: 1.5.4
5 
+Date: 2016-07-20
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

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
Showing1 changed files
DESCRIPTION
History View file @bbc69d1
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.2
5 
-Date: 2016-05-02
4 
+Version: 1.5.3
5 
+Date: 2016-06-23
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
... ... 
@@ -19,7 +19,7 @@ Copyright: See file inst/COPYRIGHT
19 19 
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20 20 
 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21 
         S4Vectors, tools
22 
-Suggests: Biobase, knitr, seqinr
22 
+Suggests: Biobase, knitr, seqinr, ape, phangorn
23 23 
 LinkingTo: Rcpp
24 24 
 SystemRequirements: GNU make
25 25 
 VignetteBuilder: knitr
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @d83a50c
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.1
4 
+Version: 1.5.2
5 5 
 Date: 2016-05-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

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

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

Dan Tenenbaum authored on 11/05/2016 23:05:31
Showing1 changed files
DESCRIPTION
History View file @9134353
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.5.0
4 
+Version: 1.5.1
5 5 
 Date: 2016-05-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

bump version after creating 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:30:44
Showing1 changed files
DESCRIPTION
History View file @9667b92
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.4.0
4 
+Version: 1.5.0
5 5 
 Date: 2016-05-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
Showing1 changed files
DESCRIPTION
History View file @cb96c2a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.7
4 
+Version: 1.4.0
5 5 
 Date: 2016-05-02
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @48323c5
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.6
5 
-Date: 2016-04-18
4 
+Version: 1.3.7
5 
+Date: 2016-05-02
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

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
Showing1 changed files
DESCRIPTION
History View file @8674fd7
... ... 
@@ -1,12 +1,12 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.5
5 
-Date: 2016-04-07
4 
+Version: 1.3.6
5 
+Date: 2016-04-18
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 to the
9 
-	     multiple sequence alignment algorithms ClustalW, ClustalOmega,
8 
+Description: The 'msa' package provides a unified R/Bioconductor interface to
9 
+             the multiple sequence alignment algorithms ClustalW, ClustalOmega,
10 10 
 	     and Muscle. All three algorithms are integrated in the package,
11 11 
 	     therefore, they do not depend on any external software tools
12 12 
 	     and are available for all major platforms. The multiple sequence
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @297b13a
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.4
5 
-Date: 2016-04-06
4 
+Version: 1.3.5
5 
+Date: 2016-04-07
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
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @faf12a4
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.3
5 
-Date: 2016-02-25
4 
+Version: 1.3.4
5 
+Date: 2016-04-06
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
... ... 
@@ -27,7 +27,7 @@ LazyLoad: yes
27 27 
 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28 28 
         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29 29 
         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30 
-        msaClustalOmega.R msaConvert.R
30 
+        msaClustalOmega.R msaConvert.R msaCheckNames.R
31 31 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
32 32 
         Sequencing
33 33 
 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
Showing1 changed files
DESCRIPTION
History View file @8db2d6e
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.2
5 
-Date: 2015-12-21
4 
+Version: 1.3.3
5 
+Date: 2016-02-25
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
... ... 
@@ -19,7 +19,7 @@ Copyright: See file inst/COPYRIGHT
19 19 
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20 20 
 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21 
         S4Vectors, tools
22 
-Suggests: Biobase, knitr
22 
+Suggests: Biobase, knitr, seqinr
23 23 
 LinkingTo: Rcpp
24 24 
 SystemRequirements: GNU make
25 25 
 VignetteBuilder: knitr
... ... 
@@ -27,7 +27,7 @@ LazyLoad: yes
27 27 
 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
28 28 
         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
29 29 
         print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
30 
-        msaClustalOmega.R
30 
+        msaClustalOmega.R msaConvert.R
31 31 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
32 32 
         Sequencing
33 33 
 NeedsCompilation: yes
Browse code

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
Showing1 changed files
DESCRIPTION
History View file @fd1f660
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.1
5 
-Date: 2015-10-13
4 
+Version: 1.3.2
5 
+Date: 2015-12-21
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
... ... 
@@ -21,7 +21,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 21 
         S4Vectors, tools
22 22 
 Suggests: Biobase, knitr
23 23 
 LinkingTo: Rcpp
24 
-SystemRequirements:
24 
+SystemRequirements: GNU make
25 25 
 VignetteBuilder: knitr
26 26 
 LazyLoad: yes
27 27 
 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
... ... 
@@ -31,4 +31,3 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
31 31 
 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
32 32 
         Sequencing
33 33 
 NeedsCompilation: yes
34 
-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
Showing1 changed files
DESCRIPTION
History View file @8d8e4c6
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.3.0
4 
+Version: 1.3.1
5 5 
 Date: 2015-10-13
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 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
Showing1 changed files
DESCRIPTION
History View file @c833e2f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.2.0
4 
+Version: 1.3.0
5 5 
 Date: 2015-10-13
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 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
Showing1 changed files
DESCRIPTION
History View file @8729769
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.1.3
4 
+Version: 1.2.0
5 5 
 Date: 2015-10-13
6 6 
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7 
 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
Showing1 changed files
DESCRIPTION
History View file @6f4b1bb
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.1.2
5 
-Date: 2015-10-10
4 
+Version: 1.1.3
5 
+Date: 2015-10-13
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
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
Showing1 changed files
DESCRIPTION
History View file @12f5100
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.1.1
5 
-Date: 2015-06-12
4 
+Version: 1.1.2
5 
+Date: 2015-10-10
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)
18 18 
 Copyright: See file inst/COPYRIGHT
19 19 
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20 
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
21 
-	 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 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,
32 
+        Sequencing
33 
+NeedsCompilation: yes
34 
+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
Showing1 changed files
DESCRIPTION
History View file @1fa6285
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.1.0
5 
-Date: 2015-04-16
4 
+Version: 1.1.1
5 
+Date: 2015-06-12
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
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
Showing1 changed files
DESCRIPTION
History View file @137a20a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 1.0.0
4 
+Version: 1.1.0
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

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
Showing1 changed files
DESCRIPTION
History View file @f938e2f
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 0.99.7
4 
+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
Showing1 changed files
DESCRIPTION
History View file @b885918
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 0.99.6
5 
-Date: 2015-04-15
4 
+Version: 0.99.7
5 
+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/
17 17 
 License: GPL (>= 2)
18 18 
 Copyright: See file inst/COPYRIGHT
19 19 
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20 
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
21 
-        S4Vectors, tools
20 
+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
21 
+	 tools
22 22 
 Suggests: Biobase, knitr
23 23 
 LinkingTo: Rcpp
24 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,
32 
-        Sequencing
33 
-NeedsCompilation: yes
34 
-Packaged: 2015-04-15 13:16:43 UTC; bodenhof
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
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
Showing1 changed files
DESCRIPTION
History View file @b5f31f0
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 0.99.5
5 
-Date: 2015-04-12
4 
+Version: 0.99.6
5 
+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)
18 18 
 Copyright: See file inst/COPYRIGHT
19 19 
 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)
20 
-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
21 
-	 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,
32 
+        Sequencing
33 
+NeedsCompilation: yes
34 
+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
Showing1 changed files
DESCRIPTION
History View file @3fda9f7
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 0.99.4
5 
-Date: 2015-04-11
4 
+Version: 0.99.5
5 
+Date: 2015-04-12
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
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
Showing1 changed files
DESCRIPTION
History View file @3b2854a
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: msa
2 2 
 Type: Package
3 3 
 Title: Multiple Sequence Alignment
4 
-Version: 0.99.3
5 
-Date: 2015-04-10
4 
+Version: 0.99.4
5 
+Date: 2015-04-11
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
... ... 
@@ -13,21 +13,19 @@ Description: This package provides a unified R/Bioconductor interface to the
13 13 
 	     alignment algorithms are complemented by a function for
14 14 
 	     pretty-printing multiple sequence alignments using the LaTeX
15 15 
 	     package TeXshade.
16 
+URL: http://www.bioinf.jku.at/software/msa/
16 17 
 License: GPL (>= 2)
17 18 
 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),
20 
-        S4Vectors, tools
20 
+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,
21 
+	 tools
21 22 
 Suggests: Biobase, knitr
22 23 
 LinkingTo: Rcpp
23 24 
 SystemRequirements: GNU make
24 25 
 VignetteBuilder: knitr
25 26 
 LazyLoad: yes
26 
-Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R
27 
-        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R
28 
-        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R
29 
-        msaClustalOmega.R
30 
-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
31 
-        Sequencing
32 
-NeedsCompilation: yes
33 
-Packaged: 2015-04-10 22:07:02 UTC; bodenhof
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
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
DESCRIPTION
History View file @d1e1d04
... ... 
@@ -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
21 21 
 Suggests: Biobase, knitr
22 22 
 LinkingTo: Rcpp
23 
+SystemRequirements: GNU make
23 24 
 VignetteBuilder: knitr
24 25 
 LazyLoad: yes
25 26 
 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
Showing1 changed files
DESCRIPTION
History View file @dafeef0
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