1. bsseq
  2. DESCRIPTION
Browse code

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

J Wokaty authored on 01/11/2022 15:07:09
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DESCRIPTION
History View file @ ed8b19c
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.34.0
2 
+Version: 1.35.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 15:07:09
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DESCRIPTION
History View file @ 98239c0
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.33.0
2 
+Version: 1.34.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

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

Nitesh Turaga authored on 26/04/2022 15:11:30
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DESCRIPTION
History View file @ 67c93e4
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.32.0
2 
+Version: 1.33.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 15:11:30
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DESCRIPTION
History View file @ a0c1eac
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.31.1
2 
+Version: 1.32.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Use && instead of & in if condition

&& is always preferred over & in if conditions as it prevents the
right operand of the && operation from being unnecessarily evaluated.
In this particular case this change preventively repairs the
updateObject() method for BSseq objects that will otherwise break
on objects with DataFrame instances in them when DataFrame becomes
a virtual class in the S4Vectors package (will happen soon).

Hervé Pagès authored on 02/11/2021 01:52:48
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DESCRIPTION
History View file @ b9e8130
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.31.0
2 
+Version: 1.31.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

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

Nitesh Turaga authored on 26/10/2021 16:03:49
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DESCRIPTION
History View file @ cad6343
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.30.0
2 
+Version: 1.31.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 16:03:49
Showing 1 changed files
DESCRIPTION
History View file @ 7eb5223
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.29.0
2 
+Version: 1.30.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

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

Nitesh Turaga authored on 19/05/2021 15:53:03
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DESCRIPTION
History View file @ facefd5
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.28.0
2 
+Version: 1.29.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 15:53:03
Showing 1 changed files
DESCRIPTION
History View file @ 57084fa
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.5
2 
+Version: 1.28.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

resync with HDF5Array 1.19.11

Hervé Pagès authored on 26/04/2021 05:55:03
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DESCRIPTION
History View file @ 83564cb
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.4
2 
+Version: 1.27.5
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -34,7 +34,7 @@ Imports:
34 34 
     BSgenome,
35 35 
     Biostrings,
36 36 
     utils,
37 
-    HDF5Array (>= 1.15.19),
37 
+    HDF5Array (>= 1.19.11),
38 38 
     rhdf5
39 39 
 Suggests:
40 40 
     testthat,
Browse code

Update serialized BSseq object BS.chr22

The object was loaded and updated with updateObject(), and then
reserialized. This had the effect of replacing all DataFrame instances
contained in the object with DFrame instances.
Note that starting with S4Vectors 0.24.0, all DataFrame instances
should be replaced with DFrame instances.

Hervé Pagès authored on 06/04/2021 01:37:29
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DESCRIPTION
History View file @ 2408c92
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.3
2 
+Version: 1.27.4
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

more environment fix

kasperdanielhansen authored on 23/03/2021 08:07:57
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DESCRIPTION
History View file @ 1aa857c
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.2
2 
+Version: 1.27.3
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

fixing a test error

Kasper Daniel Hansen authored on 15/03/2021 23:01:13
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DESCRIPTION
History View file @ 72bf72b
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.1
2 
+Version: 1.27.2
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

bugfix (requiring changing all.equal(--) to all.equal(--, check.environment=FALSE)) in combineList()

kasperdanielhansen authored on 09/02/2021 09:35:19
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DESCRIPTION
History View file @ aa2086e
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.27.0
2 
+Version: 1.27.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:46:25
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DESCRIPTION
History View file @ e0089b4
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.26.0
2 
+Version: 1.27.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 14:46:25
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DESCRIPTION
History View file @ fae3229
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.7
2 
+Version: 1.26.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

resync with DelayedArray 0.15.16

Hervé Pagès authored on 09/10/2020 05:05:28
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DESCRIPTION
History View file @ 89ac286
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.6
2 
+Version: 1.25.7
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -28,7 +28,7 @@ Imports:
28 28 
     DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
30 30 
     limma,
31 
-    DelayedArray (>= 0.15.10),
31 
+    DelayedArray (>= 0.15.16),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 34 
     BSgenome,
Browse code

Resync with DelayedArray 0.15.10

Hervé Pagès authored on 27/09/2020 01:24:50
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DESCRIPTION
History View file @ 49fd88d
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.5
2 
+Version: 1.25.6
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -28,7 +28,7 @@ Imports:
28 28 
     DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
30 30 
     limma,
31 
-    DelayedArray (>= 0.9.8),
31 
+    DelayedArray (>= 0.15.10),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 34 
     BSgenome,
Browse code

Version bump

Peter Hickey authored on 29/06/2020 01:21:07
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DESCRIPTION
History View file @ f2728b7
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.4
2 
+Version: 1.25.5
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Bump minimum versions of dependencies

Peter Hickey authored on 29/06/2020 01:21:02
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DESCRIPTION
History View file @ 2eafdd6
... ... 
@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
8 8 
     email = "kasperdanielhansen@gmail.com"),
9 9 
     person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))
10 10 
 Depends:
11 
-    R (>= 3.5),
11 
+    R (>= 4.0),
12 12 
     methods,
13 13 
     BiocGenerics,
14 14 
     GenomicRanges (>= 1.41.5),
... ... 
@@ -34,7 +34,7 @@ Imports:
34 34 
     BSgenome,
35 35 
     Biostrings,
36 36 
     utils,
37 
-    HDF5Array (>= 1.11.9),
37 
+    HDF5Array (>= 1.15.19),
38 38 
     rhdf5
39 39 
 Suggests:
40 40 
     testthat,
Browse code

Resync with latest internal changes to S4Vectors and IRanges

Hervé Pagès authored on 09/06/2020 01:36:15
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DESCRIPTION
History View file @ d336f4c
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.3
2 
+Version: 1.25.4
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -11,10 +11,10 @@ Depends:
11 11 
     R (>= 3.5),
12 12 
     methods,
13 13 
     BiocGenerics,
14 
-    GenomicRanges (>= 1.33.6),
15 
-    SummarizedExperiment (>= 1.17.4)
14 
+    GenomicRanges (>= 1.41.5),
15 
+    SummarizedExperiment (>= 1.19.5)
16 16 
 Imports:
17 
-    IRanges (>= 2.23.5),
17 
+    IRanges (>= 2.23.9),
18 18 
     GenomeInfoDb,
19 19 
     scales,
20 20 
     stats,
... ... 
@@ -23,7 +23,7 @@ Imports:
23 23 
     locfit,
24 24 
     gtools,
25 25 
     data.table (>= 1.11.8),
26 
-    S4Vectors (>= 0.25.14),
26 
+    S4Vectors (>= 0.27.12),
27 27 
     R.utils (>= 2.0.0),
28 28 
     DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
Browse code

Version bump

Peter Hickey authored on 04/06/2020 03:06:29
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DESCRIPTION
History View file @ fd51762
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.2
2 
+Version: 1.25.3
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Version bump

Peter Hickey authored on 01/06/2020 09:36:15
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DESCRIPTION
History View file @ 4a7fb5c
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.1
2 
+Version: 1.25.2
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Repair subsetByOverlaps() on hasGRanges derivatives

Also add overlapsAny() methods and improve granges() method for
hasGRanges derivatives.

Hervé Pagès authored on 20/05/2020 22:23:58
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DESCRIPTION
History View file @ 659aee2
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.25.0
2 
+Version: 1.25.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -14,7 +14,7 @@ Depends:
14 14 
     GenomicRanges (>= 1.33.6),
15 15 
     SummarizedExperiment (>= 1.17.4)
16 16 
 Imports:
17 
-    IRanges (>= 2.21.6),
17 
+    IRanges (>= 2.23.5),
18 18 
     GenomeInfoDb,
19 19 
     scales,
20 20 
     stats,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:30:19
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DESCRIPTION
History View file @ 7a12784
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.24.0
2 
+Version: 1.25.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 18:30:19
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DESCRIPTION
History View file @ 070662a
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.23.4
2 
+Version: 1.24.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Woops, skipped the wrong test with previous commit

Peter Hickey authored on 24/04/2020 04:34:15
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DESCRIPTION
History View file @ 674e7a4
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.23.3
2 
+Version: 1.23.4
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Skip Windows-specific failing test

PeteHaitch authored on 24/04/2020 03:23:25
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DESCRIPTION
History View file @ 841ce47
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.23.2
2 
+Version: 1.23.3
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -81,4 +81,4 @@ biocViews: DNAMethylation
81 81 
 SystemRequirements: C++11
82 82 
 LinkingTo: Rcpp, beachmat
83 83 
 NeedsCompilation: yes
84 
-RoxygenNote: 6.1.0
84 
+RoxygenNote: 7.1.0
Browse code

bumping version

kasperdanielhansen authored on 06/04/2020 16:21:59
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DESCRIPTION
History View file @ 43961f7
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.23.1
2 
+Version: 1.23.2
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -76,8 +76,6 @@ Collate:
76 76 
 License: Artistic-2.0
77 77 
 VignetteBuilder: knitr
78 78 
 URL: https://github.com/kasperdanielhansen/bsseq
79 
-LazyData: yes
80 
-LazyDataCompression: xz
81 79 
 BugReports: https://github.com/kasperdanielhansen/bsseq/issues
82 80 
 biocViews: DNAMethylation
83 81 
 SystemRequirements: C++11
Browse code

parallelSlotNames() was renamed vertical_slot_names() in S4Vectors 0.25.14

Hervé Pagès authored on 24/03/2020 06:15:16
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DESCRIPTION
History View file @ 59617ab
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.23.0
2 
+Version: 1.23.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -11,10 +11,10 @@ Depends:
11 11 
     R (>= 3.5),
12 12 
     methods,
13 13 
     BiocGenerics,
14 
-    GenomicRanges (>= 1.29.14),
15 
-    SummarizedExperiment (>= 1.9.18)
14 
+    GenomicRanges (>= 1.33.6),
15 
+    SummarizedExperiment (>= 1.17.4)
16 16 
 Imports:
17 
-    IRanges (>= 2.11.16),
17 
+    IRanges (>= 2.21.6),
18 18 
     GenomeInfoDb,
19 19 
     scales,
20 20 
     stats,
... ... 
@@ -23,7 +23,7 @@ Imports:
23 23 
     locfit,
24 24 
     gtools,
25 25 
     data.table (>= 1.11.8),
26 
-    S4Vectors (>= 0.23.11),
26 
+    S4Vectors (>= 0.25.14),
27 27 
     R.utils (>= 2.0.0),
28 28 
     DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:36:17
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DESCRIPTION
History View file @ b2e70be
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.22.0
2 
+Version: 1.23.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 17:08:33
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DESCRIPTION
History View file @ d4f7301
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.21.1
2 
+Version: 1.22.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Use S4Vectors:::normarg_names() instead of S4Vectors:::normalize_names_replacement_value()

Hervé Pagès authored on 12/06/2019 15:24:37
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DESCRIPTION
History View file @ 8691f7a
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.21.0
2 
+Version: 1.21.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -23,7 +23,7 @@ Imports:
23 23 
     locfit,
24 24 
     gtools,
25 25 
     data.table (>= 1.11.8),
26 
-    S4Vectors,
26 
+    S4Vectors (>= 0.23.11),
27 27 
     R.utils (>= 2.0.0),
28 28 
     DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:11:13
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DESCRIPTION
History View file @ 4f0bfd9
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.20.0
2 
+Version: 1.21.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
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 15:53:37
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DESCRIPTION
History View file @ 07e398b
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.5
2 
+Version: 1.20.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Version bump

Peter Hickey authored on 23/04/2019 02:34:09
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DESCRIPTION
History View file @ 66219bf
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.4
2 
+Version: 1.19.5
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Version bump

Peter Hickey authored on 23/04/2019 01:24:19
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DESCRIPTION
History View file @ 4d7d7dd
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.3
2 
+Version: 1.19.4
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Merge remote-tracking branch 'upstream/master'

Peter Hickey authored on 23/04/2019 01:04:08
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Browse code

Transition to beachmat version 2

Peter Hickey authored on 23/04/2019 01:03:45
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DESCRIPTION
History View file @ 9135fdb
... ... 
@@ -81,6 +81,6 @@ LazyDataCompression: xz
81 81 
 BugReports: https://github.com/kasperdanielhansen/bsseq/issues
82 82 
 biocViews: DNAMethylation
83 83 
 SystemRequirements: C++11
84 
-LinkingTo: Rcpp, Rhdf5lib, beachmat
84 
+LinkingTo: Rcpp, beachmat
85 85 
 NeedsCompilation: yes
86 86 
 RoxygenNote: 6.1.0
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The rowsum() and colsum() generics are now defined in DelayedArray

Hervé Pagès authored on 31/01/2019 22:38:18
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DESCRIPTION
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.2
2 
+Version: 1.19.3
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -25,10 +25,10 @@ Imports:
25 25 
     data.table (>= 1.11.8),
26 26 
     S4Vectors,
27 27 
     R.utils (>= 2.0.0),
28 
-    DelayedMatrixStats (>= 1.3.6),
28 
+    DelayedMatrixStats (>= 1.5.2),
29 29 
     permute,
30 30 
     limma,
31 
-    DelayedArray (>= 0.7.15),
31 
+    DelayedArray (>= 0.9.8),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 34 
     BSgenome,
Browse code

Bump minimum beachmat version on advice of Aaron

Peter Hickey authored on 15/01/2019 05:58:24
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DESCRIPTION
History View file @ c93310e
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.1
2 
+Version: 1.19.2
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -46,7 +46,7 @@ Suggests:
46 46 
     doParallel,
47 47 
     rtracklayer,
48 48 
     BSgenome.Hsapiens.UCSC.hg38,
49 
-    beachmat,
49 
+    beachmat (>= 1.5.2),
50 50 
     BatchJobs
51 51 
 Collate:
52 52 
     utils.R
Browse code

Merge remote-tracking branch 'upstream/master'

Peter Hickey authored on 15/01/2019 05:55:22
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resync with latest changes to HDF5Array package

Hervé Pagès authored on 13/12/2018 20:18:12
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DESCRIPTION
History View file @ d654f9b
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.19.0
2 
+Version: 1.19.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -34,7 +34,7 @@ Imports:
34 34 
     BSgenome,
35 35 
     Biostrings,
36 36 
     utils,
37 
-    HDF5Array,
37 
+    HDF5Array (>= 1.11.9),
38 38 
     rhdf5
39 39 
 Suggests:
40 40 
     testthat,
Browse code

Merge remote-tracking branch 'bioc/master'

Peter Hickey authored on 30/10/2018 20:40:12
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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 15:54:30
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DESCRIPTION
History View file @ 5ee292a
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.18.0
2 
+Version: 1.19.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:49
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DESCRIPTION
History View file @ aa2e1a9
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.8
2 
+Version: 1.18.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

added BatchJobs to Suggests

Kasper Daniel Hansen authored on 30/10/2018 02:51:14
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DESCRIPTION
History View file @ fb5b6ff
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.8
2 
+Version: 1.17.9
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -46,7 +46,8 @@ Suggests:
46 46 
     doParallel,
47 47 
     rtracklayer,
48 48 
     BSgenome.Hsapiens.UCSC.hg38,
49 
-    beachmat
49 
+    beachmat,
50 
+    BatchJobs
50 51 
 Collate:
51 52 
     utils.R
52 53 
     hasGRanges.R
Browse code

fixing warnings

Kasper Daniel Hansen authored on 30/10/2018 00:57:46
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DESCRIPTION
History View file @ c4abf2a
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.7
2 
+Version: 1.17.8
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -35,7 +35,7 @@ Imports:
35 35 
     Biostrings,
36 36 
     utils,
37 37 
     HDF5Array,
38 
-    beachmat
38 
+    rhdf5
39 39 
 Suggests:
40 40 
     testthat,
41 41 
     bsseqData,
... ... 
@@ -45,7 +45,8 @@ Suggests:
45 45 
     Matrix,
46 46 
     doParallel,
47 47 
     rtracklayer,
48 
-    BSgenome.Hsapiens.UCSC.hg38
48 
+    BSgenome.Hsapiens.UCSC.hg38,
49 
+    beachmat
49 50 
 Collate:
50 51 
     utils.R
51 52 
     hasGRanges.R
Browse code

Small tweak to pass tests on Windows

Peter Hickey authored on 24/10/2018 20:21:55
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DESCRIPTION
History View file @ 6ec91bb
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.6
2 
+Version: 1.17.7
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Close issue #74

- Small tweak to default @trans function in BSseq() and combine().
- Add unit test

Peter Hickey authored on 15/10/2018 05:04:53
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DESCRIPTION
History View file @ e0a4750
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.5
2 
+Version: 1.17.6
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Tighten up .isHDF5BackendBSseqUpdatable()

Peter Hickey authored on 14/10/2018 22:45:48
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DESCRIPTION
History View file @ ff02bcf
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.4
2 
+Version: 1.17.5
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Improvements to read.bismark()

- Now uses fread()'s native support of compressed files
- Supports fread()'s nThreads argument

Peter Hickey authored on 07/10/2018 03:37:11
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DESCRIPTION
History View file @ 3e0adc4
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.3
2 
+Version: 1.17.4
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -22,7 +22,7 @@ Imports:
22 22 
     Biobase,
23 23 
     locfit,
24 24 
     gtools,
25 
-    data.table,
25 
+    data.table (>= 1.11.8),
26 26 
     S4Vectors,
27 27 
     R.utils (>= 2.0.0),
28 28 
     DelayedMatrixStats (>= 1.3.6),
Browse code

Version bump

Peter Hickey authored on 17/09/2018 11:47:23
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DESCRIPTION
History View file @ fb28afa
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.2
2 
+Version: 1.17.3
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Merge refactor branch into master

Peter Hickey authored on 17/09/2018 11:17:52
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Update DESCRIPTION

Peter Hickey authored on 17/09/2018 11:08:03
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DESCRIPTION
History View file @ b8c41a9
... ... 
@@ -43,7 +43,9 @@ Suggests:
43 43 
     rmarkdown,
44 44 
     knitr,
45 45 
     Matrix,
46 
-    doParallel
46 
+    doParallel,
47 
+    rtracklayer,
48 
+    BSgenome.Hsapiens.UCSC.hg38
47 49 
 Collate:
48 50 
     utils.R
49 51 
     hasGRanges.R
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Rename findCytosines as findLoci and document

Peter Hickey authored on 17/09/2018 11:02:52
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DESCRIPTION
History View file @ 57cc26c
... ... 
@@ -68,7 +68,7 @@ Collate:
68 68 
     collapseBSseq.R
69 69 
     FWIRanges-class.R
70 70 
     FWGRanges-class.R
71 
-    findCytosines.R
71 
+    findLoci.R
72 72 
 License: Artistic-2.0
73 73 
 VignetteBuilder: knitr
74 74 
 URL: https://github.com/kasperdanielhansen/bsseq
Browse code

remove useDevel mention

LiNk-NY authored on 07/09/2018 18:03:11
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DESCRIPTION
History View file @ 3345828
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.1
2 
+Version: 1.17.2
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:45:52
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DESCRIPTION
History View file @ e04391b
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@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.0
2 
+Version: 1.17.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Regenerate NAMESPACE

Peter Hickey authored on 21/08/2018 03:47:21
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DESCRIPTION
History View file @ 296c907
... ... 
@@ -25,7 +25,7 @@ Imports:
25 25 
     data.table,
26 26 
     S4Vectors,
27 27 
     R.utils (>= 2.0.0),
28 
-    DelayedMatrixStats (>= 1.3.4),
28 
+    DelayedMatrixStats (>= 1.3.6),
29 29 
     permute,
30 30 
     limma,
31 31 
     DelayedArray (>= 0.7.15),
... ... 
@@ -79,3 +79,4 @@ biocViews: DNAMethylation
79 79 
 SystemRequirements: C++11
80 80 
 LinkingTo: Rcpp, Rhdf5lib, beachmat
81 81 
 NeedsCompilation: yes
82 
+RoxygenNote: 6.1.0
Browse code

Remove readr dependency

Found that `readr::read_tsv()` was painfully slow for large gzipped Bismark files (e.g., mCH loci).
Instead, now use:
- If file is gzipped and `gzip` is available at the command line, then use `data.table::fread()`.
- If file is gzipped and `gzip` is **not** available at the command line, then use `utils::read.table()`.
- If file is not gzipped (plain text) use `data.table::fread()`.

There are still some kinks to work out and tradeoffs to explore.

Peter Hickey authored on 04/07/2018 02:41:15
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DESCRIPTION
History View file @ 868a6f2
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@@ -31,7 +31,6 @@ Imports:
31 31 
     DelayedArray (>= 0.7.15),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 
-    readr,
35 34 
     BSgenome,
36 35 
     Biostrings,
37 36 
     utils,
Browse code

colGrid() and rowGrid() moved to DelayedMatrixStats as of v1.3.4

Peter Hickey authored on 29/06/2018 14:30:47
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DESCRIPTION
History View file @ 627e033
... ... 
@@ -25,7 +25,7 @@ Imports:
25 25 
     data.table,
26 26 
     S4Vectors,
27 27 
     R.utils (>= 2.0.0),
28 
-    DelayedMatrixStats (>= 1.3.1),
28 
+    DelayedMatrixStats (>= 1.3.4),
29 29 
     permute,
30 30 
     limma,
31 31 
     DelayedArray (>= 0.7.15),
Browse code

write_block_to_sink() was replaced with write_block() in DelayedArray 0.7.15

Peter Hickey authored on 28/06/2018 16:03:26
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DESCRIPTION
History View file @ fc52a8d
... ... 
@@ -28,7 +28,7 @@ Imports:
28 28 
     DelayedMatrixStats (>= 1.3.1),
29 29 
     permute,
30 30 
     limma,
31 
-    DelayedArray (>= 0.7.6),
31 
+    DelayedArray (>= 0.7.15),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 34 
     readr,
Browse code

Tweak DESCRIPTION and NAMESPACE

- HDF5Array and beachmat in Imports rather than Suggests

Peter Hickey authored on 14/06/2018 20:43:20
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DESCRIPTION
History View file @ 61dabc4
... ... 
@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
8 8 
     email = "kasperdanielhansen@gmail.com"),
9 9 
     person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))
10 10 
 Depends:
11 
-    R (>= 3.3),
11 
+    R (>= 3.5),
12 12 
     methods,
13 13 
     BiocGenerics,
14 14 
     GenomicRanges (>= 1.29.14),
... ... 
@@ -25,25 +25,25 @@ Imports:
25 25 
     data.table,
26 26 
     S4Vectors,
27 27 
     R.utils (>= 2.0.0),
28 
-    DelayedMatrixStats (>= 1.1.12),
28 
+    DelayedMatrixStats (>= 1.3.1),
29 29 
     permute,
30 30 
     limma,
31 
-    DelayedArray (>= 0.5.34),
31 
+    DelayedArray (>= 0.7.6),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 34 
     readr,
35 35 
     BSgenome,
36 36 
     Biostrings,
37 
-    utils
37 
+    utils,
38 
+    HDF5Array,
39 
+    beachmat
38 40 
 Suggests:
39 41 
     testthat,
40 42 
     bsseqData,
41 43 
     BiocStyle,
42 44 
     rmarkdown,
43 45 
     knitr,
44 
-    beachmat,
45 46 
     Matrix,
46 
-    HDF5Array,
47 47 
     doParallel
48 48 
 Collate:
49 49 
     utils.R
Browse code

Quieten R CMD check

Peter Hickey authored on 14/06/2018 19:39:15
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DESCRIPTION
History View file @ 1823d04
... ... 
@@ -33,7 +33,8 @@ Imports:
33 33 
     BiocParallel,
34 34 
     readr,
35 35 
     BSgenome,
36 
-    Biostrings
36 
+    Biostrings,
37 
+    utils
37 38 
 Suggests:
38 39 
     testthat,
39 40 
     bsseqData,
Browse code

Improve `findCytosines()`

- Make generic with methods for _BSgenome_ and _DNAStringSet_ (e.g., a FASTA file imported with `rtracklayer::import()`)

Peter Hickey authored on 13/06/2018 14:17:09
Showing 1 changed files
DESCRIPTION
History View file @ 5aa8515
... ... 
@@ -31,7 +31,9 @@ Imports:
31 31 
     DelayedArray (>= 0.5.34),
32 32 
     Rcpp,
33 33 
     BiocParallel,
34 
-    readr
34 
+    readr,
35 
+    BSgenome,
36 
+    Biostrings
35 37 
 Suggests:
36 38 
     testthat,
37 39 
     bsseqData,
Browse code

Formatting

Peter Hickey authored on 12/06/2018 19:56:44
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DESCRIPTION
History View file @ 0155772
... ... 
@@ -41,8 +41,7 @@ Suggests:
41 41 
     beachmat,
42 42 
     Matrix,
43 43 
     HDF5Array,
44 
-    doParallel,
45 
-    testthat
44 
+    doParallel
46 45 
 Collate:
47 46 
     utils.R
48 47 
     hasGRanges.R
Browse code

Update 'Collate' in DESCRIPTION

Peter Hickey authored on 10/06/2018 14:37:16
Showing 1 changed files
DESCRIPTION
History View file @ b2034fc
... ... 
@@ -67,6 +67,7 @@ Collate:
67 67 
     collapseBSseq.R
68 68 
     FWIRanges-class.R
69 69 
     FWGRanges-class.R
70 
+    findCytosines.R
70 71 
 License: Artistic-2.0
71 72 
 VignetteBuilder: knitr
72 73 
 URL: https://github.com/kasperdanielhansen/bsseq
Browse code

Remove loci_dt and bsseq_dt

These are superseded by FWGRanges, which implement the correct strand-matching behaviour that is surprisingly difficult to achieve otherwise.
Long term, I'd like to support FWGRanges as the rowRanges in a BSseq object.

Peter Hickey authored on 05/06/2018 20:28:32
Showing 1 changed files
DESCRIPTION
History View file @ 65f8a16
... ... 
@@ -65,8 +65,6 @@ Collate:
65 65 
     hdf5_utils.R
66 66 
     DelayedArray_utils.R
67 67 
     collapseBSseq.R
68 
-    BSseqDT.R
69 
-    lociDT.R
70 68 
     FWIRanges-class.R
71 69 
     FWGRanges-class.R
72 70 
 License: Artistic-2.0
Browse code

Add FWIRanges and FWGRanges, use in read.bismark()

Peter Hickey authored on 05/06/2018 18:36:20
Showing 1 changed files
DESCRIPTION
History View file @ 1aef3bd
... ... 
@@ -67,6 +67,8 @@ Collate:
67 67 
     collapseBSseq.R
68 68 
     BSseqDT.R
69 69 
     lociDT.R
70 
+    FWIRanges-class.R
71 
+    FWGRanges-class.R
70 72 
 License: Artistic-2.0
71 73 
 VignetteBuilder: knitr
72 74 
 URL: https://github.com/kasperdanielhansen/bsseq
Browse code

Split out R/read.bismark.R

Slightly formalise intermediate objects lociDT and BSseqDT.
Split these out into their own files.
Refine construction of 'gr' from Bismark files.

Peter Hickey authored on 31/05/2018 19:23:24
Showing 1 changed files
DESCRIPTION
History View file @ 3c2dce4
... ... 
@@ -65,6 +65,8 @@ Collate:
65 65 
     hdf5_utils.R
66 66 
     DelayedArray_utils.R
67 67 
     collapseBSseq.R
68 
+    BSseqDT.R
69 
+    lociDT.R
68 70 
 License: Artistic-2.0
69 71 
 VignetteBuilder: knitr
70 72 
 URL: https://github.com/kasperdanielhansen/bsseq
Browse code

Merge branch 'refactor-read.bismark' into refactor

Peter Hickey authored on 29/05/2018 12:56:37
Showing 0 changed files
Browse code

Work in progress: refactoring bsseq

- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
- Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
- Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
- Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
- Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
- Detailed and extensive job logging facilities.
- Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring.

Peter Hickey authored on 28/05/2018 23:42:18
Showing 1 changed files
DESCRIPTION
History View file @ 866ab76
... ... 
@@ -12,8 +12,7 @@ Depends:
12 12 
     methods,
13 13 
     BiocGenerics,
14 14 
     GenomicRanges (>= 1.29.14),
15 
-    SummarizedExperiment (>= 1.9.18),
16 
-    parallel
15 
+    SummarizedExperiment (>= 1.9.18)
17 16 
 Imports:
18 17 
     IRanges (>= 2.11.16),
19 18 
     GenomeInfoDb,
... ... 
@@ -30,17 +29,24 @@ Imports:
30 29 
     permute,
31 30 
     limma,
32 31 
     DelayedArray (>= 0.5.34),
33 
-    HDF5Array
32 
+    Rcpp,
33 
+    BiocParallel,
34 
+    readr
34 35 
 Suggests:
35 
-    RUnit,
36 
+    testthat,
36 37 
     bsseqData,
37 38 
     BiocStyle,
38 39 
     rmarkdown,
39 40 
     knitr,
41 
+    beachmat,
42 
+    Matrix,
43 
+    HDF5Array,
44 
+    doParallel,
45 
+    testthat
40 46 
 Collate:
41 47 
     utils.R
42 48 
     hasGRanges.R
43 
-    BSseq_class.R
49 
+    BSseq-class.R
44 50 
     BSseqTstat_class.R
45 51 
     BSseq_utils.R
46 52 
     combine.R
... ... 
@@ -57,8 +63,8 @@ Collate:
57 63 
     BSseqStat_class.R
58 64 
     getStats.R
59 65 
     hdf5_utils.R
60 
-    combine_utils.R
61 66 
     DelayedArray_utils.R
67 
+    collapseBSseq.R
62 68 
 License: Artistic-2.0
63 69 
 VignetteBuilder: knitr
64 70 
 URL: https://github.com/kasperdanielhansen/bsseq
... ... 
@@ -66,3 +72,6 @@ LazyData: yes
66 72 
 LazyDataCompression: xz
67 73 
 BugReports: https://github.com/kasperdanielhansen/bsseq/issues
68 74 
 biocViews: DNAMethylation
75 
+SystemRequirements: C++11
76 
+LinkingTo: Rcpp, Rhdf5lib, beachmat
77 
+NeedsCompilation: yes
Browse code

Initial re-write of read.bismark()

Peter Hickey authored on 04/05/2018 18:31:03
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DESCRIPTION
History View file @ 3b038a9
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.17.0
2 
+Version: 1.17.1
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -30,7 +30,8 @@ Imports:
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     permute,
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     limma,
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     DelayedArray (>= 0.5.34),
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-    HDF5Array
33 
+    HDF5Array,
34 
+    readr
34 35 
 Suggests:
35 36 
     RUnit,
36 37 
     bsseqData,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:38
Showing 1 changed files
DESCRIPTION
History View file @ 2cfeed6
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.16.0
2 
+Version: 1.17.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:25
Showing 1 changed files
DESCRIPTION
History View file @ fab81bd
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.15.6
2 
+Version: 1.16.0
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Run updateObject() on included dataset

Peter Hickey authored on 27/04/2018 15:38:40
Showing 1 changed files
DESCRIPTION
History View file @ 36ecd4a
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.15.5
2 
+Version: 1.15.6
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
Browse code

Small tweak to "updateObject" method for BSseq objects

The method now calls the "updateObject" method for RangedSummarizedExperiment
objects (via callNextMethod()) early rather than late. The earlier the better
because very few things actually work in general on an outdated BSseq object
before that call is made. In particular the endoapply() loop that now follows
the call to callNextMethod() was failing if the BSseq object had "old"
DelayedArray objects in its assays.

Hervé Pagès authored on 27/04/2018 05:47:48
Showing 1 changed files
DESCRIPTION
History View file @ c70c9e3
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: bsseq
2 
-Version: 1.15.4
2 
+Version: 1.15.5
3 3 
 Encoding: UTF-8
4 4 
 Title: Analyze, manage and store bisulfite sequencing data
5 5 
 Description: A collection of tools for analyzing and visualizing bisulfite
... ... 
@@ -12,7 +12,7 @@ Depends:
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     methods,
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     BiocGenerics,
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     GenomicRanges (>= 1.29.14),
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-    SummarizedExperiment (>= 1.7.8),
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+    SummarizedExperiment (>= 1.9.18),
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     parallel
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 Imports:
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     IRanges (>= 2.11.16),
... ... 
@@ -29,7 +29,7 @@ Imports:
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     DelayedMatrixStats (>= 1.1.12),
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     permute,
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     limma,
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-    DelayedArray (>= 0.5.27),
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+    DelayedArray (>= 0.5.34),
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     HDF5Array
34 34 
 Suggests:
35 35 
     RUnit,
Browse code

Another NAMESPACE/DESCRIPTION tweak

Peter Hickey authored on 24/04/2018 18:55:36
Showing 1 changed files
DESCRIPTION
History View file @ 6995930
... ... 
@@ -29,14 +29,14 @@ Imports:
29 29 
     DelayedMatrixStats (>= 1.1.12),
30 30 
     permute,
31 31 
     limma,
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-    DelayedArray (>= 0.5.27)
32 
+    DelayedArray (>= 0.5.27),