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

J Wokaty authored on 01/11/2022 15:07:09
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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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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
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:30
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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
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:11:30
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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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@@ -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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@@ -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
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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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@@ -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
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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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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... ...
@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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@@ -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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... ...
@@ -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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... ...
@@ -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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... ...
@@ -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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... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing0 changed files
Browse code

Transition to beachmat version 2

Peter Hickey authored on 23/04/2019 01:03:45
Showing1 changed files
... ...
@@ -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
Browse code

The rowsum() and colsum() generics are now defined in DelayedArray

Hervé Pagès authored on 31/01/2019 22:38:18
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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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@@ -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
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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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@@ -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,
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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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@@ -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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@@ -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
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added BatchJobs to Suggests

Kasper Daniel Hansen authored on 30/10/2018 02:51:14
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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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@@ -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
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Small tweak to pass tests on Windows

Peter Hickey authored on 24/10/2018 20:21:55
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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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@@ -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
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Tighten up .isHDF5BackendBSseqUpdatable()

Peter Hickey authored on 14/10/2018 22:45:48
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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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@@ -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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@@ -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
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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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... ...
@@ -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
Browse code

Rename findCytosines as findLoci and document

Peter Hickey authored on 17/09/2018 11:02:52
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@@ -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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@@ -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
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:45:52
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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
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Regenerate NAMESPACE

Peter Hickey authored on 21/08/2018 03:47:21
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@@ -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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@@ -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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... ...
@@ -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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... ...
@@ -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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... ...
@@ -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,
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-    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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... ...
@@ -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
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... ...
@@ -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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@@ -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
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... ...
@@ -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
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... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
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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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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:
30 30
     permute,
31 31
     limma,
32 32
     DelayedArray (>= 0.5.34),
33
-    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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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:
12 12
     methods,
13 13
     BiocGenerics,
14 14
     GenomicRanges (>= 1.29.14),
15
-    SummarizedExperiment (>= 1.7.8),
15
+    SummarizedExperiment (>= 1.9.18),
16 16
     parallel
17 17
 Imports:
18 18
     IRanges (>= 2.11.16),
... ...
@@ -29,7 +29,7 @@ Imports:
29 29
     DelayedMatrixStats (>= 1.1.12),
30 30
     permute,
31 31
     limma,
32
-    DelayedArray (>= 0.5.27),
32
+    DelayedArray (>= 0.5.34),
33 33
     HDF5Array
34 34
 Suggests:
35 35
     RUnit,
Browse code

Another NAMESPACE/DESCRIPTION tweak

Peter Hickey authored on 24/04/2018 18:55:36
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@@ -29,14 +29,14 @@ Imports:
29 29
     DelayedMatrixStats (>= 1.1.12),
30 30
     permute,
31 31
     limma,
32
-    DelayedArray (>= 0.5.27)
32
+    DelayedArray (>= 0.5.27),
33
+    HDF5Array
33 34
 Suggests:
34 35
     RUnit,
35 36
     bsseqData,
36 37
     BiocStyle,
37 38
     rmarkdown,
38 39
     knitr,
39
-    HDF5Array
40 40
 Collate:
41 41
     utils.R
42 42
     hasGRanges.R
Browse code

Tweak DESCRIPTION

Peter Hickey authored on 24/04/2018 18:35:01
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@@ -29,14 +29,14 @@ Imports:
29 29
     DelayedMatrixStats (>= 1.1.12),
30 30
     permute,
31 31
     limma,
32
-    DelayedArray (>= 0.5.27),
33
-    HDF5Array
32
+    DelayedArray (>= 0.5.27)
34 33
 Suggests:
35 34
     RUnit,
36 35
     bsseqData,
37 36
     BiocStyle,
38 37
     rmarkdown,
39 38
     knitr,
39
+    HDF5Array
40 40
 Collate:
41 41
     utils.R
42 42
     hasGRanges.R
Browse code

Replace base/matrixStats/DelayedArray by DelayedMatrixStats

This is a straight find and replace of (col|row)(Sums|Means) with DelayedMatrixStats equivalents. Immediately, this is to work around an apparent bug in DelayedArray,rowSums-method (https://github.com/Bioconductor/DelayedArray/issues/16) but long term want to be using the optimised implementations in DelayedMatrixStat (e.g., using `cols` and `rows` args).

Peter Hickey authored on 24/04/2018 17:53:48
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1 1
 Package: bsseq
2
-Version: 1.15.3
2
+Version: 1.15.4
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
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@@ -26,7 +26,7 @@ Imports:
26 26
     data.table,
27 27
     S4Vectors,
28 28
     R.utils (>= 2.0.0),
29
-    matrixStats (>= 0.50.0),
29
+    DelayedMatrixStats (>= 1.1.12),
30 30
     permute,
31 31
     limma,
32 32
     DelayedArray (>= 0.5.27),
Browse code

Bump version

Peter Hickey authored on 17/04/2018 16:30:05
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1 1
 Package: bsseq
2
-Version: 1.15.2
2
+Version: 1.15.3
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

Update BS.chr.22 data

Update BS.chr22 assays (to use new DelayedArray internal representation) and rowRanges, and re-serialize it.

Peter Hickey authored on 08/04/2018 19:57:58
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.15.1
2
+Version: 1.15.2
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

Merge remote-tracking branch 'bioc/master'

Peter Hickey authored on 08/04/2018 19:10:33
Showing0 changed files
Browse code

Re-sync with DelayedArray

Peter Hickey authored on 08/04/2018 18:47:50
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.9
2
+Version: 1.13.10
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
... ...
@@ -29,7 +29,7 @@ Imports:
29 29
     matrixStats (>= 0.50.0),
30 30
     permute,
31 31
     limma,
32
-    DelayedArray,
32
+    DelayedArray (>= 0.5.27),
33 33
     HDF5Array
34 34
 Suggests:
35 35
     RUnit,
Browse code

Update BS.chr22 assays to use new DelayedArray internal representation (which changed in DelayedArray 0.5.11), and re-serialize it.

Hervé Pagès authored on 11/01/2018 07:51:59
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.15.0
2
+Version: 1.15.1
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
... ...
@@ -29,7 +29,7 @@ Imports:
29 29
     matrixStats (>= 0.50.0),
30 30
     permute,
31 31
     limma,
32
-    DelayedArray,
32
+    DelayedArray (>= 0.5.16),
33 33
     HDF5Array
34 34
 Suggests:
35 35
     RUnit,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:20
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.14.0
2
+Version: 1.15.0
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_6 branch

Hervé Pagès authored on 30/10/2017 16:39:45
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.9
2
+Version: 1.14.0
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

Kasper Daniel Hansen authored on 17/10/2017 02:21:38
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.8
2
+Version: 1.13.9
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
Browse code

moved vignettes into Rmd

Kasper Daniel Hansen authored on 17/10/2017 02:21:02
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... ...
@@ -35,6 +35,7 @@ Suggests:
35 35
     RUnit,
36 36
     bsseqData,
37 37
     BiocStyle,
38
+    rmarkdown,
38 39
     knitr,
39 40
 Collate:
40 41
     utils.R
Browse code

Version bump to test Bioc git

Kasper Daniel Hansen authored on 16/10/2017 18:54:12
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.7
2
+Version: 1.13.8
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
Browse code

- Use new 'maxgap' and 'minoverlap' defaults in "findOverlaps" method for hasGRanges objects. - Remove "subsetByOverlaps" methods for hasGRanges objects. They are redundant with the default "subsetByOverlaps" method defined in the IRanges package. The default method works out-of-the-box on any object that supports findOverlaps() and linear subsetting ([), which is the case for hasGRanges objects.

Hervé Pagès authored on 18/09/2017 15:02:27
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.6
2
+Version: 1.13.7
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
... ...
@@ -11,11 +11,11 @@ Depends:
11 11
     R (>= 3.3),
12 12
     methods,
13 13
     BiocGenerics,
14
-    GenomicRanges (>= 1.23.7),
15
-    SummarizedExperiment (>= 0.1.1),
14
+    GenomicRanges (>= 1.29.14),
15
+    SummarizedExperiment (>= 1.7.8),
16 16
     parallel
17 17
 Imports:
18
-    IRanges (>= 2.5.17),
18
+    IRanges (>= 2.11.16),
19 19
     GenomeInfoDb,
20 20
     scales,
21 21
     stats,
Browse code

version 1.13.6 from GitHub. Numerous bugfixes, including one critical

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@131465 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 21/07/2017 12:17:16
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.3
2
+Version: 1.13.6
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

Bump version of packages that define RangedSummarizedExperiment derivatives (direct or indirect). Will help get rid of those class definitions that are cached on the user machines and became stale after GenomicRangesORGRangesList was renamed GenomicRanges_OR_GRangesList (on June 18, commit 130486).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@130713 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 27/06/2017 17:05:27
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.2
2
+Version: 1.13.3
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

resync with latest changes to DelayedArray

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129436 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 06/05/2017 06:23:15
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.1
2
+Version: 1.13.2
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

use pruning.mode="coarse" instead of force=TRUE when calling seqlevels() setter

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@129282 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 29/04/2017 20:29:37
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.13.0
2
+Version: 1.13.1
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 versions to odd y after creation of 3_5 branch

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

Herve Pages authored on 24/04/2017 19:50:57
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.12.0
2
+Version: 1.13.0
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 3_5 branch

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

Herve Pages authored on 24/04/2017 19:25:24
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... ...
@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.11.2
2
+Version: 1.12.0
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

bsseq 1.11.2 from GitHub. This adds the usage of DelayedArray and HDF5 backend

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@128540 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 11/04/2017 13:48:47
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... ...
@@ -1,19 +1,19 @@
1 1
 Package: bsseq
2
-Version: 1.11.0
2
+Version: 1.11.2
3
+Encoding: UTF-8
3 4
 Title: Analyze, manage and store bisulfite sequencing data
4 5
 Description: A collection of tools for analyzing and visualizing bisulfite
5 6
     sequencing data.
6 7
 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
7 8
     email = "kasperdanielhansen@gmail.com"),
8
-    person("Peter", "Hickey", role = "ctb", email = "peter.hickey@gmail.com"))
9
+    person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))
9 10
 Depends:
10 11
     R (>= 3.3),
11 12
     methods,
12 13
     BiocGenerics,
13 14
     GenomicRanges (>= 1.23.7),
14 15
     SummarizedExperiment (>= 0.1.1),
15
-    parallel,
16
-    limma
16
+    parallel
17 17
 Imports:
18 18
     IRanges (>= 2.5.17),
19 19
     GenomeInfoDb,
... ...
@@ -27,19 +27,22 @@ Imports:
27 27
     S4Vectors,
28 28
     R.utils (>= 2.0.0),
29 29
     matrixStats (>= 0.50.0),
30
-    permute
30
+    permute,
31
+    limma,
32
+    DelayedArray,
33
+    HDF5Array
31 34
 Suggests:
32 35
     RUnit,
33 36
     bsseqData,
34 37
     BiocStyle,
35
-    knitr
38
+    knitr,
36 39
 Collate:
40
+    utils.R
37 41
     hasGRanges.R
38 42
     BSseq_class.R
39 43
     BSseqTstat_class.R
40 44
     BSseq_utils.R
41 45
     combine.R
42
-    utils.R
43 46
     read.bsmooth.R
44 47
     read.bismark.R
45 48
     BSmooth.R
... ...
@@ -52,6 +55,9 @@ Collate:
52 55
     BSmooth.fstat.R
53 56
     BSseqStat_class.R
54 57
     getStats.R
58
+    hdf5_utils.R
59
+    combine_utils.R
60
+    DelayedArray_utils.R
55 61
 License: Artistic-2.0
56 62
 VignetteBuilder: knitr
57 63
 URL: https://github.com/kasperdanielhansen/bsseq
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/bsseq@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.10.0
2
+Version: 1.11.0
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
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/bsseq@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.9.2
2
+Version: 1.10.0
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
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/bsseq@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 15/05/2016 20:14:22
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1 1
 Package: bsseq
2
-Version: 1.9.1
2
+Version: 1.9.2
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
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/bsseq@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/05/2016 23:05:31
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1 1
 Package: bsseq
2
-Version: 1.9.0
2
+Version: 1.9.1
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
Browse code

bump version after creating 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:30:44
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.8.0
2
+Version: 1.9.0
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
Browse code

Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.7.13
2
+Version: 1.8.0
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
Browse code

updates from master

From: Kasper Daniel Hansen <khansen@Tanngrisnir.local>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@116910 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 29/04/2016 04:18:31
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.7.7
2
+Version: 1.7.13
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
... ...
@@ -7,7 +7,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
7 7
     email = "kasperdanielhansen@gmail.com"),
8 8
     person("Peter", "Hickey", role = "ctb", email = "peter.hickey@gmail.com"))
9 9
 Depends:
10
-    R (>= 2.15),
10
+    R (>= 3.3),
11 11
     methods,
12 12
     BiocGenerics,
13 13
     GenomicRanges (>= 1.23.7),
... ...
@@ -26,7 +26,7 @@ Imports:
26 26
     data.table,
27 27
     S4Vectors,
28 28
     R.utils (>= 2.0.0),
29
-    matrixStats,
29
+    matrixStats (>= 0.50.0),
30 30
     permute
31 31
 Suggests:
32 32
     RUnit,
Browse code

fixing merge

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114621 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 10/03/2016 17:06:33
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.7.6
2
+Version: 1.7.7
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
Browse code

merge conflicts

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@114581 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 10/03/2016 02:44:17
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@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.7.2
2
+Version: 1.7.6
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
... ...
@@ -26,7 +26,8 @@ Imports:
26 26
     data.table,
27 27
     S4Vectors,
28 28
     R.utils (>= 2.0.0),
29
-    matrixStats
29
+    matrixStats,
30
+    permute
30 31
 Suggests:
31 32
     RUnit,
32 33
     bsseqData,
Browse code

findOverlaps() and subsetByOverlaps() have no 'algorithm' argument anymore

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@111565 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/12/2015 21:21:51
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1 1
 Package: bsseq
2
-Version: 1.7.1
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+Version: 1.7.2
3 3
 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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     sequencing data.
... ...
@@ -10,12 +10,12 @@ Depends:
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     R (>= 2.15),
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     methods,
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     BiocGenerics,
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-    GenomicRanges (>= 1.19.6),
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+    GenomicRanges (>= 1.23.7),
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     SummarizedExperiment (>= 0.1.1),
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     parallel,
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     limma
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 Imports:
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-    IRanges (>= 2.1.10),
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+    IRanges (>= 2.5.17),
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     GenomeInfoDb,
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     scales,
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     stats,
Browse code

fixed conflict

From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@110074 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 29/10/2015 19:12:43
Showing1 changed files
... ...
@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.7.0
2
+Version: 1.7.1
3 3
 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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     sequencing data.
... ...
@@ -10,12 +10,13 @@ Depends:
10 10
     R (>= 2.15),
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     methods,
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     BiocGenerics,
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-    IRanges (>= 2.1.10),
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     GenomicRanges (>= 1.19.6),
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     SummarizedExperiment (>= 0.1.1),
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     parallel,
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-    GenomeInfoDb
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+    limma
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 Imports:
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+    IRanges (>= 2.1.10),
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+    GenomeInfoDb,
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     scales,
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     stats,
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     graphics,
... ...
@@ -29,7 +30,8 @@ Imports:
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 Suggests:
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     RUnit,
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     bsseqData,
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-    BiocStyle
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+    BiocStyle,
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+    knitr
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 Collate:
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     hasGRanges.R
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     BSseq_class.R
... ...
@@ -47,8 +49,12 @@ Collate:
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     fisher.R
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     permutations.R
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     BSmooth.fstat.R
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+    BSseqStat_class.R
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+    getStats.R
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 License: Artistic-2.0
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+VignetteBuilder: knitr
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 URL: https://github.com/kasperdanielhansen/bsseq
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-BugReports: https://github.com/kasperdanielhansen/bsseq/issues
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 LazyData: yes
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+LazyDataCompression: xz
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+BugReports: https://github.com/kasperdanielhansen/bsseq/issues
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 biocViews: DNAMethylation
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/bsseq@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
Showing1 changed files
... ...
@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.6.0
2
+Version: 1.7.0
3 3
 Title: Analyze, manage and store bisulfite sequencing data
4 4
 Description: A collection of tools for analyzing and visualizing bisulfite
5 5
     sequencing data.
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/bsseq@109589 bc3139a8-67e5-031