Browse code

Merge remote-tracking branch 'upstream/master'

Peter Hickey authored on 23/04/2019 01:04:08
Showing7 changed files

... ...
@@ -1,5 +1,5 @@
1 1
 Package: bsseq
2
-Version: 1.19.0
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
... ...
@@ -25,16 +25,16 @@ 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,
35 35
     Biostrings,
36 36
     utils,
37
-    HDF5Array,
37
+    HDF5Array (>= 1.11.9),
38 38
     rhdf5
39 39
 Suggests:
40 40
     testthat,
... ...
@@ -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
... ...
@@ -25,7 +25,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
25 25
 import(parallel)
26 26
 importFrom(locfit, "locfit", "lp")
27 27
 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
28
-           "rowSums2", "rowMeans2", "rowAlls", "rowsum", "colsum")
28
+           "rowSums2", "rowMeans2", "rowAlls")
29 29
 
30 30
 importFrom(scales, "alpha")
31 31
 importClassesFrom(Biobase, "AnnotatedDataFrame")
... ...
@@ -326,7 +326,7 @@ BSmooth <- function(BSseq,
326 326
         #       HDF5Array::saveHDF5SummarizedExperiment().
327 327
         dir <- dirname(h5_path)
328 328
         x <- BSseq
329
-        x@assays <- HDF5Array:::.shorten_h5_paths(x@assays)
329
+        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
330 330
         saveRDS(x, file = file.path(dir, "se.rds"))
331 331
     }
332 332
     BSseq
... ...
@@ -250,7 +250,11 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
250 250
         if (!isTRUEorFALSE(replace)) {
251 251
             stop("'replace' must be TRUE or FALSE")
252 252
         }
253
-        HDF5Array:::.create_dir(dir = dir, replace = replace)
253
+        if (!dir.exists(dir)) {
254
+            HDF5Array:::.create_dir(dir)
255
+        } else {
256
+            HDF5Array:::.replace_dir(dir, replace)
257
+        }
254 258
         h5_path <- file.path(dir, "assays.h5")
255 259
     } else if (identical(BACKEND, NULL)) {
256 260
         h5_path <- NULL
... ...
@@ -305,7 +309,7 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
305 309
         # NOTE: Save BSseq object; mimicing
306 310
         #       HDF5Array::saveHDF5SummarizedExperiment().
307 311
         x <- bsseq
308
-        x@assays <- HDF5Array:::.shorten_h5_paths(x@assays)
312
+        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
309 313
         saveRDS(x, file = file.path(dir, "se.rds"))
310 314
     }
311 315
     bsseq
... ...
@@ -86,7 +86,11 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(),
86 86
         if (!isTRUEorFALSE(replace)) {
87 87
             stop("'replace' must be TRUE or FALSE")
88 88
         }
89
-        HDF5Array:::.create_dir(dir = dir, replace = replace)
89
+        if (!dir.exists(dir)) {
90
+            HDF5Array:::.create_dir(dir)
91
+        } else {
92
+            HDF5Array:::.replace_dir(dir, replace)
93
+        }
90 94
         h5_path <- file.path(dir, "assays.h5")
91 95
     } else if (identical(BACKEND, NULL)) {
92 96
         h5_path <- NULL
... ...
@@ -138,7 +142,7 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(),
138 142
         # NOTE: Save BSseq object; mimicing
139 143
         #       HDF5Array::saveHDF5SummarizedExperiment().
140 144
         x <- bsseq
141
-        x@assays <- HDF5Array:::.shorten_h5_paths(x@assays)
145
+        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
142 146
         saveRDS(x, file = file.path(dir, "se.rds"))
143 147
     }
144 148
     bsseq
... ...
@@ -422,7 +422,11 @@ read.bismark <- function(files,
422 422
         if (!isTRUEorFALSE(replace)) {
423 423
             stop("'replace' must be TRUE or FALSE")
424 424
         }
425
-        HDF5Array:::.create_dir(dir = dir, replace = replace)
425
+        if (!dir.exists(dir)) {
426
+            HDF5Array:::.create_dir(dir)
427
+        } else {
428
+            HDF5Array:::.replace_dir(dir, replace)
429
+        }
426 430
     }
427 431
     # Set verbosity used by internal functions.
428 432
     subverbose <- as.logical(max(verbose - 1L, 0L))
... ...
@@ -533,7 +537,7 @@ read.bismark <- function(files,
533 537
         # NOTE: Save BSseq object; mimicing
534 538
         #       HDF5Array::saveHDF5SummarizedExperiment().
535 539
         x <- bsseq
536
-        x@assays <- HDF5Array:::.shorten_h5_paths(x@assays)
540
+        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
537 541
         saveRDS(x, file = file.path(dir, "se.rds"))
538 542
     }
539 543
     bsseq
... ...
@@ -11,5 +11,5 @@ BiocManager::install("bsseq", version = "devel")
11 11
 | Resource:     | Bioconductor        | Travis CI     |
12 12
 | ------------- | ------------------- | ------------- |
13 13
 | _Platforms:_  | _Multiple_          | _Linux_       |
14
-| R CMD check   | <a href="http://bioconductor.org/checkResults/release/bioc-LATEST/bsseq/"><img border="0" src="http://bioconductor.org/shields/build/release/bioc/bsseq.svg" alt="Build status"></a> (release)</br><a href="http://bioconductor.org/checkResults/devel/bioc-LATEST/bsseq/"><img border="0" src="http://bioconductor.org/shields/build/devel/bioc/bsseq.svg" alt="Build status"></a> (devel) | <a href="https://travis-ci.org/kasperdanielhansen/bsseq"><img src="https://travis-ci.org/kasperdanielhansen/bsseq.svg" alt="Build status"></a> |
15
-| Test coverage |                     | <a href="https://codecov.io/github/kasperdanielhansen/bsseq?branch=master"><img src="https://codecov.io/github/kasperdanielhansen/bsseq/coverage.svg?branch=master" alt="Coverage Status"/></a>   |                  |
14
+| R CMD check   | <a href="http://bioconductor.org/checkResults/release/bioc-LATEST/bsseq/"><img border="0" src="http://bioconductor.org/shields/build/release/bioc/bsseq.svg" alt="Build status"></a> (release)</br><a href="http://bioconductor.org/checkResults/devel/bioc-LATEST/bsseq/"><img border="0" src="http://bioconductor.org/shields/build/devel/bioc/bsseq.svg" alt="Build status"></a> (devel) | <a href="https://travis-ci.org/hansenlab/bsseq"><img src="https://travis-ci.org/hansenlab/bsseq.svg" alt="Build status"></a> |
15
+| Test coverage |                     | <a href="https://codecov.io/github/hansenlab/bsseq?branch=master"><img src="https://codecov.io/github/hansenlab/bsseq/coverage.svg?branch=master" alt="Coverage Status"/></a>   |                  |