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resync with HDF5Array 1.19.11

Hervé Pagès authored on 26/04/2021 05:55:03
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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 1.27.4
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+Version: 1.27.5
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 Encoding: UTF-8
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 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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@@ -34,7 +34,7 @@ Imports:
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     BSgenome,
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     Biostrings,
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     utils,
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-    HDF5Array (>= 1.15.19),
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+    HDF5Array (>= 1.19.11),
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     rhdf5
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 Suggests:
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     testthat,
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@@ -326,7 +326,7 @@ BSmooth <- function(BSseq,
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         #       HDF5Array::saveHDF5SummarizedExperiment().
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         dir <- dirname(h5_path)
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         x <- BSseq
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-        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
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+        x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
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         saveRDS(x, file = file.path(dir, "se.rds"))
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     }
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     BSseq
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@@ -252,9 +252,9 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
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             stop("'replace' must be TRUE or FALSE")
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         }
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         if (!dir.exists(dir)) {
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-            HDF5Array:::.create_dir(dir)
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+            HDF5Array::create_dir(dir)
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         } else {
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-            HDF5Array:::.replace_dir(dir, replace)
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+            HDF5Array::replace_dir(dir, replace)
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         }
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         h5_path <- file.path(dir, "assays.h5")
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     } else if (identical(BACKEND, NULL)) {
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@@ -310,7 +310,7 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
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         # NOTE: Save BSseq object; mimicing
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         #       HDF5Array::saveHDF5SummarizedExperiment().
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         x <- bsseq
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-        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
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+        x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
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         saveRDS(x, file = file.path(dir, "se.rds"))
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     }
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     bsseq
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@@ -87,9 +87,9 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(),
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             stop("'replace' must be TRUE or FALSE")
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         }
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         if (!dir.exists(dir)) {
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-            HDF5Array:::.create_dir(dir)
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+            HDF5Array::create_dir(dir)
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         } else {
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-            HDF5Array:::.replace_dir(dir, replace)
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+            HDF5Array::replace_dir(dir, replace)
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         }
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         h5_path <- file.path(dir, "assays.h5")
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     } else if (identical(BACKEND, NULL)) {
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@@ -144,7 +144,7 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(),
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         # NOTE: Save BSseq object; mimicing
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         #       HDF5Array::saveHDF5SummarizedExperiment().
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         x <- bsseq
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-        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
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+        x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
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         saveRDS(x, file = file.path(dir, "se.rds"))
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     }
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     bsseq
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@@ -423,9 +423,9 @@ read.bismark <- function(files,
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             stop("'replace' must be TRUE or FALSE")
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         }
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         if (!dir.exists(dir)) {
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-            HDF5Array:::.create_dir(dir)
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+            HDF5Array::create_dir(dir)
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         } else {
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-            HDF5Array:::.replace_dir(dir, replace)
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+            HDF5Array::replace_dir(dir, replace)
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         }
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     }
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     # Set verbosity used by internal functions.
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@@ -537,7 +537,7 @@ read.bismark <- function(files,
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         # NOTE: Save BSseq object; mimicing
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         #       HDF5Array::saveHDF5SummarizedExperiment().
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         x <- bsseq
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-        x@assays <- HDF5Array:::.shorten_assay2h5_links(x@assays)
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+        x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
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         saveRDS(x, file = file.path(dir, "se.rds"))
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     }
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     bsseq