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 @@
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 Package: bsseq
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-Version: 1.25.6
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+Version: 1.25.7
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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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@@ -28,7 +28,7 @@ Imports:
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     DelayedMatrixStats (>= 1.5.2),
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     permute,
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     limma,
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-    DelayedArray (>= 0.15.10),
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+    DelayedArray (>= 0.15.16),
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     Rcpp,
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     BiocParallel,
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     BSgenome,
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@@ -102,10 +102,10 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {
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     }
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     # Write to coef_sink and se.coef_sink while respecting the IPC lock.
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     ipclock(sink_lock)
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-    write_block(x = coef_sink, viewport = grid[[b]], block = as.matrix(coef))
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+    write_block(coef_sink, viewport = grid[[b]], block = as.matrix(coef))
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     if (keep.se) {
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         write_block(
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-            x = se.coef_sink,
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+            se.coef_sink,
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             viewport = grid[[b]],
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             block = as.matrix(se.coef))
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     }
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@@ -109,7 +109,7 @@
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                         ncol = 1)
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                 }
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                 ipclock(sink_lock)
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-                write_block(x = sink, viewport = sink_grid[[b]], block = ans)
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+                write_block(sink, viewport = sink_grid[[b]], block = ans)
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                 ipcunlock(sink_lock)
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                 NULL
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             },
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@@ -194,7 +194,7 @@
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                         nrow = 1)
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                 }
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                 ipclock(sink_lock)
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-                write_block(x = sink, viewport = sink_grid[[b]], block = ans)
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+                write_block(sink, viewport = sink_grid[[b]], block = ans)
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                 ipcunlock(sink_lock)
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                 NULL
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             },
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@@ -272,7 +272,7 @@ blockApplyWithRealization <- function(x, FUN, ..., sink = NULL, x_grid = NULL,
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         block_ans <- FUN(block, ...)
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         # NOTE: This is the only part different from DelayedArray::blockApply()
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         if (!is.null(sink)) {
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-            write_block(x = sink, viewport = sink_viewport, block = block_ans)
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+            write_block(sink, viewport = sink_viewport, block = block_ans)
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             block_ans <- NULL
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         }
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         if (DelayedArray:::get_verbose_block_processing()) {
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@@ -84,7 +84,7 @@
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             x = block_x,
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             x_rowRanges = block_rowRanges,
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             ans_rowRanges = ans_rowRanges)
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-        write_block(x = sink, viewport = sink_viewport, block = block_ans)
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+        write_block(sink, viewport = sink_viewport, block = block_ans)
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     }
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     as(sink, "DelayedArray")
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@@ -210,8 +210,8 @@
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     # Write to M_sink and Cov_sink while respecting the IPC lock.
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     viewport <- grid[[b]]
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     ipclock(sink_lock)
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-    write_block(x = M_sink, viewport = viewport, block = M)
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-    write_block(x = Cov_sink, viewport = viewport, block = Cov)
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+    write_block(M_sink, viewport = viewport, block = M)
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+    write_block(Cov_sink, viewport = viewport, block = Cov)
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     ipcunlock(sink_lock)
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     NULL
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 }