[med-svn] [r-bioc-shortread] 01/04: New upstream version 1.36.0

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-shortread.

commit 3fe8b81cd5d13c409bd09cfbf06c36005afa8605
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 9 08:44:22 2017 +0100

    New upstream version 1.36.0
---
 DESCRIPTION                  |   6 +++---
 R/SnapshotFunction-helpers.R |   2 +-
 R/spViewPerFeature.R         |   2 +-
 inst/doc/Overview.pdf        | Bin 132945 -> 174760 bytes
 man/Snapshot-class.Rd        |   2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 51a8af4..166b0f2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ShortRead
 Type: Package
 Title: FASTQ input and manipulation
-Version: 1.34.2
+Version: 1.36.0
 Author: Martin Morgan, Michael Lawrence, Simon Anders
 Maintainer: Bioconductor Package Maintainer
  <maintainer at bioconductor.org>
@@ -14,7 +14,7 @@ Description: This package implements sampling, iteration, and input of
         alignment formats.
 License: Artistic-2.0
 LazyLoad: yes
-Depends: BiocGenerics (>= 0.22.1), BiocParallel, Biostrings (>=
+Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
         2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
 Imports: Biobase, S4Vectors (>= 0.13.8), IRanges (>= 2.3.7),
         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter,
@@ -23,4 +23,4 @@ Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
 LinkingTo: S4Vectors, IRanges, XVector, Biostrings
 biocViews: DataImport, Sequencing, QualityControl
 NeedsCompilation: yes
-Packaged: 2017-10-07 22:41:16 UTC; biocbuild
+Packaged: 2017-10-30 22:51:24 UTC; biocbuild
diff --git a/R/SnapshotFunction-helpers.R b/R/SnapshotFunction-helpers.R
index d3028a0..2aaf41f 100644
--- a/R/SnapshotFunction-helpers.R
+++ b/R/SnapshotFunction-helpers.R
@@ -183,7 +183,7 @@
     ignore.strand <- ignore.strand(x)
     if (any(seqnames(anntrack)@values %in% seqlevels(rng))) {
         gr <- anntrack
-        seqlevels(gr, force=TRUE) <- seqlevels(vrange(x))
+        seqlevels(gr, pruning.mode="coarse") <- seqlevels(vrange(x))
     } else  {
         message(paste(strwrap("SnapshotFunction-helper: seqname of
            'annTrack' does not match the imported range. Annotation
diff --git a/R/spViewPerFeature.R b/R/spViewPerFeature.R
index 9af88e8..9f366c9 100644
--- a/R/spViewPerFeature.R
+++ b/R/spViewPerFeature.R
@@ -28,7 +28,7 @@ spViewPerFeature <- function(GRL,
         stop(sprintf("element named '%s' does not exist", name))
     
     gr <- GRL[[name]]
-    seqlevels(gr, force=TRUE) <- levels(seqnames(gr))
+    seqlevels(gr, pruning.mode="coarse") <- levels(seqnames(gr))
     which <- reduce(range(gr))
     annTrack <- gr
     
diff --git a/inst/doc/Overview.pdf b/inst/doc/Overview.pdf
index ce01005..c5bb7f0 100644
Binary files a/inst/doc/Overview.pdf and b/inst/doc/Overview.pdf differ
diff --git a/man/Snapshot-class.Rd b/man/Snapshot-class.Rd
index c794631..1223d97 100644
--- a/man/Snapshot-class.Rd
+++ b/man/Snapshot-class.Rd
@@ -235,7 +235,7 @@ library(GenomicFeatures)
 
 getAnnGR <- function(txdb, which) {
     ex <- exonsBy(txdb, by="gene")
-    seqlevels(ex, force=TRUE) <- seqlevels(which)
+    seqlevels(ex, pruning.mode="coarse") <- seqlevels(which)
     r <- range(ex)
     gr <- unlist(r)
     values(gr)[["gene_id"]] <- rep.int(names(r), times=lengths(r))

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