[med-svn] [r-bioc-summarizedexperiment] 08/12: * Exclude more parts of test suite which fail due to missing data package * debhelper 10 * d/watch: version=4

[Andreas Tille]

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

commit 736fd5eb262c3667a0b902b099725a1694242990
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jan 15 17:53:47 2017 +0000

      * Exclude more parts of test suite which fail due to missing data package
      * debhelper 10
      * d/watch: version=4
---
 debian/changelog                                   |  8 ++++
 debian/compat                                      |  2 +-
 debian/control                                     |  2 +-
 .../skip_test_needing_not_packaged_database.patch  | 45 +++++++++++++++++++---
 debian/watch                                       |  2 +-
 5 files changed, 51 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 3aaf199..687fd3d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+r-bioc-summarizedexperiment (1.4.0-2) unstable; urgency=medium
+
+  * Exclude more parts of test suite which fail due to missing data package
+  * debhelper 10
+  * d/watch: version=4
+
+ -- Andreas Tille <tille at debian.org>  Sun, 15 Jan 2017 18:43:53 +0100
+
 r-bioc-summarizedexperiment (1.4.0-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/compat b/debian/compat
index ec63514..f599e28 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10
diff --git a/debian/control b/debian/control
index 05a1162..e418759 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
                dh-r,
                r-base-dev,
                r-bioc-biobase (>= 2.26.0),
diff --git a/debian/patches/skip_test_needing_not_packaged_database.patch b/debian/patches/skip_test_needing_not_packaged_database.patch
index 74c4014..639d1db 100644
--- a/debian/patches/skip_test_needing_not_packaged_database.patch
+++ b/debian/patches/skip_test_needing_not_packaged_database.patch
@@ -4,10 +4,45 @@ Last-Update: Tue, 03 May 2016 20:27:21 +0200
 
 --- a/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
 +++ b/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
-@@ -176,12 +176,5 @@ test_GenomicRanges_SummarizedExperiment_
-             makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
-                 geneRangeMapper(NULL))))
+@@ -141,47 +141,3 @@ test_GenomicRanges_SummarizedExperiment_
+                        sampleNames(eset5))
+ }
  
+-test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions <- function()
+-{
+-    ## naiveRangeMapper
+-    ## valid object from empty object
+-    checkTrue(validObject(makeSummarizedExperimentFromExpressionSet(ExpressionSet())))
+-
+-    ## valid object from sample ExpressionSet
+-    data("sample.ExpressionSet", package = "Biobase")
+-    eset1 <- sample.ExpressionSet
+-    checkTrue(validObject(makeSummarizedExperimentFromExpressionSet(eset1)))
+-
+-    ## makeSummarizedExperimentFromExpressionSet should be the same as `as`
+-    ## with default args
+-    checkEquals(makeSummarizedExperimentFromExpressionSet(eset1),
+-                as(eset1, "RangedSummarizedExperiment"))
+-
+-    ## probeRangeMapper
+-    ## valid object from empty object
+-    checkTrue(validObject(
+-            makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
+-                probeRangeMapper)))
+-
+-    ## valid object from sample ExpressionSet
+-    se1 <- makeSummarizedExperimentFromExpressionSet(eset1, probeRangeMapper)
+-    checkTrue(validObject(se1))
+-
+-    ## Granges returned have rownames that were from the featureNames
+-    checkTrue(all(rownames(rowRanges(se1)) %in% featureNames(eset1)))
+-
+-    ## geneRangeMapper
+-    ## valid object from empty object
+-    checkTrue(validObject(
+-            makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
+-                geneRangeMapper(NULL))))
+-
 -    ## valid object from sample ExpressionSet
 -    se2 <- makeSummarizedExperimentFromExpressionSet(eset1,
 -        geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
@@ -15,5 +50,5 @@ Last-Update: Tue, 03 May 2016 20:27:21 +0200
 -
 -    ## Granges returned have rownames that were from the featureNames
 -    checkTrue(all(rownames(rowRanges(se2)) %in% featureNames(eset1)))
- }
- 
+-}
+-
diff --git a/debian/watch b/debian/watch
index f5bb84c..9eacbd4 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,3 @@
-version=3
+version=4
 opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
  http://www.bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html .*/SummarizedExperiment_([\d\.]+)\.tar\.gz

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