[med-svn] r23599 - in trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2017-01-15 17:53:47 +0000 (Sun, 15 Jan 2017)
New Revision: 23599

Modified:
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/compat
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/control
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/watch
Log:
  * Exclude more parts of test suite which fail due to missing data package
  * debhelper 10
  * d/watch: version=4


Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog	2017-01-15 17:18:16 UTC (rev 23598)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog	2017-01-15 17:53:47 UTC (rev 23599)
@@ -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

Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/compat	2017-01-15 17:18:16 UTC (rev 23598)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/compat	2017-01-15 17:53:47 UTC (rev 23599)
@@ -1 +1 @@
-9
+10

Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/control	2017-01-15 17:18:16 UTC (rev 23598)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/control	2017-01-15 17:53:47 UTC (rev 23599)
@@ -3,7 +3,7 @@
 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),

Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch	2017-01-15 17:18:16 UTC (rev 23598)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch	2017-01-15 17:53:47 UTC (rev 23599)
@@ -4,16 +4,51 @@
 
 --- 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"))
 -    checkTrue(validObject(se2))
 -
 -    ## Granges returned have rownames that were from the featureNames
 -    checkTrue(all(rownames(rowRanges(se2)) %in% featureNames(eset1)))
- }
- 
+-}
+-

Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/watch	2017-01-15 17:18:16 UTC (rev 23598)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/watch	2017-01-15 17:53:47 UTC (rev 23599)
@@ -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