[med-svn] r21848 - in trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-05-03 18:56:06 +0000 (Tue, 03 May 2016)
New Revision: 21848

Added:
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/series
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch
Modified:
   trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog
Log:
Skip test needing unpackaged database


Modified: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog	2016-05-03 12:14:07 UTC (rev 21847)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/changelog	2016-05-03 18:56:06 UTC (rev 21848)
@@ -1,3 +1,10 @@
+r-bioc-summarizedexperiment (1.0.2-3) unstable; urgency=medium
+
+  * Skip test needing unpackaged database (thanks to Gordon Ball
+    <gordon at chronitis.net> for the hint)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 03 May 2016 20:27:21 +0200
+
 r-bioc-summarizedexperiment (1.0.2-2) unstable; urgency=medium
 
   * Add missing Depends to autopkgtest

Added: trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/series	2016-05-03 18:56:06 UTC (rev 21848)
@@ -0,0 +1 @@
+skip_test_needing_not_packaged_database.patch

Added: 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	                        (rev 0)
+++ trunk/packages/R/r-bioc-summarizedexperiment/trunk/debian/patches/skip_test_needing_not_packaged_database.patch	2016-05-03 18:56:06 UTC (rev 21848)
@@ -0,0 +1,19 @@
+Description: Skip test needing unpackaged database
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 03 May 2016 20:27:21 +0200
+
+--- a/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
++++ b/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
+@@ -172,12 +172,5 @@ test_GenomicRanges_SummarizedExperiment_
+             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)))
+ }
+