[med-svn] [r-bioc-biobase] 09/09: Add autopkgtest

[Andreas Tille]

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

commit df9b2e1b8a86660162c3b104f5924a2f2c9d4f17
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 10 13:08:24 2014 +0200

    Add autopkgtest
---
 debian/README.test                              | 17 +++++++++
 debian/changelog                                |  3 +-
 debian/docs                                     |  1 +
 debian/patches/exclude_testing_golubEsets.patch | 51 +++++++++++++++++++++++++
 debian/patches/series                           |  1 +
 5 files changed, 71 insertions(+), 2 deletions(-)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..6533fdb
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,17 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("Biobase")
+EOT
+
+in order to confirm its integrity.
+
+Please note that the test that needs experiment data from
+   http://www.bioconductor.org/packages/release/data/experiment/html/golubEsets.html
+is deactivated since Debian has no package for this
+data sets.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 10 Jun 2014 11:01:29 +0200
diff --git a/debian/changelog b/debian/changelog
index dc8f196..5f70fca 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -9,8 +9,7 @@ r-bioc-biobase (2.24.0-1) UNRELEASED; urgency=low
   * Remove outdated README.Debian
   * cme fix dpkg-control
   * debian/source/format: 3.0 (quilt)
-  * Add autopkgtest
-    TODO: Test needs http://www.bioconductor.org/packages/release/data/experiment/html/golubEsets.html
+  * Add autopkgtest (Exclude unit test requiring golubEsets data)
 
  -- Andreas Tille <tille at debian.org>  Tue, 10 Jun 2014 11:01:29 +0200
 
diff --git a/debian/docs b/debian/docs
index edc0071..c3f0f84 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,2 @@
 NEWS
+debian/README.test
diff --git a/debian/patches/exclude_testing_golubEsets.patch b/debian/patches/exclude_testing_golubEsets.patch
new file mode 100644
index 0000000..984dd96
--- /dev/null
+++ b/debian/patches/exclude_testing_golubEsets.patch
@@ -0,0 +1,51 @@
+Author: Andreas Tille <tille at debian.org>
+Description: Tue, 10 Jun 2014 11:01:29 +0200
+Description: Enable running testsuite without error by disabling
+ a test which needs external data.
+ If you have installed experiment data from
+   http://www.bioconductor.org/packages/release/data/experiment/html/golubEsets.html
+ you can remove comments below.  Since Debian has no package for this
+ data sets it must be excluded from the global test framework
+
+
+--- a/inst/unitTests/test_EsetSubclasses.R
++++ b/inst/unitTests/test_EsetSubclasses.R
+@@ -427,20 +427,24 @@ testSetAs <- function() {
+   suppressMessages(e <- as(exprSet,"ExpressionSet"))
+   checkNewAndOld(e,exprSet)
+ 
+-  library(golubEsets)
+-  data(Golub_Merge)
+-  gm <- as(Golub_Merge,"ExpressionSet")
+-  checkNewGolubMerge(gm,Golub_Merge)
+-  pubMedIds(gm) = "10521349"
+-  checkNewGolubMerge(gm,Golub_Merge)
+-
+-  fp <- system.file(package="Biobase", "unitTests",
+-                    "VersionedClass_data", "devel", "sample.eSet.rda")
+-  load(fp)
+-  suppressMessages(es <- updateOldESet(sample.eSet, "SwirlSet"))
+-  checkNewSampleEset(es, sample.eSet)
+-  options(opts)
+-  removeClass("SwirlSet", where=.GlobalEnv)
++## If you have installed experiment data from
++##   http://www.bioconductor.org/packages/release/data/experiment/html/golubEsets.html
++## you can remove comments below.  Since Debian has no package for this
++## data sets it must be excluded from the global test framework
++#  library(golubEsets)
++#  data(Golub_Merge)
++#  gm <- as(Golub_Merge,"ExpressionSet")
++#  checkNewGolubMerge(gm,Golub_Merge)
++#  pubMedIds(gm) = "10521349"
++#  checkNewGolubMerge(gm,Golub_Merge)
++#
++#  fp <- system.file(package="Biobase", "unitTests",
++#                    "VersionedClass_data", "devel", "sample.eSet.rda")
++#  load(fp)
++#  suppressMessages(es <- updateOldESet(sample.eSet, "SwirlSet"))
++#  checkNewSampleEset(es, sample.eSet)
++#  options(opts)
++#  removeClass("SwirlSet", where=.GlobalEnv)
+ }
+ 
+ testFeatureNamesReplace <- function() {
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..645bc6d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+exclude_testing_golubEsets.patch

-- 
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