[med-svn] r17145 - in trunk/packages/R/r-bioc-biostrings/trunk/debian: . patches tests

[Andreas Tille]

Author: tille
Date: 2014-06-13 09:37:31 +0000 (Fri, 13 Jun 2014)
New Revision: 17145

Added:
   trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/
   trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/control
   trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-biostrings/trunk/debian/README.test
   trunk/packages/R/r-bioc-biostrings/trunk/debian/changelog
   trunk/packages/R/r-bioc-biostrings/trunk/debian/control
   trunk/packages/R/r-bioc-biostrings/trunk/debian/docs
   trunk/packages/R/r-bioc-biostrings/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
Add autopkgtest


Modified: trunk/packages/R/r-bioc-biostrings/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/README.test	2014-06-13 08:48:10 UTC (rev 17144)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/README.test	2014-06-13 09:37:31 UTC (rev 17145)
@@ -1,5 +1,8 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package can be tested by loading it into R with the command
-‘library(Biostrings)’ in order to confirm its integrity.
+To run the unit tests provided by the package you can do
+
+   sh  run-unit-test
+
+in this directory.

Modified: trunk/packages/R/r-bioc-biostrings/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/changelog	2014-06-13 08:48:10 UTC (rev 17144)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/changelog	2014-06-13 09:37:31 UTC (rev 17145)
@@ -1,8 +1,9 @@
-r-bioc-biostrings (2.32.0-1) UNRELEASED; urgency=medium
+r-bioc-biostrings (2.32.0-1) unstable; urgency=medium
 
   * New upstream version
   * Patch to use Debian packaged zlib
   * Versioned (Build-)Depends from r-bioc-xvector
+  * Add autopkgtest
 
  -- Andreas Tille <tille at debian.org>  Fri, 13 Jun 2014 09:57:40 +0200
 

Modified: trunk/packages/R/r-bioc-biostrings/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/control	2014-06-13 08:48:10 UTC (rev 17144)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/control	2014-06-13 09:37:31 UTC (rev 17145)
@@ -3,6 +3,7 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,

Modified: trunk/packages/R/r-bioc-biostrings/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/docs	2014-06-13 08:48:10 UTC (rev 17144)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/docs	2014-06-13 09:37:31 UTC (rev 17145)
@@ -1 +1,2 @@
 debian/README.test
+debian/tests/run-unit-test

Modified: trunk/packages/R/r-bioc-biostrings/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-13 08:48:10 UTC (rev 17144)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-13 09:37:31 UTC (rev 17145)
@@ -1,3 +1,8 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Sun, 08 Jun 2014 14:24:15 +0200
+Description: If the systems includes zlib natively there is no point in
+ requiring the import of zlibbioc
+
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
 @@ -12,7 +12,7 @@ biocViews: SequenceMatching, Genetics, S

Added: trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/control	2014-06-13 09:37:31 UTC (rev 17145)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-biostrings/trunk/debian/tests/run-unit-test	2014-06-13 09:37:31 UTC (rev 17145)
@@ -0,0 +1,12 @@
+#!/bin/sh -e
+
+pkg=r-bioc-biostrings
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/lib/R/site-library/Biostrings/UnitTests/* $ADTTMP
+for runtest in `ls *.R` ; do
+    R --no-save < $runtest
+done
+rm -f $ADTTMP/*