[med-svn] r18358 - in trunk/packages/R/r-bioc-biomart/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-10-20 16:35:06 +0000 (Mon, 20 Oct 2014)
New Revision: 18358

Added:
   trunk/packages/R/r-bioc-biomart/trunk/debian/examples
   trunk/packages/R/r-bioc-biomart/trunk/debian/tests/
   trunk/packages/R/r-bioc-biomart/trunk/debian/tests/control_unused
   trunk/packages/R/r-bioc-biomart/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-biomart/trunk/debian/README.test
   trunk/packages/R/r-bioc-biomart/trunk/debian/changelog
   trunk/packages/R/r-bioc-biomart/trunk/debian/control
   trunk/packages/R/r-bioc-biomart/trunk/debian/copyright
   trunk/packages/R/r-bioc-biomart/trunk/debian/docs
Log:
New upstream version including autopkgtest


Modified: trunk/packages/R/r-bioc-biomart/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/README.test	2014-10-20 16:15:50 UTC (rev 18357)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/README.test	2014-10-20 16:35:06 UTC (rev 18358)
@@ -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(biomaRt)’ 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-biomart/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/changelog	2014-10-20 16:15:50 UTC (rev 18357)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/changelog	2014-10-20 16:35:06 UTC (rev 18358)
@@ -1,3 +1,11 @@
+r-bioc-biomart (2.22.0-1) experimental; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-control
+  * Add autopkgtest
+
+ -- Andreas Tille <tille at debian.org>  Mon, 20 Oct 2014 18:17:09 +0200
+
 r-bioc-biomart (2.20.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-biomart/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/control	2014-10-20 16:15:50 UTC (rev 18357)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/control	2014-10-20 16:35:06 UTC (rev 18358)
@@ -6,11 +6,10 @@
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
-               r-bioc-biobase,
-               r-bioc-annotationdbi,
+               r-bioc-annotationdbi (>= 1.28.0),
                r-cran-xml,
                r-cran-rcurl
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biomart/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biomart/trunk/
 Homepage: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html
@@ -19,8 +18,7 @@
 Architecture: all
 Depends: ${R:Depends},
          ${misc:Depends},
-         r-bioc-biobase,
-         r-bioc-annotationdbi,
+         r-bioc-annotationdbi (>= 1.28.0),
          r-cran-xml,
          r-cran-rcurl
 Description: GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

Modified: trunk/packages/R/r-bioc-biomart/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/copyright	2014-10-20 16:15:50 UTC (rev 18357)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/copyright	2014-10-20 16:35:06 UTC (rev 18358)
@@ -4,13 +4,13 @@
 Source: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html
 
 Files: *
-Copyright: © 2006-2013 Steffen Durinck <sdurinck at gmail.com>,
+Copyright: © 2006-2014 Steffen Durinck <sdurinck at gmail.com>,
                        Wolfgang Huber <huber at ebi.ac.uk> 
 License: Artistic-2.0
 
 
 Files: debian/*
-Copyright: 2013 Andreas Tille <tille at debian.org>
+Copyright: 2013-2014 Andreas Tille <tille at debian.org>
 License: Artistic-2.0
 
 License: Artistic-2.0

Modified: trunk/packages/R/r-bioc-biomart/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/docs	2014-10-20 16:15:50 UTC (rev 18357)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/docs	2014-10-20 16:35:06 UTC (rev 18358)
@@ -1 +1,2 @@
 debian/README.test
+debian/tests/run-unit-test

Added: trunk/packages/R/r-bioc-biomart/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/examples	                        (rev 0)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/examples	2014-10-20 16:35:06 UTC (rev 18358)
@@ -0,0 +1 @@
+vignettes

Added: trunk/packages/R/r-bioc-biomart/trunk/debian/tests/control_unused
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/tests/control_unused	                        (rev 0)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/tests/control_unused	2014-10-20 16:35:06 UTC (rev 18358)
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+# The following dependencies are not available so this autopkgtest is disabled
+Depends: @, r-bioc-biocstyle, r-bioc-bsgenome.hsapiens.ucsc.hg19
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-biomart/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-biomart/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-biomart/trunk/debian/tests/run-unit-test	2014-10-20 16:35:06 UTC (rev 18358)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+oname=biomaRt
+pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
+for rnw in `ls *.[rR]nw` ; do
+rfile=`echo $rnw | sed 's/\.[rR]nw/.R/'`
+R --no-save <<EOT
+  Stangle("$rnw")
+  source("$rfile", echo=TRUE)
+EOT
+done
+# rm -rf *